PDF Output of CLIC (Clustering by Inferred Co-Expression)

PDF Output of CLIC (clustering by inferred co-expression)

Dataset: Num of genes in input gene set: 93 Total number of genes: 16493

CLIC PDF output has three sections:

1) Overview of Co-Expression Modules (CEMs) Heatmap shows pairwise correlations between all genes in the input query gene set.

Red lines shows the partition of input genes into CEMs, ordered by CEM strength.

Each row shows one gene, and the brightness of squares indicates its correlations with other genes.

Gene symbols are shown at left side and on the top of the heatmap.

2) Details of each CEM and its expansion CEM+ Top panel shows the posterior selection probability (dataset weights) for top GEO series datasets.

Bottom panel shows the CEM genes (blue rows) as well as expanded CEM+ genes (green rows).

Each column is one GEO series dataset, sorted by their posterior probability of being selected.

The brightness of squares indicates the gene's correlations with CEM genes in the corresponding dataset.

CEM+ includes genes that co-express with CEM genes in high-weight datasets, measured by LLR score.

3) Details of each GEO series dataset and its expression profile: Top panel shows the detailed information (e.g. title, summary) for the GEO series dataset.

Bottom panel shows the background distribution and the expression profile for CEM genes in this dataset. Num ofGenesinQueryGeneset:93.CEMs:1. Overview ofCo-ExpressionModules(CEMs)withDatasetWeighting Anapc10 Anapc11 Anapc13 Rps6ka6 Rps6ka3 Rps6ka2 Rps6ka1 Ppp2r5d Ppp2r1b Ppp2r5b Ppp2r5e Ppp2r5a Ppp2r1a Camk2b Camk2g Camk2d Camk2a Fbxw11 Mapk12 Ppp3cb Ppp1cb Anapc4 Ppp2cb Anapc7 Anapc2 Anapc5 Anapc1 Ppp1ca Ppp3cc Ppp3ca Ppp2ca Pkmyt1 Cdc25c Fbxo43 Mad2l2 Ppp3r2 Ppp3r1 Prkacb Prkaca Smc1b Calml3 Smc1a Ywhab Ywhaq Ywhag Ywhah Ywhae Ywhaz Cpeb1 Ccnb1 Ccnb2 Adcy2 Calm4 Adcy1 Cdc23 Adcy5 Cdc16 Spdya Cdc27 Cdc26 Adcy3 Adcy7 Adcy8 Adcy9 Adcy6 Adcy4 Ccne1 Ccne2 Cdc20 Fbxo5 Aurka Stag3 Sgol1 Smc3 Espl1 Plcz1 Chp2 Pttg1 Bub1 Cdk2 Rec8 Prkx Itpr2 Itpr3 Itpr1 Plk1 Ins2 Mos Btrc Igf1 Pgr Slk Ar

Aurka Bub1 Plk1 Cdc20 Ccnb2 Sgol1 Espl1 Fbxo5 Cdc25c Ccne2 Ccne1 Pkmyt1 Smc1a Ccnb1 Smc3 Anapc1 Anapc5 Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 0.0 Singletons CEM 1(626datasets) Scale ofaveragePearsoncorrelations 0.2 0.4 0.6 0.8 1.0 Symbol Num ofCEMGenes:17.Predicted546.SelectedDatasets:626.Strength:79.0 CEM 1,Geneset"[K]Oocytemeiosis",Page1 Mis18bp1 Racgap1 Ncapd2 Shcbp1 Nusap1 Anapc5 Anapc1 Pkmyt1 Cdc25c Smc1a Incenp Bub1b Ncaph Cenpe Ncapg Ccnb1 Ccnb2 Rad51 Spag5 Cdca5 Cdca8 Ube2c Kif20a Ccna2 Ccne1 Ccne2 Cdc20 Fbxo5 Aurkb Aurka Cenpf Mki67 Asf1b Cenpi Aspm Sgol1 Smc3 Espl1 Birc5 Bub1 Kif22 Kif11 Cdk1 Tpx2 Melk Nuf2 Prc1 Plk1 Kif4 Pbk 0.0 1.0

GSE40513 [6] GSE16874 [12]

GSE17266 [59] Only showingfirst200datasets-Seetxtoutputforfulldetails. GSE53916 [6] GSE17794 [44] GSE39621 [51] GSE54215 [13] GSE6998 [32] GSE13225 [6] GSE46797 [6] GSE21224 [16] GSE57543 [6] GSE44260 [10] GSE13874 [14] GSE15303 [11] GSE31028 [6] GSE4694 [6] GSE27605 [8] GSE17796 [39] GSE48382 [10] GSE51385 [8] GSE17316 [12] GSE26290 [12] GSE30192 [6] GSE51883 [30] GSE20954 [14] GSE54490 [12] GSE51243 [7] GSE39449 [6] GSE7875 [16] GSE34839 [6] GSE25257 [6] GSE27786 [20] GSE21299 [12] GSE51075 [12] GSE12454 [13] GSE6957 [12] GSE54653 [6] GSE9287 [8] GSE29241 [6] GSE33308 [10] GSE15741 [6] GSE46185 [6] GSE6837 [8] GSE23845 [15] GSE26616 [6] GSE12498 [12] GSE21716 [28] GSE6875 [8] GSE12881 [6] GSE18135 [18] GSE21309 [9] GSE52474 [154] GSE32386 [13] GSE39034 [9] GSE16675 [72] GSE9763 [20] GSE45051 [18] GSE41342 [26] GSE17509 [57] GSE47959 [8] GSE12993 [6] GSE7020 [8] GSE45143 [6] GSE46209 [21] GSE31359 [8] GSE28621 [21] GSE46090 [12] GSE21900 [12] GSE30160 [6] GSE14769 [24] GSE12001 [6] GSE21379 [10] GSE10525 [18] GSE39082 [6] GSE22774 [6] GSE20302 [12] GSE11220 [44] GSE48397 [10] GSE24512 [29] GSE46606 [30] GSE28457 [24] GSE16684 [6] GSE34324 [12] GSE4260 [6] GSE8039 [32] GSE10176 [6] GSE6689 [12] GSE22180 [60] GSE28417 [12] GSE23502 [8] GSE15326 [10] GSE51628 [15] GSE13873 [27] GSE18326 [8] GSE7694 [12] GSE24628 [16] GSE4535 [6] GSE23505 [10] GSE8678 [6] GSE32330 [12] GSE27901 [23] GSE17745 [6] GSE21278 [48] GSE13611 [8] GSE15610 [12] GSE18115 [8] GSE13693 [9] GSE20100 [15] GSE33471 [12] GSE22124 [18] GSE50813 [24] GSE30745 [12] GSE39984 [18] GSE30485 [15] GSE18993 [13] GSE7657 [12] GSE30962 [16] GSE22005 [23] GSE11222 [42] GSE26355 [6] GSE23925 [6] GSE9247 [15] GSE19729 [14] GSE8660 [6] GSE13259 [10] GSE8960 [18] GSE32277 [33] GSE19885 [9] GSE20500 [6] GSE8025 [21] GSE31099 [24] GSE15872 [18] GSE31313 [22] GSE34729 [6] GSE20696 [8] GSE4768 [18] GSE28389 [20] GSE19925 [6] GSE27379 [6] GSE5041 [8] GSE5891 [6] GSE7460 [52] GSE45465 [39] GSE18534 [15] GSE40856 [8] GSE19004 [9] GSE13692 [8] GSE21491 [9] GSE49194 [14] GSE15267 [8] GSE43419 [20] GSE11201 [18] GSE18460 [16] CEM+ CEM GSE7503 [6] GSE24210 [16] GSE11818 [6] GSE48004 [6] GSE38031 [8] GSE27546 [51] 0.0 GSE7897 [60] GSE21711 [6]

GSE47421 [24] Scale ofaveragePearsoncorrelations GSE9975 [36] GSE19369 [8] GSE13635 [6] GSE1435 [27] GSE12518 [6] GSE51608 [6] 0.2 GSE15580 [14] GSE7225 [9] GSE11186 [33] GSE42021 [27] GSE3126 [6] GSE2019 [12] GSE30083 [12] GSE12465 [14] GSE4142 [14] 0.4 GSE36530 [6] GSE12581 [16] GSE18281 [33] GSE14012 [24] GSE8156 [6] GSE51804 [10] GSE24121 [9] GSE45895 [27] GSE21054 [8] 0.6 GSE53951 [10] GSE45820 [6] GSE21393 [6] GSE11110 [11] GSE13563 [6] GSE46242 [12] GSE17097 [20] GSE29318 [9] GSE48203 [9] 0.8 GSE11382 [10] GSE31598 [12] GSE13149 [25] GSE33156 [18] Score 213.97 215.07 215.65 217.13 219.76 221.45 222.06 224.16 226.00 226.01 226.51 226.74 229.94 230.12 230.21 234.31 234.74 234.74 234.92 237.00 237.31 237.94 240.03 241.68 241.75 242.39 245.71 248.11 250.11 250.98 252.77 256.09 261.40 1.0 Notes Symbol Num ofCEMGenes:17.Predicted546.SelectedDatasets:626.Strength:79.0 CEM 1,Geneset"[K]Oocytemeiosis",Page2 Arhgap11a Rad51ap1 Depdc1a Ncapg2 Ckap2l Zwilch Cenpp Cenpn Cenph Kpna2 Cenpk Kif18b Ercc6l Kif18a Cks1b Cdc45 Cep55 Cdca2 Ckap2 Ndc80 Esco2 Spc24 Fignl1 Mcm7 Mcm5 Gins1 Prim1 Brca1 Atad2 Kntc1 Spdl1 Sgol2 Uhrf1 Rrm2 Rrm1 Cdc6 Cks2 Exo1 Nek2 Ska3 Dbf4 Anln Ccnf Rfc5 Pole Ect2 Plk4 Lig1 Tk1 Stil 0.0 1.0

GSE40513 [6] GSE16874 [12]

GSE47421 [24] Scale ofaveragePearsoncorrelations GSE9975 [36] GSE19369 [8] GSE13635 [6] GSE1435 [27] GSE12518 [6] GSE51608 [6] 0.2 GSE15580 [14] GSE7225 [9] GSE11186 [33] GSE42021 [27] GSE3126 [6] GSE2019 [12] GSE30083 [12] GSE12465 [14] GSE4142 [14] 0.4 GSE36530 [6] GSE12581 [16] GSE18281 [33] GSE14012 [24] GSE8156 [6] GSE51804 [10] GSE24121 [9] GSE45895 [27] GSE21054 [8] 0.6 GSE53951 [10] GSE45820 [6] GSE21393 [6] GSE11110 [11] GSE13563 [6] GSE46242 [12] GSE17097 [20] GSE29318 [9] GSE48203 [9] 0.8 GSE11382 [10] GSE31598 [12] GSE13149 [25] GSE33156 [18] Score 176.94 177.48 177.60 177.85 178.59 178.96 179.72 179.72 181.77 182.86 186.04 186.53 187.04 188.34 188.58 188.81 190.47 191.07 191.66 192.53 193.20 193.67 193.89 195.17 196.65 196.68 196.78 197.84 198.13 200.22 200.22 200.45 202.02 203.08 203.16 204.41 205.02 205.17 205.83 206.29 206.54 207.68 207.86 208.77 208.80 208.80 209.81 211.62 213.03 213.86 1.0 Notes Symbol Num ofCEMGenes:17.Predicted546.SelectedDatasets:626.Strength:79.0 CEM 1,Geneset"[K]Oocytemeiosis",Page3 BC055324 Arhgef39 Depdc1b Suv39h1 Mms22l Rad54b Topbp1 Parpbp Chaf1b Cenpm Wdhd1 Cenpw Iqgap3 Dnmt1 Cenpu Chtf18 Cdkn3 Trip13 Casc5 Gmnn Hirip3 Mcm6 Mcm2 Mcm4 Mybl2 Gins2 Prim2 Cenpl Atad5 Ube2t H2afx Pole2 Eme1 Pola1 Tcf19 Prr11 Mastl Gsg2 Rpa2 Pcna Hells Tipin Ezh2 Fen1 Oip5 Rfc4 E2f8 E2f7 Blm Pif1 0.0 1.0

GSE40513 [6] GSE16874 [12]

GSE47421 [24] Scale ofaveragePearsoncorrelations GSE9975 [36] GSE19369 [8] GSE13635 [6] GSE1435 [27] GSE12518 [6] GSE51608 [6] 0.2 GSE15580 [14] GSE7225 [9] GSE11186 [33] GSE42021 [27] GSE3126 [6] GSE2019 [12] GSE30083 [12] GSE12465 [14] GSE4142 [14] 0.4 GSE36530 [6] GSE12581 [16] GSE18281 [33] GSE14012 [24] GSE8156 [6] GSE51804 [10] GSE24121 [9] GSE45895 [27] GSE21054 [8] 0.6 GSE53951 [10] GSE45820 [6] GSE21393 [6] GSE11110 [11] GSE13563 [6] GSE46242 [12] GSE17097 [20] GSE29318 [9] GSE48203 [9] 0.8 GSE11382 [10] GSE31598 [12] GSE13149 [25] GSE33156 [18] Score 138.80 139.76 140.07 140.22 141.58 143.02 143.83 144.73 145.25 146.26 146.31 146.32 147.50 148.19 148.59 149.06 149.60 150.19 150.22 150.70 151.41 152.12 152.65 154.24 154.93 156.04 156.69 157.05 157.95 160.60 160.71 162.54 162.76 164.79 165.62 166.83 168.08 168.91 169.44 170.11 172.38 172.50 172.90 173.01 173.58 173.88 173.97 174.12 175.69 175.89 1.0 Notes 4930579G24Rik 2700094K13Rik 2810417H13Rik Symbol Num ofCEMGenes:17.Predicted546.SelectedDatasets:626.Strength:79.0 CEM 1,Geneset"[K]Oocytemeiosis",Page4 Rnaseh2b Timeless Fam83d Fam64a Nup133 Nup107 Sapcd2 Hmgb3 Dlgap5 Dnajc9 Trim59 Rad54l Lmnb1 Whsc1 Cenpq Apitd1 Nup85 Stmn1 Haus1 Haus5 Rfwd3 Poc1a Sass6 Mcm8 Gtse1 Brca2 Pold1 Diap3 Tfdp1 Fanci Brip1 Gen1 Cdc7 Dsn1 Mtfr2 Skp2 Neil3 Ska2 Orc6 Orc1 Cdt1 Rfc3 Rbl1 Hat1 Dhfr Ttf2 Cit 0.0 1.0

GSE40513 [6] GSE16874 [12]

GSE47421 [24] Scale ofaveragePearsoncorrelations GSE9975 [36] GSE19369 [8] GSE13635 [6] GSE1435 [27] GSE12518 [6] GSE51608 [6] 0.2 GSE15580 [14] GSE7225 [9] GSE11186 [33] GSE42021 [27] GSE3126 [6] GSE2019 [12] GSE30083 [12] GSE12465 [14] GSE4142 [14] 0.4 GSE36530 [6] GSE12581 [16] GSE18281 [33] GSE14012 [24] GSE8156 [6] GSE51804 [10] GSE24121 [9] GSE45895 [27] GSE21054 [8] 0.6 GSE53951 [10] GSE45820 [6] GSE21393 [6] GSE11110 [11] GSE13563 [6] GSE46242 [12] GSE17097 [20] GSE29318 [9] GSE48203 [9] 0.8 GSE11382 [10] GSE31598 [12] GSE13149 [25] GSE33156 [18] Score 106.26 107.01 107.97 108.69 108.91 109.02 111.31 112.26 112.69 113.25 113.61 113.93 114.18 115.30 115.50 117.43 118.39 118.98 119.54 120.04 120.05 120.23 120.74 121.83 122.25 123.11 123.27 123.53 123.55 123.63 123.77 123.80 123.91 124.81 125.34 125.87 125.90 126.29 129.03 129.04 129.85 130.06 130.57 131.04 134.43 136.74 136.88 137.93 138.08 138.57 1.0 Notes 2700029M09Rik 4632434I11Rik Symbol Num ofCEMGenes:17.Predicted546.SelectedDatasets:626.Strength:79.0 CEM 1,Geneset"[K]Oocytemeiosis",Page5 BC030867 Hnrnpab Snrnp40 Ranbp1 Anp32b Anp32e Nup155 Ccdc34 Cep192 Nudt21 Hmgb2 Mis18a Dnaaf2 Recql4 Ankle1 Rqcd1 Nup93 Dtymk Chek2 Haus4 Actl6a Cdca4 Ddx39 Cdca7 Fancb Syce2 Gins4 Ssrp1 Rnf26 Pold2 Clhc1 Palb2 Smc4 Cse1l H2afz Lsm3 Lsm2 G2e3 Nde1 Rpa1 Rpa3 Rcc1 Ppil1 Mtbp Pask Nxt1 Rfc2 Lbr 0.0 1.0

GSE40513 [6] GSE16874 [12]

GSE47421 [24] Scale ofaveragePearsoncorrelations GSE9975 [36] GSE19369 [8] GSE13635 [6] GSE1435 [27] GSE12518 [6] GSE51608 [6] 0.2 GSE15580 [14] GSE7225 [9] GSE11186 [33] GSE42021 [27] GSE3126 [6] GSE2019 [12] GSE30083 [12] GSE12465 [14] GSE4142 [14] 0.4 GSE36530 [6] GSE12581 [16] GSE18281 [33] GSE14012 [24] GSE8156 [6] GSE51804 [10] GSE24121 [9] GSE45895 [27] GSE21054 [8] 0.6 GSE53951 [10] GSE45820 [6] GSE21393 [6] GSE11110 [11] GSE13563 [6] GSE46242 [12] GSE17097 [20] GSE29318 [9] GSE48203 [9] 0.8 GSE11382 [10] GSE31598 [12] GSE13149 [25] GSE33156 [18] Score 83.17 83.36 83.68 83.81 83.93 84.08 84.63 85.11 85.25 85.62 85.68 86.46 86.60 87.08 87.47 88.01 88.48 89.30 89.44 91.38 92.01 92.07 92.37 92.46 93.95 94.42 94.46 95.51 95.87 95.96 96.63 97.19 97.67 99.43 100.02 100.09 100.49 100.73 100.76 100.79 101.42 101.46 101.72 101.74 103.04 103.60 104.39 105.30 105.49 105.67 1.0 Notes Symbol Num ofCEMGenes:17.Predicted546.SelectedDatasets:626.Strength:79.0 CEM 1,Geneset"[K]Oocytemeiosis",Page6 Suv39h2 Psmc3ip Efcab11 Fam72a Rbmxl1 Cdc25b Nup160 Ncaph2 Tubb4b Nucks1 Cep128 Gpsm2 Snrpa1 Rbmx2 Lmnb2 Zfp367 Lrrc40 Rpp30 Nup43 Nup62 Wdr90 Reep4 Haus3 Rad18 Tubg1 Lrwd1 Fanca Hmmr Alyref Gins3 Banf1 Phf5a Larp7 Psip1 Sf3a3 Tonsl Mxd3 Msh6 Mns1 Usp1 Uba2 Aaas Tdp1 Bora Rfc1 Dis3 Nrm Ung Eri1 Eri2 0.0 1.0

GSE40513 [6] GSE16874 [12]

GSE47421 [24] Scale ofaveragePearsoncorrelations GSE9975 [36] GSE19369 [8] GSE13635 [6] GSE1435 [27] GSE12518 [6] GSE51608 [6] 0.2 GSE15580 [14] GSE7225 [9] GSE11186 [33] GSE42021 [27] GSE3126 [6] GSE2019 [12] GSE30083 [12] GSE12465 [14] GSE4142 [14] 0.4 GSE36530 [6] GSE12581 [16] GSE18281 [33] GSE14012 [24] GSE8156 [6] GSE51804 [10] GSE24121 [9] GSE45895 [27] GSE21054 [8] 0.6 GSE53951 [10] GSE45820 [6] GSE21393 [6] GSE11110 [11] GSE13563 [6] GSE46242 [12] GSE17097 [20] GSE29318 [9] GSE48203 [9] 0.8 GSE11382 [10] GSE31598 [12] GSE13149 [25] GSE33156 [18] Score 62.24 62.50 62.79 63.25 63.49 63.88 64.00 64.43 64.88 64.95 65.28 65.31 65.37 66.01 66.19 66.96 67.07 67.26 67.95 67.97 69.49 69.61 70.00 70.02 70.08 70.18 70.22 70.56 70.73 71.83 71.99 72.12 73.19 73.47 74.73 75.37 75.74 76.96 77.13 77.44 77.60 77.76 78.42 78.52 79.12 79.34 80.21 80.74 81.04 81.96 1.0 Notes 4930422G04Rik 2610318N02Rik Symbol Num ofCEMGenes:17.Predicted546.SelectedDatasets:626.Strength:79.0 CEM 1,Geneset"[K]Oocytemeiosis",Page7 Rnaseh2a Tmem194 Fam111a Anapc15 Tamm41 Sephs1 Ccp110 Mthfd1l Dctpp1 Ruvbl2 Ppm1g Zbtbd6 Gas2l3 Cdca7l Mcph1 Kpnb1 Rbbp8 Nup35 Cep76 Enkd1 Haus8 Cep57 Pbdc1 Ddx11 Dpy30 Tex30 Tacc3 Gmps Xrcc6 Uchl5 Pold3 Defa3 Pms2 Pole3 Smc2 Siva1 Lin54 Msh2 Xpo1 Ints7 Tcp1 Hn1l E2f1 Lyar Taf5 Lin9 Lrr1 Fxn 0.0 1.0

GSE40513 [6] GSE16874 [12]

GSE47421 [24] Scale ofaveragePearsoncorrelations GSE9975 [36] GSE19369 [8] GSE13635 [6] GSE1435 [27] GSE12518 [6] GSE51608 [6] 0.2 GSE15580 [14] GSE7225 [9] GSE11186 [33] GSE42021 [27] GSE3126 [6] GSE2019 [12] GSE30083 [12] GSE12465 [14] GSE4142 [14] 0.4 GSE36530 [6] GSE12581 [16] GSE18281 [33] GSE14012 [24] GSE8156 [6] GSE51804 [10] GSE24121 [9] GSE45895 [27] GSE21054 [8] 0.6 GSE53951 [10] GSE45820 [6] GSE21393 [6] GSE11110 [11] GSE13563 [6] GSE46242 [12] GSE17097 [20] GSE29318 [9] GSE48203 [9] 0.8 GSE11382 [10] GSE31598 [12] GSE13149 [25] GSE33156 [18] Score 45.60 45.70 46.97 47.63 47.77 47.96 48.27 48.54 48.74 49.07 49.11 49.31 49.72 50.56 50.62 52.05 52.38 52.38 52.69 52.91 53.16 53.22 53.22 53.32 54.25 54.27 54.42 55.04 55.27 55.48 55.99 56.06 56.07 56.67 56.73 56.80 58.07 58.72 59.38 60.06 60.10 61.01 61.26 61.39 61.49 61.61 61.78 61.84 61.92 62.16 1.0 Notes 4930427A07Rik Symbol Num ofCEMGenes:17.Predicted546.SelectedDatasets:626.Strength:79.0 CEM 1,Geneset"[K]Oocytemeiosis",Page8 Nsmce4a Tubgcp2 Snrnp25 Hnrnpm Donson Cenpc1 Ccdc77 Rad51c Cdc25a Hnrnpu Exosc2 Dazap1 Rnf168 Ruvbl1 Trim28 Trim37 Mrpl18 Magoh Rbbp7 Ncbp1 Kifc5b Nelfcd Haus6 Usp39 Rad21 Snrpb Snrpc Snrpe Cenpt Hmbs Psrc1 Asf1a Tmpo Etaa1 Wee1 Lsm4 Fancl Snrpf Srsf1 Srsf4 Ndc1 Pmf1 Pfas Ipo5 Gart Fzr1 Dck Srrt Ttk 0.0 1.0

GSE40513 [6] GSE16874 [12]

GSE47421 [24] Scale ofaveragePearsoncorrelations GSE9975 [36] GSE19369 [8] GSE13635 [6] GSE1435 [27] GSE12518 [6] GSE51608 [6] 0.2 GSE15580 [14] GSE7225 [9] GSE11186 [33] GSE42021 [27] GSE3126 [6] GSE2019 [12] GSE30083 [12] GSE12465 [14] GSE4142 [14] 0.4 GSE36530 [6] GSE12581 [16] GSE18281 [33] GSE14012 [24] GSE8156 [6] GSE51804 [10] GSE24121 [9] GSE45895 [27] GSE21054 [8] 0.6 GSE53951 [10] GSE45820 [6] GSE21393 [6] GSE11110 [11] GSE13563 [6] GSE46242 [12] GSE17097 [20] GSE29318 [9] GSE48203 [9] 0.8 GSE11382 [10] GSE31598 [12] GSE13149 [25] GSE33156 [18] Score 32.49 32.69 32.77 32.77 32.81 33.30 33.95 34.11 34.42 34.52 34.60 34.73 34.97 35.06 35.70 36.08 36.23 36.31 36.35 37.12 37.53 37.63 38.03 38.35 38.52 38.72 38.85 39.08 39.19 39.37 39.81 39.82 40.51 40.73 40.83 41.07 41.15 41.20 41.35 41.50 41.54 41.81 42.80 43.31 43.45 43.66 44.92 44.99 45.06 45.57 1.0 Notes Symbol Num ofCEMGenes:17.Predicted546.SelectedDatasets:626.Strength:79.0 CEM 1,Geneset"[K]Oocytemeiosis",Page9 Zmynd19 Cdk2ap1 Tbc1d31 Ankrd32 Gemin2 Cdkn2c Cdc123 Cep152 Metap2 Ppp1r8 Ppp1r7 Rbm8a Nt5dc2 Supt16 Cmss1 Tcerg1 Knstrn G3bp1 Prpf31 Cenpo Dnph1 Nup50 Cpsf3l Nop56 Nedd1 Ddx20 Pa2g4 Snrpg Myef2 Bard1 Gstcd Nudt1 Parp2 Dars2 Mis12 Xrcc2 Emg1 Paics Mnd1 Myg1 Nelfe Ddx1 Terf1 Dkc1 Hdgf Cct7 Ipo9 Dut Ncl Ilf2 0.0 1.0

GSE40513 [6] GSE16874 [12]

GSE47421 [24] Scale ofaveragePearsoncorrelations GSE9975 [36] GSE19369 [8] GSE13635 [6] GSE1435 [27] GSE12518 [6] GSE51608 [6] 0.2 GSE15580 [14] GSE7225 [9] GSE11186 [33] GSE42021 [27] GSE3126 [6] GSE2019 [12] GSE30083 [12] GSE12465 [14] GSE4142 [14] 0.4 GSE36530 [6] GSE12581 [16] GSE18281 [33] GSE14012 [24] GSE8156 [6] GSE51804 [10] GSE24121 [9] GSE45895 [27] GSE21054 [8] 0.6 GSE53951 [10] GSE45820 [6] GSE21393 [6] GSE11110 [11] GSE13563 [6] GSE46242 [12] GSE17097 [20] GSE29318 [9] GSE48203 [9] 0.8 GSE11382 [10] GSE31598 [12] GSE13149 [25] GSE33156 [18] Score 19.88 20.21 20.35 20.48 20.99 21.02 21.72 22.11 23.11 23.11 23.15 23.80 23.81 23.85 23.85 23.91 24.24 24.82 25.11 25.39 25.55 25.81 26.37 26.40 26.44 27.03 27.16 27.39 27.50 27.64 27.72 28.03 28.06 28.36 28.74 28.85 29.00 29.50 29.63 29.71 30.06 30.68 30.83 31.32 31.50 31.53 31.58 31.66 31.90 31.90 1.0 Notes D030056L22Rik Symbol Num ofCEMGenes:17.Predicted546.SelectedDatasets:626.Strength:79.0 CEM 1,Geneset"[K]Oocytemeiosis",Page10 Casp8ap2 Tmem209 Smarca5 Nfatc2ip Nudcd2 Nup188 Mcmbp Skiv2l2 Aarsd1 Hmgn5 Pradc1 Stoml2 Mthfd1 Gtf2e2 Polr2b Med14 Nup88 Nup54 Nop58 Cops3 Pdap1 Rad50 Cep72 Ssna1 Naa10 Thoc6 Prmt1 Parp1 Troap Clspn Recql U2af1 Noc4l Lsm6 Mdc1 Prpf3 Nop9 Dna2 Dcps Ctps Utp6 Sfpq Vars Cct5 E2f2 Eif3l Me2 Ctcf Dtl 0.0 1.0

GSE40513 [6] GSE16874 [12]

GSE47421 [24] Scale ofaveragePearsoncorrelations GSE9975 [36] GSE19369 [8] GSE13635 [6] GSE1435 [27] GSE12518 [6] GSE51608 [6] 0.2 GSE15580 [14] GSE7225 [9] GSE11186 [33] GSE42021 [27] GSE3126 [6] GSE2019 [12] GSE30083 [12] GSE12465 [14] GSE4142 [14] 0.4 GSE36530 [6] GSE12581 [16] GSE18281 [33] GSE14012 [24] GSE8156 [6] GSE51804 [10] GSE24121 [9] GSE45895 [27] GSE21054 [8] 0.6 GSE53951 [10] GSE45820 [6] GSE21393 [6] GSE11110 [11] GSE13563 [6] GSE46242 [12] GSE17097 [20] GSE29318 [9] GSE48203 [9] 0.8 GSE11382 [10] GSE31598 [12] GSE13149 [25] GSE33156 [18] Score 9.33 9.38 9.49 9.66 10.03 10.59 11.00 11.05 11.12 11.16 11.21 11.96 12.00 12.01 12.29 12.32 12.43 12.48 12.56 12.57 12.73 12.85 13.11 13.38 13.55 13.74 14.89 14.97 15.18 15.28 15.47 15.55 15.66 15.69 16.04 16.33 16.39 16.47 16.54 17.48 17.72 18.03 18.09 18.26 18.33 18.37 18.92 18.99 19.08 19.68 1.0 Notes 1600002H07Rik Symbol Num ofCEMGenes:17.Predicted546.SelectedDatasets:626.Strength:79.0 CEM 1,Geneset"[K]Oocytemeiosis",Page11 Tmem107 Eif4enif1 Magohb Prpf38a Wrap53 Zmym1 Rprd1b Zcchc8 Snrpd3 Arl6ip6 Wbp11 Mthfd2 Polr2d Pitrm1 Nubp1 Cenpa Aimp2 Cactin Apex1 Alms1 Dhx15 Hdac1 Tubb5 Znhit3 Thoc3 Mbnl3 Gspt1 Cct6a Nol11 Phf10 Ipo11 Prpf4 Srsf9 Nanp Cstf2 Nhp2 Nudc Hus1 Rcc2 Orc2 Mlh1 Iws1 Adsl Ctc1 Alg8 Taf9 Hn1 Atic Set 0.0 1.0

GSE40513 [6] GSE16874 [12]

GSE47421 [24] Scale ofaveragePearsoncorrelations GSE9975 [36] GSE19369 [8] GSE13635 [6] GSE1435 [27] GSE12518 [6] GSE51608 [6] 0.2 GSE15580 [14] GSE7225 [9] GSE11186 [33] GSE42021 [27] GSE3126 [6] GSE2019 [12] GSE30083 [12] GSE12465 [14] GSE4142 [14] 0.4 GSE36530 [6] GSE12581 [16] GSE18281 [33] GSE14012 [24] GSE8156 [6] GSE51804 [10] GSE24121 [9] GSE45895 [27] GSE21054 [8] 0.6 GSE53951 [10] GSE45820 [6] GSE21393 [6] GSE11110 [11] GSE13563 [6] GSE46242 [12] GSE17097 [20] GSE29318 [9] GSE48203 [9] 0.8 GSE11382 [10] GSE31598 [12] GSE13149 [25] GSE33156 [18] Score 2.03 2.06 2.49 2.50 2.65 2.78 2.86 2.91 2.94 2.99 3.11 3.13 3.27 3.30 3.38 3.40 3.58 3.59 3.60 4.22 4.30 4.37 4.43 4.52 4.66 4.69 4.80 5.52 6.02 6.15 6.21 6.27 6.37 6.39 6.43 6.74 7.04 7.36 7.58 7.62 7.86 7.94 8.42 8.51 8.53 8.53 8.56 8.93 9.26 9.31 1.0 Notes Symbol Num ofCEMGenes:17.Predicted546.SelectedDatasets:626.Strength:79.0 CEM 1,Geneset"[K]Oocytemeiosis",Page12 Ebna1bp2 Rnaseh2c Psmd14 Exosc3 Hnrnpf Psmc3 Ubap2 Cep78 Pds5b Xrcc1 Sf3b3 Sf3b5 Ttll12 0.0 1.0

GSE40513 [6] GSE16874 [12]

GSE17266 [59] Only showingfirst200datasets-Seetxtoutputforfulldetails . GSE53916 [6] GSE17794 [44] GSE39621 [51] GSE54215 [13] GSE6998 [32] GSE13225 [6] GSE46797 [6] GSE21224 [16] GSE57543 [6] GSE44260 [10] GSE13874 [14] GSE15303 [11] GSE31028 [6] GSE4694 [6] GSE27605 [8] GSE17796 [39] GSE48382 [10] GSE51385 [8] GSE17316 [12] GSE26290 [12] GSE30192 [6] GSE51883 [30] GSE20954 [14] GSE54490 [12] GSE51243 [7] GSE39449 [6] GSE7875 [16] GSE34839 [6] GSE25257 [6] GSE27786 [20] GSE21299 [12] GSE51075 [12] GSE12454 [13] GSE6957 [12] GSE54653 [6] GSE9287 [8] GSE29241 [6] GSE33308 [10] GSE15741 [6] GSE46185 [6] GSE6837 [8] GSE23845 [15] GSE26616 [6] GSE12498 [12] GSE21716 [28] GSE6875 [8] GSE12881 [6] GSE18135 [18] GSE21309 [9] GSE52474 [154] GSE32386 [13] GSE39034 [9] GSE16675 [72] GSE9763 [20] GSE45051 [18] GSE41342 [26] GSE17509 [57] GSE47959 [8] GSE12993 [6] GSE7020 [8] GSE45143 [6] GSE46209 [21] GSE31359 [8] GSE28621 [21] GSE46090 [12] GSE21900 [12] GSE30160 [6] GSE14769 [24] GSE12001 [6] GSE21379 [10] GSE10525 [18] GSE39082 [6] GSE22774 [6] GSE20302 [12] GSE11220 [44] GSE48397 [10] GSE24512 [29] GSE46606 [30] GSE28457 [24] GSE16684 [6] GSE34324 [12] GSE4260 [6] GSE8039 [32] GSE10176 [6] GSE6689 [12] GSE22180 [60] GSE28417 [12] GSE23502 [8] GSE15326 [10] GSE51628 [15] GSE13873 [27] GSE18326 [8] GSE7694 [12] GSE24628 [16] GSE4535 [6] GSE23505 [10] GSE8678 [6] GSE32330 [12] GSE27901 [23] GSE17745 [6] GSE21278 [48] GSE13611 [8] GSE15610 [12] GSE18115 [8] GSE13693 [9] GSE20100 [15] GSE33471 [12] GSE22124 [18] GSE50813 [24] GSE30745 [12] GSE39984 [18] GSE30485 [15] GSE18993 [13] GSE7657 [12] GSE30962 [16] GSE22005 [23] GSE11222 [42] GSE26355 [6] GSE23925 [6] GSE9247 [15] GSE19729 [14] GSE8660 [6] GSE13259 [10] GSE8960 [18] GSE32277 [33] GSE19885 [9] GSE20500 [6] GSE8025 [21] GSE31099 [24] GSE15872 [18] GSE31313 [22] GSE34729 [6] GSE20696 [8] GSE4768 [18] GSE28389 [20] GSE19925 [6] GSE27379 [6] GSE5041 [8] GSE5891 [6] GSE7460 [52] GSE45465 [39] GSE18534 [15] GSE40856 [8] GSE19004 [9] GSE13692 [8] GSE21491 [9] GSE49194 [14] GSE15267 [8] GSE43419 [20] GSE11201 [18] GSE18460 [16] CEM+ CEM GSE7503 [6] GSE24210 [16] GSE11818 [6] GSE48004 [6] GSE38031 [8] GSE27546 [51] 0.0 GSE7897 [60] GSE21711 [6]

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40513 Status: Public on Oct 16 2012 Title: Gene expression profile of mouse breast cancer V720 cells treated with vehicle or PD 0332991 Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 23079655 Summary & Design: Summary: D-cyclins represent components of cell cycle machinery. To test the efficacy of targeting D-cyclins in cancer treatment, we engineered mouse strains which allow acute and global ablation of individual D-cyclins in a living animal. Ubiquitous shutdown of cyclin D1 or inhibition of cyclin D associated kinase activity in mice bearing ErbB2-driven mammary carcinomas halted cancer progression and triggered tumor-specific senescence, without compromising the animals' health. Ablation of cyclin D3 in mice bearing T-cell acute lymphoblastic leukemias (T-ALL) triggered tumorspecific apoptosis. Such selective killing of leukemic cells can be also achieved by inhibiting cyclin D associated kinase activity in mouse and human T-ALL models. Hence, contrary to what one might expect from ablation of a cell cycle protein, acute shutdown of a D-cyclin leads not only to cell cycle arrest, but it also triggers tumor cell senescence or apoptosis, and it affects different tumor types through distinct cellular mechanisms. Inhibiting cyclin D-activity represents a highly-selective anticancer strategy which specifically targets cancer cells without significantly affecting normal tissues.

Overall design: Mouse breast cancer V720 cells were cultured in the presence of the CDK4/6 inhibitor PD 0332991 (PD; 1 microM) or vehicle (VO) for 24 hrs. Experiment was done in biological triplicate. A total of 6 RNA samples (3 vehicle treated and 3 PD 0332991 treated samples) were used for microarray expression analysis.

Background corr dist: KL-Divergence = 0.0313, L1-Distance = 0.0429, L2-Distance = 0.0022, Normal std = 0.7225

0.600 Kernel fit Pairwise Correlations Normal fit

Density 0.300

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

V720_vehicle_rep1V720_vehicle_rep2V720_vehicle_rep3 (0.137719)V720_PD0332991_rep1 (0.190402)V720_PD0332991_rep2 (0.180573)V720_PD0332991_rep3 (0.15944) (0.182382) (0.149485)[ min ] [ medium ] [ max ] CEM 1 Aurka 363.4 1211.2 1255.2 P ( S | Z, I ) = 1.00 Bub1 608.4 2150.6 2190.0 Mean Corr = 0.97905 Plk1 349.1 1399.8 1503.9 Cdc20 496.4 1665.5 1799.1 Ccnb2 1006.2 3675.2 3821.0 Sgol1 297.9 1092.2 1197.8 Espl1 82.9 335.0 367.1 Fbxo5 583.7 2013.3 2067.8 Cdc25c 195.8 798.2 845.5 Ccne2 296.1 828.8 844.3 Ccne1 278.7 415.6 468.5 Pkmyt1 226.7 317.2 347.9 Smc1a 1938.5 2681.8 2848.8 Ccnb1 33.3 94.2 96.7 Smc3 1998.5 2623.3 2800.2 Anapc1 1565.4 1865.6 1964.7 Anapc5 2611.8 3413.9 3523.7 Ccna2 1538.2 4738.1 5049.6 Cdk1 3175.7 6326.4 6472.5 Birc5 1585.2 4564.5 4643.2 Kif20a 459.2 1928.7 2075.8 Tpx2 536.7 1735.9 1836.1 CEM 1 + Ncapg 514.7 1834.8 1920.4 Top 10 Genes Ube2c 1224.8 4056.0 4311.9 Nusap1 779.4 3043.5 3067.2 Shcbp1 799.9 2916.3 2967.0 Kif11 231.2 856.2 872.6

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE16874" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 12 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16874 Status: Public on Dec 07 2010 Title: Expression in wild type and TgDREAM mouse B cells unstimulated or 2 days after LPS+IL4 stimulation Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21059893 Summary & Design: Summary: DREAM/KChIP-3 is a calcium-dependent transcriptional repressor highly expressed in immune cells. Transgenic mice expressing a dominant active DREAM mutant show reduced serum immunoglobulin levels. In vitro assays show that reduced immunoglobulin secretion is an intrinsic defect of transgenic B cells that occurs without impairment in plasma cell differentiation but with an accelerated entry in cell division and an increase in class switch recombination. B cells from DREAM knockout mice did not show any phenotype, due to compensation by endogenous KChIP-2. Expression arrays revealed modified expression of Edem1 and Derlin3, two proteins related to the ER-associated degradation pathway and of Klf9, a cell-cycle regulator. Our results disclose a function of DREAM and KChIP-2 in Ig subclass production in B lymphocytes.

Overall design: We used Affymetrix microarrays (GeneChip Mouse Genome 430 2.0) to compare global gene expression in wild type (WT) versus transgenic B cells (Tg), unstimulated and 2 days after LPS + IL4 stimulation. For ech type of sample three hybridizations were carried-out (independent biological replicates).

Background corr dist: KL-Divergence = 0.0300, L1-Distance = 0.0974, L2-Distance = 0.0115, Normal std = 0.9421

0.423 Kernel fit Pairwise Correlations Normal fit

Density 0.212

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

BCells_WildType_day0_REP1BCells_WildType_day0_REP2BCells_WildType_day0_REP3BCells_Transgenic_day0_REP1 BCells_Transgenic_day0_REP2(0.10565) BCells_Transgenic_day0_REP3(0.0889229) BCells_WildType_day2_REP1(0.0881205)BCells_WildType_day2_REP2 (0.0853605)BCells_WildType_day2_REP3 (0.0752302)BCells_Transgenic_day2_REP1 (0.0983158) BCells_Transgenic_day2_REP2(0.074158) BCells_Transgenic_day2_REP3(0.0760756) (0.0861239) (0.0649034) (0.0671853)[ (0.0899536)min ] [ medium ] [ max ] CEM 1 Aurka 225.3 2390.6 2566.1 P ( S | Z, I ) = 1.00 Bub1 119.1 3295.7 4133.5 Mean Corr = 0.96504 Plk1 521.3 2838.6 3435.7 Cdc20 601.9 6001.0 6729.9 Ccnb2 409.0 4755.4 5805.3 Sgol1 194.8 1839.8 2166.3 Espl1 251.3 2280.8 3117.9 Fbxo5 414.0 1786.8 2379.4 Cdc25c 144.5 559.1 610.2 Ccne2 57.8 722.3 832.3 Ccne1 313.7 1039.0 1357.2 Pkmyt1 627.4 800.8 1000.9 Smc1a 3531.0 5276.4 5685.8 Ccnb1 108.8 214.2 260.8 Smc3 985.9 2101.3 2354.1 Anapc1 1353.7 2772.6 3207.2 Anapc5 4376.1 9482.1 11162.6 Ccna2 488.9 4715.3 5698.6 Cdk1 389.6 5943.4 6640.3 Birc5 351.1 5246.1 6541.2 Kif20a 103.4 827.8 1434.5 Tpx2 172.0 2731.3 3127.9 CEM 1 + Ncapg 149.7 1829.2 2101.3 Top 10 Genes Ube2c 509.6 6874.7 8751.7 Nusap1 507.0 2612.1 3248.0 Shcbp1 314.3 3507.9 3745.6 Kif11 196.2 1292.0 1451.3

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE17266" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 59 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17266 Status: Public on Jan 12 2010 Title: Expression data from B6C3F1 mice treated with baclofen Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 19812364 Summary & Design: Summary: Mice were treated with either 100mg/kg baclofen or 0.5% methylcellulose alone by oral gavage for 1 or 5 days.

Overall design: Mice were sacrificed by cervical dislocation after either a single dose (1day) or 5 daily doses (5 days) of either baclofen or 0.5% methylcellulose two hours after the last dose. The bone marrow from the right humerus, a portion of the left lateral liver lobe and half a cross-section of the spleen were harvested and the RNA was isolated from these tissues using standard Qiagen reagents. Standard Affymetrix protocols were used for GeneChip probe preparations. 59 arrays.

Background corr dist: KL-Divergence = 0.0198, L1-Distance = 0.0483, L2-Distance = 0.0033, Normal std = 0.7864

0.507 Kernel fit Pairwise Correlations Normal fit

Density 0.254

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

liver-vehicle-1day-repliver-baclofen-1day-repliver-baclofen-1day-rep 1liver-vehicle-1day-rep (0.0235203)liver-baclofen-1day-rep 1 (0.0251928)liver-vehicle-1day-rep 2 (0.0242373) 2liver-baclofen-1day-rep (0.0211279)liver-vehicle-5day-rep 3 (0.0236393) 3liver-baclofen-5day-rep (0.0212788)liver-vehicle-5day-rep 4 (0.0211892) 1liver-baclofen-5day-rep (0.0217325)liver-vehicle-5day-rep 1 (0.0212389) 2liver-baclofen-5day-rep (0.0203277)liver-vehicle-5day-rep 2 (0.0227866) 3liver-baclofen-5day-rep (0.0222591)liver-baclofen-5day-rep 3 (0.022122) 4liver-baclofen-5day-rep (0.0202844)liver-baclofen-5day-rep 4 (0.0205918)liver-baclofen-5day-rep 5 (0.0220147)bone 6 (0.022775) marrow-vehicle-1day-repbone 7 (0.0212145) marrow-baclofen-1day-repbone 8 (0.0220453) marrow-vehicle-1day-repbone marrow-baclofen-1day-repbone 1 (0.0193947) marrow-vehicle-1day-repbone 1 (0.0177535) marrow-baclofen-1day-repbone 2 (0.0154875) marrow-vehicle-1day-repbone 2 (0.0148102) marrow-baclofen-1day-repbone 3 (0.0166325) marrow-vehicle-5day-repbone 3 (0.0154467) marrow-baclofen-5day-repbone 4 (0.0151549) marrow-vehicle-5day-repbone 4 (0.0175068) marrow-baclofen-5day-repbone 1 (0.0197765) marrow-vehicle-5day-repbone 1 (0.0190282) marrow-baclofen-5day-repbone 2 (0.0163711) marrow-vehicle-5day-repbone 2 (0.0170183) marrow-baclofen-5day-repbone 3 (0.0170948) marrow-baclofen-5day-repbone 3 (0.0182251) marrow-baclofen-5day-repbone 4 (0.0150092) marrow-baclofen-5day-repbone 4 (0.0143396) marrow-baclofen-5day-repspleen-vehicle-1day-rep 5 (0.0199902)spleen-baclofen-1day-rep 6 (0.0175522)spleen-vehicle-1day-rep 7 (0.0168601)spleen-baclofen-1day-rep 1 8 (0.0153816) (0.015605)spleen-vehicle-1day-rep 1 (0.0126186)spleen-baclofen-1day-rep 2 (0.0111501)spleen-vehicle-1day-rep 2 (0.00970615)spleen-baclofen-1day-rep 3 (0.0131395)spleen-vehicle-5day-rep 3 (0.0151049)spleen-baclofen-5day-rep 4 (0.0102568)spleen-vehicle-5day-rep 4 (0.013372)spleen-baclofen-5day-rep 1 (0.0156053)spleen-vehicle-5day-rep 1 (0.013142)spleen-baclofen-5day-rep 2 (0.0125504)spleen-vehicle-5day-rep 2 (0.0114947)spleen-baclofen-5day-rep 3 (0.012646)spleen-baclofen-5day-rep 3 (0.010803)spleen-baclofen-5day-rep 4 (0.00843429)spleen-baclofen-5day-rep 4 (0.0113667)spleen-baclofen-5day-rep 5 (0.0104362) 6 (0.0127237) 7 (0.00998391) 8 (0.0114488)[ min ] [ medium ] [ max ] CEM 1 Aurka 50.0 738.3 2867.7 P ( S | Z, I ) = 1.00 Bub1 23.5 731.5 2834.4 Mean Corr = 0.95082 Plk1 133.3 703.9 1966.5 Cdc20 80.3 1477.9 5323.1 Ccnb2 46.6 1645.9 7438.6 Sgol1 99.1 627.6 1804.1 Espl1 46.3 552.7 1460.7 Fbxo5 61.2 1386.3 4277.7 Cdc25c 28.2 135.6 391.3 Ccne2 28.5 514.8 2237.8 Ccne1 114.7 710.1 1808.1 Pkmyt1 105.9 668.7 1204.0 Smc1a 1841.6 3578.6 4686.3 Ccnb1 36.4 52.6 167.8 Smc3 641.5 1779.1 3213.8 Anapc1 1056.6 1461.4 2023.8 Anapc5 2239.2 6376.0 9909.6 Ccna2 64.5 2076.2 7532.7 Cdk1 173.3 1282.1 5654.6 Birc5 36.3 2404.1 7837.6 Kif20a 31.6 349.9 1685.4 Tpx2 40.9 780.0 3250.9 CEM 1 + Ncapg 26.3 364.2 1256.6 Top 10 Genes Ube2c 54.5 5030.8 15346.5 Nusap1 43.7 1607.3 6089.7 Shcbp1 32.1 520.0 1970.9 Kif11 44.2 394.2 2194.2

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE53916" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 6 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53916 Status: Public on Feb 17 2014 Title: Expression data from mouse bone marrow cells expressing renin driven expression of green fluorescent protein. Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 24549417 Summary & Design: Summary: Local renin antiotensin systems have been identified for many extra-renal sites. Bone marrow has been proposed as one such site, although the nature of the renin-expressing cell type(s) has not been established.

Affymetrix microarrays were used to characterize the expression profile of renin-expressing GFP positive cells.

Overall design: Green fluorescent protein positive cells were sorted from whole bone marrow collected from adult transgenic mice. Bone marrow from several mice was collected and pooled on the day of a FACS sort. A portion of this was reserved for RNA extraction while the remainder was sorted. RNA was prepared with Trizol. Bone marrow collection and sorting was performed 3 times so that microarrays could be run in triplicate.

Background corr dist: KL-Divergence = 0.0206, L1-Distance = 0.0262, L2-Distance = 0.0007, Normal std = 0.7706

0.537 Kernel fit Pairwise Correlations Normal fit

Density 0.268

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

Bone marrowBone marrow presortBone marrow sortedcellsBone biological marrow cellspresortBone biological marrow sortedcells Bonerep1 biological (0.144031) marrow cells presortrep1 biological(0.281971) sortedcells rep2 biological(0.138525) cells rep2 biological(0.142974) [rep3 min (0.150093) rep3 (0.142405)] [ medium ] [ max ] CEM 1 Aurka 322.1 2420.7 2864.8 P ( S | Z, I ) = 1.00 Bub1 321.5 2799.6 3177.3 Mean Corr = 0.94558 Plk1 232.4 1837.0 2029.4 Cdc20 953.6 5106.4 5226.2 Ccnb2 891.7 6079.0 6743.9 Sgol1 439.1 2306.1 2732.6 Espl1 199.2 1054.2 1301.1 Fbxo5 1033.1 4252.6 4820.6 Cdc25c 106.4 391.5 502.5 Ccne2 192.2 1529.1 3177.5 Ccne1 158.1 1092.6 1148.0 Pkmyt1 318.3 1108.8 1247.1 Smc1a 3309.5 6712.3 6913.3 Ccnb1 40.0 68.5 88.7 Smc3 1769.9 2609.3 2947.6 Anapc1 1166.6 1813.3 1908.2 Anapc5 3871.1 8119.0 8249.9 Ccna2 441.2 5456.4 5737.2 Cdk1 448.7 4337.9 4482.7 Birc5 234.1 2783.2 3963.6 Kif20a 166.7 1787.1 2385.7 Tpx2 368.3 3235.8 4173.9 CEM 1 + Ncapg 163.8 1343.3 1538.7 Top 10 Genes Ube2c 594.1 7691.5 10108.7 Nusap1 1156.6 8313.9 8998.0 Shcbp1 427.5 3305.5 3845.8 Kif11 339.2 3044.6 3559.5

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE17794" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 44 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17794 Status: Public on Jan 11 2010 Title: Expression data from B6C3F1 mice treated with 2-butoxyethanol Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 19812364 Summary & Design: Summary: Mice were dosed with 2-BE (900mg/kg) or vehicle by oral gavage and sacrificied either after 4 hours of a single dose or after 7 days of daily dosing.

Overall design: Mice were euthanased by cervical dislocation under ketamine / acepromazine (100 mg/kg / 5 mg/kg, I.P) anesthesia. The bone marrow from the right humerus, a portion of the left lateral liver lobe and half a cross-section of the spleen were harvested and the RNA was isolated from these tissues using standard Qiagen reagents. Standard Affymetrix protocols were used for GeneChip probe preparations. 44 arrays.

Background corr dist: KL-Divergence = 0.0249, L1-Distance = 0.0283, L2-Distance = 0.0013, Normal std = 0.6953

0.574 Kernel fit Pairwise Correlations Normal fit

Density 0.287

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

liver-vehicle-4hours-repliver-vehicle-4hours-repliver-vehicle-4hours-repliver-2BE-4hours-rep 1 (0.0223298)liver-2BE-4hours-rep 2 (0.0214321)liver-2BE-4hours-rep 3 (0.0248711) 1liver-2BE-4hours-rep (0.0224905) 2spleen-vehicle-4hours-rep (0.0267183) 3spleen-vehicle-4hours-rep (0.0231215) 4spleen-vehicle-4hours-rep (0.025096)spleen-vehicle-4hours-rep 1 (0.0160113)spleen-2BE-4hours-rep 2 (0.0191871)spleen-2BE-4hours-rep 3 (0.0150748)spleen-2BE-4hours-rep 4 (0.0157912)spleen-2BE-4hours-rep 1 (0.0158439)liver-vehicle-7days-rep 2 (0.018838)liver-vehicle-7days-rep 3 (0.0186521)liver-vehicle-7days-rep 4 (0.0189577)liver-vehicle-7days-rep 1 (0.0280629)liver-2BE-7days-rep 2 (0.0238107)liver-2BE-7days-rep 3 (0.0280705)liver-2BE-7days-rep 4 (0.0237893) 1 (0.0272046)liver-2BE-7days-rep 2 (0.0243444)liver-2BE-7days-rep 3 (0.0280211)bone 4marrow-vehicle-7days-rep (0.0264237)bone 5marrow-vehicle-7days-rep (0.0289987)bone marrow-vehicle-7days-repbone marrow-vehicle-7days-repbone 1 (0.0204758) marrow-vehicle-7days-repbone 2 (0.023297) marrow-2BE-7days-repbone 3 (0.0229132) marrow-2BE-7days-repbone 4 (0.02255) marrow-2BE-7days-repbone 5 (0.0207962) marrow-2BE-7days-rep 1bone (0.0270803) marrow-2BE-7days-rep 2spleen-vehicle-7days-rep (0.0265868) 3spleen-vehicle-7days-rep (0.022401) 4spleen-vehicle-7days-rep (0.0211487) 5spleen-vehicle-7days-rep (0.0212707) 1 (0.0184471)spleen-vehicle-7days-rep 2 (0.0167733)spleen-2BE-7days-rep 3 (0.0175161)spleen-2BE-7days-rep 4 (0.0156717)spleen-2BE-7days-rep 5 (0.0156409) spleen-2BE-7days-rep1 (0.0315893) spleen-2BE-7days-rep2 (0.0453931) 3 (0.0242894) 4 (0.0274842) 5 (0.0155339)[ min ] [ medium ] [ max ] CEM 1 Aurka 59.6 718.6 3225.8 P ( S | Z, I ) = 1.00 Bub1 25.3 718.0 2602.6 Mean Corr = 0.94448 Plk1 140.9 579.2 2109.4 Cdc20 75.3 1540.5 5348.4 Ccnb2 48.7 2288.4 9044.6 Sgol1 80.3 733.4 3602.8 Espl1 47.6 509.5 1970.5 Fbxo5 70.1 1691.0 6483.0 Cdc25c 35.5 234.9 718.2 Ccne2 30.3 584.3 3808.4 Ccne1 157.7 503.4 2309.1 Pkmyt1 95.0 642.7 1640.1 Smc1a 1582.0 2900.7 4558.0 Ccnb1 37.8 61.1 244.0 Smc3 537.9 1648.5 3211.0 Anapc1 973.4 1341.0 2173.8 Anapc5 2454.7 5945.9 10209.1 Ccna2 100.9 2548.0 10211.9 Cdk1 208.2 1490.7 6496.1 Birc5 45.2 2845.4 11317.0 Kif20a 35.0 377.6 1763.0 Tpx2 38.9 1126.5 4262.7 CEM 1 + Ncapg 26.2 530.3 2086.2 Top 10 Genes Ube2c 82.2 6172.8 22147.2 Nusap1 56.3 2241.9 7556.1 Shcbp1 44.8 480.4 1987.5 Kif11 48.6 570.5 3367.1

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE39621" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 51 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39621 Status: Public on Dec 27 2012 Title: Expression data from brain, liver and spleen of Npc1-/- mice Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 23094108 Summary & Design: Summary: Niemann-Pick Type C (NPC) disease is a rare, genetic, lysosomal disorder with progressive neurodegeneration. Poor understanding of the pathophysiology and lack of blood-based diagnostic markers are major hurdles in the treatment and management of NPC and several additional neurological, lysosomal disorders. To identify disease severity correlates, we undertook whole genome expression profiling of sentinel organs, brain, liver, and spleen of Balb/c Npc1-/- mice (Npc1nih)relative to Npc1+/- at an asymptomatic stage, as well as early- and late-symptomatic stages. Unexpectedly, we found prominent up regulation of innate immunity genes with age-dependent change in their expression, in all three organs. We shortlisted a set of 12 secretory genes whose expression steadily increased with age in both brain and liver, as potential plasma correlates for the neurological disease. Ten were innate immune genes with eight ascribed to lysosomes. Several are known to be elevated in diseased organs of murine models of other lysosomal diseases including Gauchers disease, Sandhoff disease and MPSIIIB. We validated the top candidate lysozyme, in the plasma of Npc1-/- as well as Balb/c Npc1nmf164 mice (bearing a point mutation closer to human disease mutants) and show its reduction in response to an emerging therapeutic. We further established elevation of innate immunity in Npc1-/- mice through multiple functional assays including inhibition of bacterial infection as well as cellular analysis and immunohistochemistry.

We used microarrays on the diseased organs, brain, liver and spleen of the Npc1-/- mice to unserstand the molecular changes occur during the progression of NPC diseases. From the data, we have identified 12 potential genes which can be potentially developed as blood-based biomarker. We have also discovered up regulation of innate iimunity genes in all three organs of Npc1-/- mice and functionally validated them in liver and spleen.

Overall design: Brain from 11 female Npc1/ and 16 control female mice (Npc1+/+ and Npc1+/) from 6 age groups (20-25, 37-40, 54-55, 59-62, 67-71 and 81-84 days) were surgically harvested. Liver and spleen from 6 Npc1-/- and 6 Npc1+/- female mice from three age group ( 20-25, 54-55 and 67-71 days) were surgically harvested. Organs were kept in RNA later and stored at -20 ´C until used. RNA was isolated and Affymetrix mouse 430 2.0 array hybridizations were performed by UCLA Clinical Microarray Core, UCLA, Los Angeles, CA, USA. Subsequent raw data were analyzed using DNA-Chip Analyzer (D-Chip) with the .CEL files obtained from AGCC. Data from Npc1-/- mice from all age groups were compared to control mice (Npc1+/- and/or Npc1-/- mice) from all age groups separately for brain, liver and spleen. 'Matrix Table1' corrsponds for brain, 'Matrix Table2' corresponds for liver and 'Matrix Table3' corresponds for spleen. Thresholds for selecting significant genes were set at a relative difference Â³1.5-fold, absolute difference Â³100 signal intensity units and p<0.05. Genes that met all three criteria simultaneously were considered as significant change.

Background corr dist: KL-Divergence = 0.0594, L1-Distance = 0.0598, L2-Distance = 0.0057, Normal std = 0.5712

0.698 Kernel fit Pairwise Correlations Normal fit

Density 0.349

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

WT BrainWT 20d Brain Mouse1HET 25d Brain Mouse1 HET(0.0148892) 20d Brain NPCMouse1(0.0113389) 25d Brain NPCMouse1 (0.0145344) 20d Brain HETMouse1 (0.0106688) 25d Brain HETMouse1 (0.010586) 37d Brain NPCMouse1 (0.007288) 40d Brain NPCMouse1 (0.014725) 37d Brain HETMouse1 (0.0109165) 40d Brain HETMOuse1 (0.0130123) 54d Brain NPCMouse1 (0.0088969) 55d Brain NPCMouse1 (0.0128594) 54d Brain WTMOuse1 (0.00982459) 55dBrain WTMouse1 (0.0105695) 60d Brain Mouse1HET (0.0107609) 60d Brain Mouse2 HET(0.011703) 59d Brain NPCMouse1(0.0149633) 62d Brain NPCMouse1 (0.011507) 59d Brain WTMouse1 (0.0153444) 62dBrain HETMouse1 (0.0203924) 67d Brain Mouse1NPC (0.0128794) 67d Brain HETMouse1(0.0106145) 67d Brain HETMouse1 (0.0156008) 81d Brain NPCMouse1 (0.00991553) 82d Brain NPCMouse1 (0.0099392) 82d Brain HETMouse1 (0.0109821) 84d Liver HETMouse1 (0.010644) 20d Liver Mouse1NPC (0.0116421) 25d Liver Mouse1NPC (0.0200453) 20d Liver Mouse1HET (0.0162825) 25d Liver Mouse1HET (0.0158124) 54 Liver Mouse1NPC (0.0146185) 55d Liver (0.0172313)Mouse1NPC 54d Liver Mouse1HET (0.0182169) 55d Liver Mouse1HET (0.0178408) 67d Liver Mouse1NPC (0.0232518) 67d Liver Mouse2NPC (0.0183535) 67 Liver Mouse1HET (0.0169899) 71d Spleen (0.0131481)Mouse1HET Spleen20dNPC (0.0136789) Mouse1 25dSpleenNPC Mouse1 (0.0701321) Spleen20dHET Mouse1 (0.0442846) Spleen25dHET Mouse1 (0.0608476) Spleen54dNPC Mouse1 (0.060233) 55dSpleenNPC Mouse1 (0.0269406) Spleen54dHET Mouse1 (0.0441598) Spleen55dHET Mouse1 (0.0289717) Spleen67dNPC Mouse1 (0.0196125) 67dSpleenNPC Mouse2 (0.0403178) Spleen67 Mouse1 (0.0245959) 71d (0.0246085)Mouse1 (0.0228282)[ min ] [ medium ] [ max ] CEM 1 Aurka 38.8 77.1 4734.8 P ( S | Z, I ) = 1.00 Bub1 10.9 34.8 3293.7 Mean Corr = 0.94034 Plk1 93.2 132.2 2921.2 Cdc20 42.9 136.0 4332.9 Ccnb2 32.3 90.5 10059.8 Sgol1 32.3 70.6 3453.1 Espl1 33.5 225.5 4934.6 Fbxo5 25.7 61.1 12655.8 Cdc25c 1.2 25.8 569.6 Ccne2 90.0 254.8 3419.5 Ccne1 65.8 247.9 4492.8 Pkmyt1 1.2 15.1 1531.1 Smc1a 721.9 1609.9 6718.0 Ccnb1 27.3 58.4 552.7 Smc3 518.9 1657.7 4700.7 Anapc1 529.4 868.2 3922.7 Anapc5 1477.3 2591.9 6719.9 Ccna2 84.3 210.4 22644.5 Cdk1 46.3 118.9 14774.1 Birc5 37.2 100.8 12043.1 Kif20a 15.1 40.0 1183.2 Tpx2 40.3 140.7 2835.6 CEM 1 + Ncapg 3.0 53.5 4039.5 Top 10 Genes Ube2c 23.8 74.3 17016.6 Nusap1 48.6 83.7 8844.6 Shcbp1 40.4 78.3 2205.1 Kif11 36.4 71.0 2337.4

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE54215" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 13 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54215 Status: Public on Mar 02 2014 Title: Comparison of gene expression profiles of naÃ¯ve and in vitro effector CD8+ T cells from wild-type and BATF-/- mice Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 24584090 Summary & Design: Summary: The transcription factor BATF is required for Th17 and TFH differentiation. Here, we show that BATF also has a fundamental role in regulating effector CD8+ T cell differentiation. BATF-deficient CD8+ T cells show profound defects in effector expansion and undergo proliferative and metabolic catastrophe early after antigen encounter. BATF, together with IRF4 and Jun proteins, binds to and promotes early expression of genes encoding lineage-specific transcription-factors (T-bet and Blimp-1) and cytokine receptors, while paradoxically repressing genes encoding effector molecules (IFNg and granzyme B). Thus, BATF amplifies TCR-dependent transcription factor expression and augments inflammatory signal propagation but restrains effector gene expression. This checkpoint prevents irreversible commitment to an effector fate until a critical threshold of downstream transcriptional activity has been achieved.

Overall design: P14 TCR transgenic CD8+ T cells from wild-type or BATF-/- mice were examined either as naÃ¯ve cells or after 3 days of in vitro stimulation with antibodies to CD3 and CD28 in the presence of IL-2

Background corr dist: KL-Divergence = 0.0486, L1-Distance = 0.0713, L2-Distance = 0.0070, Normal std = 0.6584

0.695 Kernel fit Pairwise Correlations Normal fit

Density 0.348

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

WT_P14_Naive_rep1WT_P14_Naive_rep2BATF_KO_P14_Naive_rep1 (0.109252)BATF_KO_P14_Naive_rep2 (0.115688)BATF_KO_P14_Naive_rep3WT_P14_D3_Effector_rep1 (0.0977852)WT_P14_D3_Effector_rep2 (0.114448)WT_P14_D3_Effector_rep3 (0.0849134)WT_P14_D3_Effector_rep4 (0.052003)BATF_KO_P14_D3_Effector_rep1 (0.0637348)BATF_KO_P14_D3_Effector_rep2 (0.076799)BATF_KO_P14_D3_Effector_rep3 (0.0615748)BATF_KO_P14_D3_Effector_rep4 (0.0687123) (0.0435848) (0.0491561)[ min (0.0623485) ] [ medium ] [ max ] CEM 1 Aurka 214.7 2362.7 2811.3 P ( S | Z, I ) = 1.00 Bub1 307.3 6553.5 7345.5 Mean Corr = 0.93381 Plk1 205.5 2008.2 2273.0 Cdc20 541.2 5446.1 5985.8 Ccnb2 657.0 8814.3 9532.9 Sgol1 224.3 2103.7 2202.5 Espl1 237.1 1845.3 2056.5 Fbxo5 851.8 4282.5 4595.6 Cdc25c 67.4 564.7 666.7 Ccne2 127.8 980.9 1281.6 Ccne1 455.1 865.6 1023.9 Pkmyt1 411.2 801.8 872.7 Smc1a 4753.9 5749.0 6257.0 Ccnb1 46.4 109.2 148.9 Smc3 1619.7 2286.7 2774.2 Anapc1 2080.3 2773.9 2930.8 Anapc5 5236.8 5833.1 6629.1 Ccna2 808.6 9437.7 10151.6 Cdk1 414.6 5158.3 5403.1 Birc5 643.0 7210.7 8109.1 Kif20a 191.4 2168.8 2337.6 Tpx2 163.4 2573.6 2878.6 CEM 1 + Ncapg 135.0 2297.7 2482.4 Top 10 Genes Ube2c 1177.2 15994.0 17816.6 Nusap1 514.0 8143.6 8967.4 Shcbp1 385.7 3268.1 3732.3 Kif11 182.4 1549.1 1781.7

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE6998" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 32 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6998 Status: Public on Feb 09 2007 Title: Expression profiling of developmental and regenerating liver in mice Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 17227769 Summary & Design: Summary: Normal adult liver is uniquely capable of renewal

and repair after injury. Whether this response

represents simple hyperplasia of various liver elements

or requires recapitulation of the genetic program of

the developing liver is not known. To study these possibilities,

we examined transcriptional programs of

adult liver after partial hepatectomy and contrasted

these with developing embryonic liver. Principal component

analysis demonstrated that the time series of

gene expression during liver regeneration does not segregate

according to developmental transcription patterns.

Gene ontology analysis revealed that liver restoration

after hepatectomy and liver development differ

dramatically with regard to transcription factors

and chromatin structure modification. In contrast, the

tissues are similar with regard to proliferationassociated

genes. Consistent with these findings, realtime

polymerase chain reaction showed transcription

factors known to be important in liver development

are not induced during liver regeneration. These three

lines of evidence suggest that at a transcriptional level,

restoration of liver mass after injury is best described

as hepatocyte hyperplasia and not true regeneration.

We speculate this novel pattern of gene expression may

underlie the unique capacity of the liver to repair itself

after injury.

Keywords: time course

Overall design: Each experimental time point is represented by two separate samples, each consisting of at least 3 pooled tissues from different animals. For example, 6 hepatectomies were performed for the 1 hour post-hepatectomy time point. Time 0 is used as control.

Background corr dist: KL-Divergence = 0.0534, L1-Distance = 0.0220, L2-Distance = 0.0006, Normal std = 0.5487

0.727 Kernel fit Pairwise Correlations Normal fit

Density 0.364

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

baselinebaseline sampleregeneration sampleat T0,regeneration rep1 at T0, (0.0196522)sampleregeneration rep2 (0.0245252) sampleatregeneration T1, rep1 sampleatregeneration T1, (0.0226779) rep2 sampleatregeneration T2, (0.0275256) rep1 sampleatregeneration T2, (0.0266849) rep2 sampleatregeneration T6, (0.0237063) rep1 sampleatregeneration T6, (0.019207) rep2 sampleatregeneration T12, (0.0187327) samplerep1atregeneration T12, (0.0187114) samplerep2atregeneration T18, (0.0417774) samplerep1atregeneration T18, (0.0187381) samplerep2atregeneration T24, (0.0325544) samplerep1atregeneration T24, (0.0174898) samplerep2atregeneration T30, (0.0229301) samplerep1atregeneration T30, (0.0186814) samplerep2atregeneration T48, (0.0157254) samplerep1atdevelopmental T48, (0.0181816) samplerep2atdevelopmental T72, (0.0692559) rep1at developmentalsample T72, (0.0151002) rep2 developmental sampleat T105,(0.0129751) developmental sampleat rep1 T105, (0.0524869) developmental sampleat rep2 T115, (0.0609155) developmental sampleat rep1 T115, (0.0482161) developmental sampleat rep2 T125, (0.0529352) developmental sampleat rep1 T125, (0.03227) developmental sampleat rep2 T135, (0.0384658) developmental sampleat rep1 T135, (0.0428918) developmental sampleat rep2 T145, (0.0417185) sampleat rep1 T145, (0.0381711) sampleat rep2 T165, (0.0407998) at rep1 T165, (0.0372469)[ rep2min (0.0290497) ] [ medium ] [ max ] CEM 1 Aurka 3.7 97.0 2669.7 P ( S | Z, I ) = 1.00 Bub1 3.3 21.6 2069.3 Mean Corr = 0.93219 Plk1 382.3 645.8 3499.1 Cdc20 3.3 237.8 3895.5 Ccnb2 3.3 82.7 4967.1 Sgol1 3.3 31.7 1404.0 Espl1 32.9 103.1 1856.3 Fbxo5 58.8 180.1 3395.4 Cdc25c 3.9 87.6 445.9 Ccne2 3.7 92.9 1781.0 Ccne1 3.4 66.9 2049.1 Pkmyt1 344.4 492.5 1056.4 Smc1a 604.5 808.5 2733.2 Ccnb1 48.2 111.2 212.2 Smc3 281.3 472.2 2883.7 Anapc1 918.9 1183.1 2853.5 Anapc5 1099.4 1481.5 6386.5 Ccna2 9.1 245.6 7042.4 Cdk1 3.3 251.9 6343.5 Birc5 3.3 105.8 5878.8 Kif20a 49.8 112.4 1235.3 Tpx2 32.8 137.0 2233.0 CEM 1 + Ncapg 3.5 109.6 2208.5 Top 10 Genes Ube2c 3.5 211.5 9837.2 Nusap1 129.8 273.1 4229.3 Shcbp1 3.3 122.4 1684.7 Kif11 3.3 82.4 1616.4

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE13225" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 6 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13225 Status: Public on Nov 30 2008 Title: (AKR/J x FVB/NJ)F1 versus (DBA/2J x FVB)F1 spleen expression data Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 19118016 Summary & Design: Summary: F1 hybrids from (AKR/J x FVB/NJ) and (DBA/2J x FVB/NJ) outcrosses display a 20-fold difference in mammary tumor metastatic capacity, due to differences in inherited polymorphisms. Expression studies were performed to determine whether polymorphism-driven gene expression signatures predictive of outcome could be generated from normal tissues

Keywords: Basal transcription profiles

Overall design: Spleen from adult F1 animals from (AKR/J x FVB/NJ) and (DBA/2J x FVB/NJ) outcrosses was collected and arrayed on Affymetrics chip to identify basal differences in gene expression between the different genotypes

Background corr dist: KL-Divergence = 0.0222, L1-Distance = 0.0130, L2-Distance = 0.0002, Normal std = 0.7145

0.558 Kernel fit Pairwise Correlations Normal fit

Density 0.279

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

spleen akr1spleen (0.157885) akr2spleen (0.124601) akr3spleen (0.205194) dba1spleen (0.113369) dba2spleen (0.195261) dba3 (0.20369) [ min ] [ medium ] [ max ] CEM 1 Aurka 283.7 741.5 1327.2 P ( S | Z, I ) = 1.00 Bub1 338.2 624.6 1331.3 Mean Corr = 0.92791 Plk1 428.5 751.4 1353.9 Cdc20 782.7 1441.0 2558.4 Ccnb2 664.0 1886.6 3455.3 Sgol1 242.9 529.1 934.6 Espl1 379.2 531.8 962.0 Fbxo5 483.1 894.0 1330.0 Cdc25c 126.2 165.6 267.7 Ccne2 77.0 247.0 446.7 Ccne1 213.7 426.8 868.4 Pkmyt1 553.8 750.1 938.4 Smc1a 3444.0 3622.9 4140.7 Ccnb1 54.1 76.7 96.6 Smc3 1251.6 1397.0 1682.1 Anapc1 1456.1 1587.7 1751.7 Anapc5 5830.1 7207.4 8684.5 Ccna2 491.1 1264.1 2389.8 Cdk1 687.6 1522.2 2847.3 Birc5 707.1 1924.6 3630.2 Kif20a 156.3 243.9 514.3 Tpx2 322.2 540.7 1081.7 CEM 1 + Ncapg 110.0 231.7 454.9 Top 10 Genes Ube2c 1662.7 5836.4 9158.9 Nusap1 534.7 1531.3 2358.9 Shcbp1 242.5 361.8 610.9 Kif11 197.9 391.8 746.7

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE46797" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 6 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE46797 Status: Public on May 10 2013 Title: Expression data from c-Myc+ Notch1 T-ALL initiating cells Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 23791182 Summary & Design: Summary: Missense FBXW7 mutations are prevalent in various tumors, including T-cell acute lymphoblastic leukemia (T-ALL). To study the effects of such lesions, we generated animals carrying regulatable Fbxw7 mutant alleles. We show here that these mutations specifically bolster cancer-initiating cell activity in collaboration with Notch1 oncogenes, but spare normal hematopoietic stem cell function. We were also able to show that FBXW7 mutations specifically affect the ubiquitylation and half-life of c-Myc protein, a key T-ALL oncogene. Using animals carrying c-Myc fusion alleles, we connected Fbxw7 function to c-Myc abundance and correlated c-Myc expression to leukemia-initiating activity.

Overall design: Three independent Notch1 T-ALL were derived on c-Myc-GFP background and sorted from the spleen of leukemic mice on the basis of GFP expression for RNA extraction and hybridization on Affymetrix microarrays

Background corr dist: KL-Divergence = 0.0376, L1-Distance = 0.0289, L2-Distance = 0.0011, Normal std = 0.6371

0.637 Kernel fit Pairwise Correlations Normal fit

Density 0.318

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

Notch1 Notch1T-ALL MycGFP Notch1T-ALL MycGFP Notch1T-ALL negative MycGFP Notch1T-ALL negative replicate MycGFP Notch1T-ALL negative replicate 1 (0.13911) MycGFP T-ALL positive replicate 2 (0.194942) MycGFP positive replicate 3 (0.184268) positive replicate 1 (0.238379)[ replicatemin 2 (0.127033) 3] (0.116269) [ medium ] [ max ] CEM 1 Aurka 98.4 762.0 1403.2 P ( S | Z, I ) = 1.00 Bub1 191.1 1610.6 3232.7 Mean Corr = 0.92463 Plk1 118.3 554.0 1113.1 Cdc20 120.2 930.4 1736.9 Ccnb2 468.2 2293.0 4314.3 Sgol1 135.4 969.1 1505.8 Espl1 38.6 350.9 599.1 Fbxo5 167.3 1134.1 2536.0 Cdc25c 50.7 626.2 997.1 Ccne2 216.0 1186.3 1605.8 Ccne1 89.9 409.8 1067.1 Pkmyt1 32.3 163.9 240.0 Smc1a 840.9 2051.0 2440.1 Ccnb1 92.2 1462.6 2540.3 Smc3 612.0 866.7 907.3 Anapc1 402.4 641.4 968.8 Anapc5 4259.0 6935.1 8591.3 Ccna2 482.3 3997.8 5699.1 Cdk1 698.1 5664.8 9993.5 Birc5 2431.9 11433.4 13218.6 Kif20a 116.6 649.0 1353.2 Tpx2 198.0 966.6 1282.9 CEM 1 + Ncapg 456.4 4796.1 6364.7 Top 10 Genes Ube2c 849.3 7235.8 11785.6 Nusap1 421.3 4213.4 7018.9 Shcbp1 163.3 1748.4 3877.4 Kif11 59.9 926.5 1219.0

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE21224" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 16 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21224 Status: Public on Oct 01 2010 Title: Transcriptional ontogeny of the developing liver Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 22260730 Summary & Design: Summary: We characterized gene expression changes in the developing mouse liver at gestational days (GD) 11.5, 12.5, 13.5, 14.5, 16.5, and 19.5 and in the neonate (postnatal day (PND) 7 and 30) using full-genome microarrays and compared these changes to that in the adult liver. The fetal liver, and to a lesser extent the neonatal liver, exhibited dramatic differences in gene expression compared to adults. Canonical pathway analysis of the fetal liver signature demonstrated increases in functions important in cell replication and DNA fidelity whereas most metabolic pathways of intermediary metabolism were suppressed. Comparison of the dataset to a number of previously published datasets revealed 1) a striking similarity between the fetal liver and that of the pancreas in both mice and humans, 2) a nucleated erythrocyte signature in the fetus and 3) suppression of most xenobiotic metabolism genes throughout development, except a number of transporters associated with expression in hematopoietic cells.

Keywords: gene expression/microarray

Overall design: We characterized gene expression changes in the developing mouse liver at gestational days (GD) 19 and in the neonate (postnatal day (PND) 7 and 30) using full-genome microarrays and compared these changes to that in the adult liver. Total RNA was isolated from liver samples and gene expression analyzed using Affymetrix Mouse 430 2.0 GeneChips. Data from 16 samples, with four mice in each of the four age groups, were analyzed.

Background corr dist: KL-Divergence = 0.0715, L1-Distance = 0.0857, L2-Distance = 0.0154, Normal std = 0.5557

0.910 Kernel fit Pairwise Correlations Normal fit

Density 0.455

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

Mouse liver_GD19_4Mouse liver_GD19_5Mouse (0.0921321) liver_GD19_10Mouse (0.100372) liver_GD19_18Mouse liver_PND7_26Mouse(0.0836226) liver_PND7_29Mouse(0.117407) liver_PND7_30Mouse(0.0377054) liver_PND7_31Mouse(0.03916) liver_PND32_33Mouse(0.0369729) liver_PND32_34Mouse(0.0409566) liver_PND32_37Mouse (0.0551539) liver_PND32_40Mouse (0.0457093) liver_PND67_45Mouse (0.0453214) liver_PND67_46Mouse (0.0457123) liver_PND67_47Mouse (0.049296) liver_PND67_49 (0.0605923) (0.0609932) (0.0888926)[ min ] [ medium ] [ max ] CEM 1 Aurka 64.8 634.5 2236.5 P ( S | Z, I ) = 1.00 Bub1 6.5 375.3 1408.1 Mean Corr = 0.92361 Plk1 27.3 422.0 1852.6 Cdc20 106.7 1106.2 2724.2 Ccnb2 8.6 1143.8 3891.8 Sgol1 6.5 63.5 1166.1 Espl1 12.8 200.2 725.3 Fbxo5 7.6 418.9 1959.3 Cdc25c 6.5 48.3 226.2 Ccne2 8.6 568.7 1729.0 Ccne1 15.4 217.1 474.4 Pkmyt1 6.5 154.0 395.4 Smc1a 1303.1 1682.3 2674.3 Ccnb1 6.5 55.9 147.3 Smc3 645.2 1313.9 2532.7 Anapc1 956.0 1095.4 1702.8 Anapc5 2915.7 4930.0 5953.2 Ccna2 8.3 1517.1 5025.6 Cdk1 104.0 2388.5 5927.0 Birc5 6.5 984.1 3969.3 Kif20a 7.6 412.0 994.3 Tpx2 55.2 484.4 1929.7 CEM 1 + Ncapg 6.5 385.5 1680.2 Top 10 Genes Ube2c 37.9 1841.5 10338.2 Nusap1 7.8 1205.0 6115.9 Shcbp1 7.6 656.7 1544.3 Kif11 11.1 294.9 1412.0

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE57543" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 6 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57543 Status: Public on May 13 2014 Title: Expression data from B6 mouse miR-142 KO and WT T cells Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: T cells are critical for modulating immune responses. miRNAs are small, noncoding RNAs and play a significant role in T cell responses. miR-142 is a hematopoietic specific miRNA. To explore the potential role of miR-142 in regulating T cell responses, we generated mutant mice bearing a targeted deletion of the miR-142 gene.

We used microarrays to detail the global programme of gene expression underlying the profile changes between miR-142 KO and WT T cell and identified distinct classes of up-regulated genes during this process.

Overall design: miR-142 KO mice and WT littermates (biological triplicates) matched with age and sex were selected. T cells were purified from spleens by negative selection and processed for RNA isolation and hybridization on Affymetrix microarrays.

Background corr dist: KL-Divergence = 0.0094, L1-Distance = 0.0206, L2-Distance = 0.0006, Normal std = 0.8842

0.451 Kernel fit Pairwise Correlations Normal fit

Density 0.226

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

WT biologicalWT biological repWT 1 biological (0.166924) repKO 2biological (0.170457) repKO 3biological (0.168597) repKO 1 biological (0.149449) rep 2 (0.264744) rep 3 (0.079829)[ min ] [ medium ] [ max ] CEM 1 Aurka 314.0 1436.6 1887.2 P ( S | Z, I ) = 1.00 Bub1 448.5 2500.6 3315.2 Mean Corr = 0.92252 Plk1 457.1 1821.6 2702.8 Cdc20 1011.7 3427.1 4863.6 Ccnb2 863.1 4166.6 5779.4 Sgol1 291.9 1357.0 1901.1 Espl1 280.4 1373.6 1697.6 Fbxo5 716.0 1642.2 2297.4 Cdc25c 94.6 291.9 487.6 Ccne2 213.6 1946.2 2899.7 Ccne1 445.0 961.9 1526.1 Pkmyt1 532.9 788.4 878.6 Smc1a 4025.0 4483.7 4936.9 Ccnb1 40.7 43.6 55.8 Smc3 1475.3 2110.2 2175.7 Anapc1 1660.8 1920.7 2323.4 Anapc5 3894.9 5620.4 6472.4 Ccna2 892.6 4896.2 6686.9 Cdk1 756.0 3521.6 4546.7 Birc5 1079.4 4492.1 6356.8 Kif20a 254.9 1222.0 1950.1 Tpx2 264.8 1491.2 2080.2 CEM 1 + Ncapg 173.3 844.7 1201.4 Top 10 Genes Ube2c 2067.9 8374.7 12303.9 Nusap1 731.3 2830.3 4061.8 Shcbp1 337.9 1423.8 1927.5 Kif11 234.6 1063.3 1622.7

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE44260" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 10 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE44260 Status: Public on Mar 06 2013 Title: Murine germinal center and naive B cells Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 23514741 Summary & Design: Summary: Gene expressions of murine germinal center and naive B cells on Affymetrix platform

Overall design: The experiment include 3 d14 GC B1-8, 3 d14 GC V23 and 4 NaÃ¯ve samples

Background corr dist: KL-Divergence = 0.0522, L1-Distance = 0.0558, L2-Distance = 0.0041, Normal std = 0.6145

0.712 Kernel fit Pairwise Correlations Normal fit

Density 0.356

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

Navie_rep1Navie_rep2 (0.140074)Navie_rep3 (0.105304)Navie_rep4 (0.130658)d14 GC(0.120623) d14B1-8_rep1 GC d14B1-8_rep2 (0.067778)GC d14B1-8_rep3 (0.0602426)GC d14V23_rep1 (0.0519268)GC d14V23_rep2 (0.088735) GC V23_rep3 (0.0920902) (0.142569) [ min ] [ medium ] [ max ] CEM 1 Aurka 185.3 1207.1 1788.3 P ( S | Z, I ) = 1.00 Bub1 187.9 2176.6 2936.7 Mean Corr = 0.92154 Plk1 141.9 1822.8 2591.9 Cdc20 290.2 4116.4 5504.5 Ccnb2 295.6 4627.3 5900.9 Sgol1 145.5 1437.1 2147.8 Espl1 141.9 1206.0 1631.2 Fbxo5 365.7 1621.6 2110.3 Cdc25c 63.2 451.6 564.6 Ccne2 93.4 1304.2 1709.1 Ccne1 216.9 613.1 821.0 Pkmyt1 708.7 977.4 1118.0 Smc1a 3377.0 5830.7 7012.5 Ccnb1 9.7 50.0 85.7 Smc3 1273.9 2728.8 3374.3 Anapc1 1626.5 2024.9 2429.1 Anapc5 3790.6 6488.3 7747.5 Ccna2 430.7 4564.9 5583.5 Cdk1 319.5 3890.5 4792.0 Birc5 310.1 4721.0 5699.5 Kif20a 108.7 1420.7 1826.4 Tpx2 187.2 2359.0 3519.5 CEM 1 + Ncapg 165.2 2923.5 3297.5 Top 10 Genes Ube2c 226.2 4429.9 5636.8 Nusap1 502.0 5949.7 7040.1 Shcbp1 303.5 3771.8 5300.2 Kif11 166.8 1619.1 2254.5

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE13874" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 14 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13874 Status: Public on Mar 05 2009 Title: microRNA-1 negatively regulates expression of the hypertrophy-associated genes calmodulin and Mef2a Organism: Mus musculus Experiment type: Non-coding RNA profiling by array Platform: GPL1261 Pubmed ID: 19188439 Summary & Design: Summary: Calcium signaling is a central regulator of cardiomyocyte growth and function. Calmodulin is a critical mediator of calcium signals. Because the amount of calmodulin within cardiomyocytes is limiting, precise regulation of calmodulin expression may be an important for regulation of calcium signaling. In this study, we show for the first time that calmodulin levels are regulated post-transcriptionally in heart failure. The cardiomyocyte-restricted microRNA miR-1 inhibited translation of calmodulin-encoding mRNAs via highly conserved target sites within their 3-untranslated regions. In keeping with its effect on calmodulin expression, miR-1 downregulated calcium-calmodulin signaling through the calcineurin to NFAT. miR-1 also negatively regulated expression of Mef2a and Gata4, key transcription factors that mediate calcium-dependent changes in gene expression. Consistent with downregulation of these hypertrophy-associated genes, miR-1 attenuated cardiomyocyte hypertrophy in cultured neonatal rat cardiomyocytes and in the intact adult heart. Our data indicate that miR-1 regulates cardiomyocyte growth responses by negatively regulating the calcium-signaling components calmodulin, Mef2a, and Gata4.

Overall design: We show that miR-1 is downregulated in a murine heart failure model. miRNAs expression changes were measured in calcineurin transgenic model of heart failure and control mice using a Luminex platform. Reduced miR-1 expression was associated with broad alteration in expression of predicted target genes. To test this, we measured miRs including miR-1 and genome wide transcriptome changes in vivo and in vitro system. Calcineurin transgenic heart was compared to nontransgenic heart (NTg vs. CNTg). We also investigated the gene expression changes during the course of cardiomyocytes differentiation using DMSO treated P19CL6 cell lines. Two time points (day 6 and day 10) were compared to identified the gene expression changes of predicted miR-1 targets (Day 6 vs. Day 10).

Background corr dist: KL-Divergence = 0.0212, L1-Distance = 0.0629, L2-Distance = 0.0054, Normal std = 0.8282

0.482 Kernel fit Pairwise Correlations Normal fit

Density 0.241

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

NTg, biologicalNTg, biologicalNTg, replicate biologicalNTg, replicate 1 (Affymetrix) biologicalCalcineurin replicate 2 (Affymetrix)Calcineurin replicate (0.0545051) 3 (Affymetrix)Tg,Calcineurin biological (0.0754553) 4 (Affymetrix)Tg,Calcineurin biological (0.0588064) replicate Tg,Differentiating biological (0.050136) replicate Tg, 1 (Affymetrix)Differentiating biological replicate 2 P19CL6(Affymetrix)Differentiating replicate (0.0522579) 3 P19CL6(Affymetrix)Differentiating cells (0.0438101) 4at P19CL6(Affymetrix)Differentiating cellsday (0.04087)6 at afterP19CL6Differentiating cellsday DMSO(0.0532064)6 at afterP19CL6 cellsday treatment, DMSO6 at afterP19CL6 cellsday treatment, DMSO10 at replicate aftercellsday treatment, 10 DMSOat replicate[ afterday 1min (Affymetrix) 10 treatment,DMSO replicate after 2 (Affymetrix)] treatment,DMSO (0.0919889)replicate 3 (Affymetrix) treatment, (0.109713)replicate [1 (Affymetrix)medium (0.118515)replicate 2 (Affymetrix) (0.0851503) 3 (Affymetrix) ] (0.0761564) (0.0894296)[ max ] CEM 1 Aurka 44.8 92.1 1958.7 P ( S | Z, I ) = 1.00 Bub1 18.7 54.8 3106.6 Mean Corr = 0.92115 Plk1 149.7 312.7 2292.1 Cdc20 244.4 399.2 3677.2 Ccnb2 46.1 176.3 2018.6 Sgol1 25.6 66.7 1080.0 Espl1 62.5 135.0 1666.9 Fbxo5 198.1 261.8 2276.2 Cdc25c 13.5 75.5 333.7 Ccne2 145.9 234.7 848.2 Ccne1 83.3 127.5 332.6 Pkmyt1 265.1 378.3 651.9 Smc1a 1038.5 1350.0 3855.9 Ccnb1 10.4 40.0 164.9 Smc3 966.4 1137.2 4299.0 Anapc1 955.3 1168.0 4514.3 Anapc5 2923.3 3664.1 9247.6 Ccna2 68.2 276.8 3189.8 Cdk1 51.2 226.4 7170.4 Birc5 19.6 207.9 4139.7 Kif20a 16.6 82.6 1534.5 Tpx2 148.4 201.2 1465.5 CEM 1 + Ncapg 10.1 41.5 1581.0 Top 10 Genes Ube2c 91.0 258.8 4368.1 Nusap1 124.5 265.5 1576.1 Shcbp1 28.1 96.8 2150.1 Kif11 86.1 108.3 1003.1

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE15303" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 11 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15303 Status: Public on May 31 2009 Title: Identification of Myelin-gene Regulatory Factor as a Critical Transcriptional Regulator Required for CNS Myelination Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 19596243 Summary & Design: Summary: The transcriptional control of CNS myelin gene expression is poorly understood. Here we identify gene model 98, which we have named Myelin-gene Regulatory Factor (MRF), as a transcriptional regulator required for CNS myelination. Within the CNS, MRF is specifically expressed by postmitotic oligodendrocytes. MRF is a nuclear protein containing an evolutionarily conserved DNA binding domain homologous to a yeast transcription factor. Knockdown of MRF in oligodendrocytes by RNA interference prevents expression of most CNS myelin genes; conversely, overexpression of MRF within cultured oligodendrocyte progenitors or the chick spinal cord promotes expression of myelin genes. In mice lacking MRF within the oligodendrocyte lineage, pre-myelinating oligodendrocytes are generated but display severe deficits in myelin gene expression and fail to myelinate. These mice display severe neurological abnormalities, and die due to seizures during the third postnatal week. These findings establish MRF as a critical transcriptional regulator essential for oligodendrocyte maturation and CNS myelination.

We used microarrays to compare cultured oligodendrocytes (differentiated in vitro for 4 days) from MRF conditional knockouts and control litteramates to look at the effects of MRF deficiency on myelin gene expression. Mouse OPCs grown in vitro in the presence of PDGF serve as a baseline for gene expression prior to differentiation.

Overall design: Mouse OPCs from MRF conditional knockout (MRF fl/fl, Olig2 wt/cre) mice and control littermates (MRF wt/fl; Olig2 wt/cre) were isolated from enzymatically dissociated P7 mouse brains as previously described (Cahoy et al., 2008), positively immunopanning for PDGFR-alpha following a depletion of microglia with BSL1. Cells were grown in defined serum-free media as previously described (Dugas et al., 2006), but with the addition of 2% B-27 (Invitrogen). Cells were proliferated for several days in the presence of PDGF-AA (10 ng/ml, PeproTech) and then differentiation induced by withdrawal of PDGF-AA and addition of triiodothyronine (T3) (40 ng/ml; Sigma). RNA was isolated from cells 4 days after induction of differentiation; OPCs maintained in PDGF-AA serve as a baseline of OPC gene expression. Total RNA was isolated from cells with the RNeasy micro kit (Qiagen, Valencia, CA) using Qiagen on-column DNase treatment to remove any contaminating genomic DNA. The integrity of RNA was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies) and RNA concentration was determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop, Rockland, DE). Biotinylated cRNAs for hybridization to Affymetrix 3'-arrays were prepared from 1ug total RNA using the Affymetrix two-cycle target labeling assay with spike in controls (Affymetrix Inc., Santa Clara, CA, 900494). Labeled-cRNA was fragmented and hybridized to Mouse Genome 430 2.0 Arrays (3'-arrays, Affymetrix, 900495) following the manufacturer's protocols. Raw image files were processed using Affymetrix GCOS 1.3 software to calculate individual probe cell intensity data and generate CEL data files. Using GCOS and the MAS 5.0 algorithm, intensity data was normalized per chip to a target intensity TGT value of 500 and expression data and present/absent calls for individual probe sets calculated. Gene symbols and names for data analyzed with the MAS 5.0 algorithm were from the Affymetrix Netaffx Mouse430_2 annotations file (http://www.affymetrix.com/support/technical/byproduct.affx?product=moe430-20). Quality control was performed by examining raw DAT image files for anomalies, confirming each GeneChip array had a background value less than 100, monitoring that the percencelle present calls was appropriate for the cell type, and inspecting the poly(A) spike in controls, housekeeping genes, and hybridization controls to confirm labeling and hybridization consistency.

Background corr dist: KL-Divergence = 0.0695, L1-Distance = 0.0313, L2-Distance = 0.0016, Normal std = 0.5115

0.795 Kernel fit Pairwise Correlations Normal fit

Density 0.398

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

MRF CKOMRF Oligodendrocyte CKOMRF Oligodendrocyte CKOMRF Oligodendrocyte controlReplicateMRF controlReplicateOligodendrocyte MRF1 (0.0555175) controlReplicateOligodendrocyte MRF2 (0.107654) controlOligodendrocyte CulturedReplicate3 (0.0560456) Oligodendrocyte CulturedReplicate OPCs 1 (0.0589809) CulturedReplicateControl OPCs 2 (0.0537226) CulturedReplicateControl ReplicateOPCs 3 (0.0703604) Control ReplicateOPCs 4 1 (0.0725492) (0.148247) Control Replicate 2 (0.069545) Replicate 3 (0.139987)[ min 4 (0.16739) ] [ medium ] [ max ] CEM 1 Aurka 86.7 269.2 2934.2 P ( S | Z, I ) = 1.00 Bub1 25.9 173.2 3977.5 Mean Corr = 0.91778 Plk1 64.0 218.2 3393.6 Cdc20 221.0 685.3 6730.9 Ccnb2 126.4 355.0 4960.2 Sgol1 5.0 77.9 1498.2 Espl1 39.1 101.3 1959.2 Fbxo5 50.4 204.8 4133.5 Cdc25c 18.7 88.2 866.4 Ccne2 54.6 259.0 1870.2 Ccne1 154.5 287.3 858.3 Pkmyt1 51.9 242.7 1203.9 Smc1a 1425.9 1786.9 5091.9 Ccnb1 11.6 32.8 126.1 Smc3 836.4 1134.7 2787.1 Anapc1 1069.6 1234.8 2055.0 Anapc5 3630.9 4112.8 8071.3 Ccna2 139.2 505.1 8211.5 Cdk1 129.2 661.5 8695.2 Birc5 143.8 320.4 5319.6 Kif20a 30.6 132.0 2407.8 Tpx2 89.2 429.4 3895.2 CEM 1 + Ncapg 43.7 133.6 1601.0 Top 10 Genes Ube2c 161.7 797.8 12671.5 Nusap1 160.1 459.2 5485.4 Shcbp1 48.3 223.4 4205.4 Kif11 59.8 212.7 2016.6

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE31028" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 6 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31028 Status: Public on Sep 02 2011 Title: Genome-wide maps of histone modifications unwind in vivo chromatin states of the hair follicle lineage Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21885018 Summary & Design: Summary: Mouse hair follicles (HFs) undergo synchronized cycles. Cyclical regeneration and hair growth is fueled by stem cells (SCs). During the rest phase, the HF-SCs remain quiescent due to extrinsic inhibitory signals within the niche. As activating cues accumulate, HF-SCs become activated, proliferate, and grow downward to form transient-amplifying matrix progenitor cells. We used microarrays to detect the relative levels of global gene expression underlying the states of hair follicle stem cells and their transient-amplifying progeny before differentiation.

Overall design: Quiescent hair follicle stem cells (qHF-SCs), activated hair follicle stem cells (aHF-SCs) and transient-amplifying matrix cells (HF-TACs) were FACS-purified for RNA extraction and hybridization on Affymetrix microarrays. To obtain homogeneous populations of expression profiles, we applied the FACS technique to purify SC and TACs according to their cell surface markers.

Background corr dist: KL-Divergence = 0.0298, L1-Distance = 0.0230, L2-Distance = 0.0006, Normal std = 0.6841

0.594 Kernel fit Pairwise Correlations Normal fit

Density 0.297

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

QuiescentQuiescent hair Activatedfollicle hair Activatedstemfollicle hair cells, follicleTransient-amplifyingstem hair rep1 cells, stemfollicleTransient-amplifying (0.1534) rep2 cells, stem (0.212328) rep1 cells, matrix (0.0891376) rep2 cells,matrix (0.14382) rep1 cells,[ (0.150508)min rep2 (0.250806) ] [ medium ] [ max ] CEM 1 Aurka 77.0 338.2 1985.7 P ( S | Z, I ) = 1.00 Bub1 28.5 355.1 2010.4 Mean Corr = 0.91734 Plk1 66.7 342.0 1944.1 Cdc20 184.4 1344.1 4831.2 Ccnb2 45.6 970.1 4485.9 Sgol1 75.2 288.0 1204.2 Espl1 90.0 326.4 1096.4 Fbxo5 181.5 328.5 1414.0 Cdc25c 45.1 175.2 671.0 Ccne2 78.3 136.7 608.0 Ccne1 92.9 210.8 701.8 Pkmyt1 297.7 533.9 950.7 Smc1a 1400.0 2048.5 2476.3 Ccnb1 60.0 119.7 218.0 Smc3 662.1 1005.9 1147.5 Anapc1 1336.8 1676.0 2846.7 Anapc5 3531.7 4739.6 8128.8 Ccna2 109.7 1026.9 4703.3 Cdk1 155.1 1624.7 7249.5 Birc5 83.1 1465.9 5926.8 Kif20a 55.2 416.5 1804.6 Tpx2 66.9 342.2 1956.7 CEM 1 + Ncapg 27.7 166.4 827.5 Top 10 Genes Ube2c 249.1 2643.2 15727.6 Nusap1 69.2 652.5 3322.4 Shcbp1 39.2 304.4 1761.8 Kif11 51.3 222.7 1119.7

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE4694" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 6 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4694 Status: Public on Apr 30 2006 Title: Expression data from myogenesis Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 17062158 Summary & Design: Summary: During muscle differentiation, myogenesis sepcific genes are differentially regulated, including Lamins that function at least in maintenance of nuclear architecture and regulation of gene expression.

We used microarrays to detail the global changes of gene expression in lamins and nuclear envelope assoicated proteins during myogenesis.

Keywords: comparative, myogenesis

Overall design: C2C12 were cultured either in 20% serum (undifferentiated) or in 2% horse serum (differentiated). Differentiated C2C12 cells were harvested on day 6 after induction of myogenesis in low serum. Affymetirx microarray raw data were further processed by GCRMA to globally normalized signal values and then subjected to analysis of Bayesian regularized t-test. Gene expression, that has a p-value less than 0.05 in the t-test and has more than 1.5 fold change, was considered siginificant.

Background corr dist: KL-Divergence = 0.0380, L1-Distance = 0.0307, L2-Distance = 0.0010, Normal std = 0.6550

0.633 Kernel fit Pairwise Correlations Normal fit

Density 0.316

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

myoblastmyoblast undifferentiatedmyoblast undifferentiatedmyotubes, undifferentiated C2C12,myotubes, differentiatedC2C12,biologicalmyotubes, differentiatedC2C12,biological rep1 C2C12, differentiated biological(0.141668) rep2 C2C12,biological (0.183885) rep3 C2C12,biological (0.172176) rep1[ min biological(0.151739) rep2 (0.159116)] rep3 (0.191416)[ medium ] [ max ] CEM 1 Aurka 232.1 2464.5 2697.9 P ( S | Z, I ) = 1.00 Bub1 74.3 1176.1 1396.4 Mean Corr = 0.91636 Plk1 245.2 2484.8 2972.7 Cdc20 420.2 4798.5 5410.9 Ccnb2 146.2 1997.4 2135.9 Sgol1 38.7 746.8 1634.3 Espl1 120.5 1240.7 1792.6 Fbxo5 119.3 1433.4 1757.4 Cdc25c 23.7 419.2 568.4 Ccne2 57.6 222.8 483.4 Ccne1 329.1 905.0 999.3 Pkmyt1 31.3 797.1 1089.1 Smc1a 1492.2 2621.4 3249.5 Ccnb1 10.2 193.0 196.3 Smc3 944.0 1298.6 1870.3 Anapc1 1500.9 2980.9 3371.3 Anapc5 4223.5 7304.0 7909.5 Ccna2 586.4 3748.6 4083.6 Cdk1 900.0 8880.1 10015.0 Birc5 273.7 5815.4 6314.6 Kif20a 147.0 1635.7 1844.4 Tpx2 310.7 1699.6 1798.2 CEM 1 + Ncapg 95.4 722.5 1094.4 Top 10 Genes Ube2c 341.2 5652.8 7193.6 Nusap1 147.6 1442.7 1669.9 Shcbp1 188.9 1321.9 1742.2 Kif11 95.6 811.5 1119.9

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE27605" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 8 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27605 Status: Public on Mar 14 2011 Title: The intestinal stem cell signature identifies colorectal cancer stem cells and predicts disease relapse Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21419747 Summary & Design: Summary: Using EphB2 or the ISC marker Lgr5, we have FACS-purified and profiled intestinal stem cells (ISCs), crypt proliferative progenitors and late transient amplifying cells to define a gene expression program specific for normal ISCs.

A frequent complication in colorectal cancer (CRC) is regeneration of the tumor after therapy. The intestinal stem cell signature predicts disease relapse in CRC and identifies a stem cell-like population that displays robust tumor- initiating capacity in immunodeficient mice as well as long-term self-renewal potential.

Overall design: We FACS purified mouse intestinal crypt cells according to their EphB2 or Lgr5 contents. We used Affymetrix chips to hybridize 2 samples from EphB2 high, 2 samples from EphB2 medium and 2 samples from EphB2 low cells (one sample from each group in a first hybridization on February 2009 plus an additional sample from each group on March 2009). Additionally, we hybridized one sample from Lgr5-EGFP high and one sample from Lgr5-EGFP low cells, obtained from Lgr5-EGFP knock-in mice (Barker et al., 2007).

Background corr dist: KL-Divergence = 0.0298, L1-Distance = 0.0338, L2-Distance = 0.0014, Normal std = 0.6870

0.614 Kernel fit Pairwise Correlations Normal fit

Density 0.307

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

intestine-Lgr5High-R1intestine-Lgr5Low-R1intestine-EphB2High-R1 intestine-EphB2Medium-R1(0.117567) (0.117582)intestine-EphB2Low-R1intestine-EphB2High-R2 (0.106219)intestine-EphB2Medium-R2 (0.0660455)intestine-EphB2Low-R2 (0.176399) (0.122328) (0.059028) (0.234832)[ min ] [ medium ] [ max ] CEM 1 Aurka 368.1 1780.5 2331.7 P ( S | Z, I ) = 1.00 Bub1 242.2 1544.5 1903.8 Mean Corr = 0.91506 Plk1 150.5 991.1 1351.0 Cdc20 447.1 2505.1 4082.7 Ccnb2 824.2 3291.8 4331.9 Sgol1 356.0 1586.2 2101.5 Espl1 69.5 376.2 544.0 Fbxo5 169.5 770.6 995.0 Cdc25c 152.3 713.9 1180.2 Ccne2 138.8 414.4 551.5 Ccne1 108.2 571.5 646.5 Pkmyt1 297.8 698.3 784.8 Smc1a 1110.3 1945.0 2315.1 Ccnb1 334.5 1585.4 2211.1 Smc3 505.8 1300.5 1406.6 Anapc1 1238.1 1670.2 1930.3 Anapc5 3953.5 6331.9 7400.8 Ccna2 982.1 3875.7 4870.2 Cdk1 773.8 3314.4 4331.3 Birc5 2365.3 6663.7 7308.3 Kif20a 198.6 1236.4 2091.7 Tpx2 238.2 1610.6 2318.3 CEM 1 + Ncapg 787.1 3310.9 4525.3 Top 10 Genes Ube2c 1087.7 4895.4 6969.2 Nusap1 553.8 2904.5 3357.1 Shcbp1 420.3 2367.0 2814.5 Kif11 91.6 591.0 810.8

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE17796" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 39 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17796 Status: Public on Jan 11 2010 Title: Expression data from B6C3F1 mice treated with reduced oxygen Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 19812364 Summary & Design: Summary: Mice received decreasing oxygen concentrations from 21% to 6% O2 for ~ 30 minutes. Then, the mice remained an additional 120 minutes at 6% O2, control mice were placed insimilarchambers but recieved normal (21%) oxygen.

Background corr dist: KL-Divergence = 0.0270, L1-Distance = 0.0739, L2-Distance = 0.0083, Normal std = 0.7950

0.502 Kernel fit Pairwise Correlations Normal fit

Density 0.251

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

liver-vehicle-2hours-repliver-vehicle-2hours-repliver-vehicle-2hours-repliver-vehicle-2hours-rep 1 (0.0223098)liver-hypoxia-2hours-rep 2 (0.0221778)liver-hypoxia-2hours-rep 3 (0.02718)liver-hypoxia-2hours-rep 4 (0.0258276)liver-hypoxia-2hours-rep 1 (0.0205059)liver-hypoxia-2hours-rep 2 (0.0215316)liver-hypoxia-2hours-rep 3 (0.0268668)liver-hypoxia-2hours-rep 4 (0.0242231)liver-hypoxia-2hours-rep 5 (0.034463)liver-vehicle-2hours-rep 6 (0.0290293)liver-vehicle-2hours-rep 7 (0.0328511)liver-vehicle-2hours-rep 8 (0.0331084)liver-vehicle-2hours-rep 5 (0.0273123)bone 6 (0.0268383) marrow-vehicle-2hours-repbone 7 (0.0305806) marrow-vehicle-2hours-repbone 8 (0.0238593) marrow-vehicle-2hours-repbone marrow-hypoxia-2hours-repbone 1 (0.0474377)marrow-hypoxia-2hours-repbone 2 (0.0420716)marrow-hypoxia-2hours-repbone 3 (0.0403749)marrow-hypoxia-2hours-repspleen-vehicle-2hours-rep 1 (0.0422453)spleen-vehicle-2hours-rep 2 (0.0346943)spleen-vehicle-2hours-rep 3 (0.0382769)spleen-vehicle-2hours-rep 41 (0.0353685)(0.0176952)spleen-hypoxia-2hours-rep 2 (0.0279432)spleen-hypoxia-2hours-rep 3 (0.0195559)spleen-hypoxia-2hours-rep 4 (0.017224)spleen-hypoxia-2hours-rep 1 (0.0252934)spleen-vehicle-2hours-rep 2 (0.0205796)spleen-hypoxia-2hours-rep 3 (0.0157652)spleen-hypoxia-2hours-rep 4 (0.031854)spleen-vehicle-2hours-rep 5 (0.0119929)spleen-vehicle-2hours-rep 7 (0.0177445)spleen-vehicle-2hours-rep 8 (0.0135056)spleen-hypoxia-2hours-rep 6 (0.0127422)spleen-hypoxia-2hours-rep 7 (0.0181931) 8 (0.0130386) 5 (0.0153846) 6 (0.0123543)[ min ] [ medium ] [ max ] CEM 1 Aurka 63.9 553.6 2748.9 P ( S | Z, I ) = 1.00 Bub1 26.6 513.3 2856.7 Mean Corr = 0.91481 Plk1 202.1 496.8 2419.4 Cdc20 120.3 1351.2 5294.6 Ccnb2 56.4 1888.2 6686.9 Sgol1 81.5 546.8 1823.5 Espl1 55.9 436.2 1494.4 Fbxo5 61.4 1431.2 4660.0 Cdc25c 36.7 188.6 472.5 Ccne2 26.0 371.9 1807.7 Ccne1 80.4 541.7 1923.9 Pkmyt1 117.0 614.7 1108.0 Smc1a 1485.6 3089.0 4866.4 Ccnb1 41.8 56.1 170.0 Smc3 431.1 1528.4 2859.4 Anapc1 1137.5 1478.6 1914.6 Anapc5 2379.3 6675.9 9538.9 Ccna2 81.1 1929.2 6905.1 Cdk1 204.1 1135.4 5325.6 Birc5 39.0 2418.7 7612.4 Kif20a 43.7 382.1 1720.0 Tpx2 57.3 683.6 3825.0 CEM 1 + Ncapg 27.8 389.3 1529.5 Top 10 Genes Ube2c 70.2 6113.2 19554.4 Nusap1 55.5 1761.3 6638.8 Shcbp1 42.1 469.1 1965.5 Kif11 60.3 495.3 2230.7

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE48382" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 10 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48382 Status: Public on Jul 01 2013 Title: ChIp-Chip using RNAP II, CREB C/EBPb and cJun antibody in undifferentiated or differentiated keratinocytes (expression) Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 24244291 Summary & Design: Summary: Combinatorial recruitment of CREB, C/EBPb and Jun determines activation of promoters upon keratinocyte differentiation

Chromatin immunoprecipitation (ChIP) of RNAP II, CREB C/EBPb and cJun in undifferentiated or differentiated keratinocytes demonstrate recruitment of RNAP II to promoters bound by combination of specific transcription factors. Analysis of mRNA expression data from contrl keratinocytes or keratinovtyes where binding of transcription factors is disrupted demonstrate functional requirements for ceratin class of promoters

Overall design: comparison of undifferentiated and differentated keratinocytes using mRNA expression data

Background corr dist: KL-Divergence = 0.0766, L1-Distance = 0.0223, L2-Distance = 0.0008, Normal std = 0.4867

0.820 Kernel fit Pairwise Correlations Normal fit

Density 0.410

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

DifferentiatedDifferentiated keratinocytesA-C/EBP keratinocytesA-C/EBP expressing treatedDifferentiated expressing treateddifferentiatedwithDifferentiated 5-AZA differentiated withkeratinocytesDifferentiated #1 5-AZA keratinocytes (0.0672204) keratinocytesDifferentiated #2 keratinocytes (0.124979)#1 keratinocytesUndifferentiated (0.0385998) #1 #2 keratinocytes(0.0688549)Undifferentiated (0.0822848) #2 #3 (0.131237) (0.0912297)keratinocytes#1 #4 (0.0556997)keratinocytes#2 (0.210211)[ min(0.129683) ] [ medium ] [ max ] CEM 1 Aurka 156.5 372.7 2589.7 P ( S | Z, I ) = 1.00 Bub1 66.1 280.2 1886.2 Mean Corr = 0.91341 Plk1 174.2 423.6 2634.8 Cdc20 298.7 730.0 4532.6 Ccnb2 108.6 478.6 2935.9 Sgol1 118.0 176.9 1073.2 Espl1 53.2 68.1 277.8 Fbxo5 117.4 314.9 1760.7 Cdc25c 56.0 70.3 200.3 Ccne2 118.6 227.7 1188.9 Ccne1 141.5 221.1 898.9 Pkmyt1 270.0 332.6 627.7 Smc1a 978.8 1478.4 1868.9 Ccnb1 42.8 47.6 53.1 Smc3 556.8 723.9 1308.0 Anapc1 1396.7 1645.0 2060.5 Anapc5 2532.9 3562.7 6170.2 Ccna2 155.8 430.5 3145.4 Cdk1 272.6 873.1 4254.3 Birc5 129.9 403.0 2555.5 Kif20a 79.6 215.8 1178.1 Tpx2 699.9 1146.7 2946.2 CEM 1 + Ncapg 29.3 72.3 674.2 Top 10 Genes Ube2c 484.4 1786.1 9256.9 Nusap1 93.5 240.0 1423.3 Shcbp1 159.5 298.0 2138.5 Kif11 44.8 72.4 358.4

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE51385" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 8 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE51385 Status: Public on Oct 18 2013 Title: Expression profiling of ProB and PreB cells in Ebf1 heterozygous mouse bone marrow Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 24078629 Summary & Design: Summary: Loss of one allele of Ebf1 impairs pre-B cell (B220+CD19+CD43low/negIgM-) expansion. In order to better understand the underlying cause of the reduced pre-B cell compartment in Ebf1+/- mice, we sorted pro-B (B220+CD19+CD43highIgM- ) as well as pre-B cells from Wt and Ebf1 heterozygote mutant mice and performed Affymetrix based microarray gene expression analysis.

While the overall gene expression patterns as well as Pax5 expression in Wt and Ebf1 pro-B cells were similar, gene set enrichment (GSE) analysis of the microarray data suggested a reduced expression of cell division (p<0.001) and mitosis (p<0.001) genes in the Ebf1+/- pre-B cells as compared to their Wt counterparts. This in combination with rather normal expression of B-lineage genes in Ebf1+/- pre-B cells opens for the possibility that the phenotypic loss of pre-B cells in Ebf1+/- mice could be a result of reduced expansion of progenitors rather than by a differentiation block.

Overall design: RNA was extracted from 20,000 or 25000 purified adult bone marrow cells using the RNAeasy microkit. RNA was labeled and amplified by dual amplification and hybridized to Affymetrix microarray MOE430_2, according to AffymetrixTM GeneChip Expression Analysis Technical Manual. Probe level expression values were calculated using the RMA algorithm.

Background corr dist: KL-Divergence = 0.0357, L1-Distance = 0.0280, L2-Distance = 0.0014, Normal std = 0.6198

0.644 Kernel fit Pairwise Correlations Normal fit

Density 0.322

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

Ebf1 heteroEbf1 PreB_1heteroEbf1 PreB_2(0.166134)heteroEbf1 ProB_2(0.181289)heteroWT PreB_2 ProB_1(0.0875212)WT PreB_1(0.101288) (0.0938705)WT ProB_1(0.104814)WT ProB_2(0.135051) (0.130032) [ min ] [ medium ] [ max ] CEM 1 Aurka 234.5 2100.8 2964.8 P ( S | Z, I ) = 1.00 Bub1 108.9 1974.9 3300.2 Mean Corr = 0.91007 Plk1 184.1 1761.9 2674.3 Cdc20 632.9 3917.4 6591.7 Ccnb2 1025.4 8715.0 12112.2 Sgol1 234.6 1715.1 1964.3 Espl1 258.5 2201.9 3485.6 Fbxo5 1034.2 4863.7 7404.2 Cdc25c 107.2 393.2 596.6 Ccne2 28.8 505.1 1062.9 Ccne1 253.3 937.2 1252.1 Pkmyt1 463.7 797.8 1252.0 Smc1a 3341.1 6667.6 7845.5 Ccnb1 97.8 230.4 318.4 Smc3 719.7 1368.1 2045.7 Anapc1 1568.3 2800.7 3156.9 Anapc5 4659.4 11719.3 14149.6 Ccna2 907.3 5812.9 9488.6 Cdk1 730.5 6867.9 8942.1 Birc5 570.1 5764.0 7911.6 Kif20a 103.4 1577.6 2371.4 Tpx2 266.6 4852.8 5864.0 CEM 1 + Ncapg 109.1 1979.1 2450.3 Top 10 Genes Ube2c 416.4 3830.1 6055.6 Nusap1 399.9 3499.0 4219.9 Shcbp1 351.0 3553.1 4016.5 Kif11 114.6 1057.9 1558.9

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE17316" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 12 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17316 Status: Public on Nov 23 2009 Title: Reprogramming of a B cell line into macrophages Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 19896445 Summary & Design: Summary: Transcription factor induced reprogramming of one specialized cell type into another is a promising approach for regenerative medicine. However, the process still remains poorly understood, in large part because of the lack of adequate experimental models. Here we describe a robust cell reprogramming system consisting of a B cell line with an inducible form of C/EBPa that can be converted into macrophages with essentially 100% efficiency in only 2 to 3 days. The conversion involves reciprocal changes in cell surface antigen expression, increase in cell granularity and size, alterations in cellular structures, formation of membrane extensions, acquisition of phagocytic capacity and an increased inflammatory responsiveness as well as migratory activity. Analysis of the transcriptome shows complex reciprocal regulation of B cell and macrophage genes, including transcription factors required for the formation of the two lineages. The fact that the cells become irreversibly committed to a macrophage fate within 1 to 2 days after activation of C/EBPa show that they are truly reprogrammed. The system should be useful to study epigenetic and cell biological mechanisms of transcription factor induced cell reprogramming.

Overall design: time points: vehicle control, 3h, 12h, 24h, 48h.

Background corr dist: KL-Divergence = 0.0922, L1-Distance = 0.0474, L2-Distance = 0.0035, Normal std = 0.4812

0.883 Kernel fit Pairwise Correlations Normal fit

Density 0.441

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

HAFTL HAFTLcell line C10cell treated linecellC10 treatedwithline cell withbetaC10 withline an estradiol cell withinduciblebetaC10 line an estradiol cell samplewithinducibleC10 formline an cell samplewith1inducibleof (0.0658067)C10 formC/EBPa,line an cell with2inducibleof (0.0765682)C10 formC/EBPa,line treatedan cell withinducibleofC10 formC/EBPa,line treatedwithan cell withinducibleof ethanolC10 formC/EBPa,line treatedwithan cell withinducibleof ethanol C10 sampleformC/EBPa,line treatedwithan cell withinducibleof beta sampleform1C/EBPa,line treatedwith(0.0756085)an estradiol withinducibleof beta form2C/EBPa, treatedwith(0.0681656)an estradiol inducibleof for beta formC/EBPa, treatedwith3 hoursestradiol of for beta [ formC/EBPa, treatedwith3 minsample hoursestradiol of for beta C/EBPa, treatedwith12 sample1 ]estradiol (0.107873)hours for beta treatedwith12 2 sampleestradiol (0.0989946)hours for beta with24[ sampleestradiol1 hoursmedium for(0.0899159) beta 24 sampleestradiol2 hours for(0.0652779) 48 sample1 hours for(0.0785995) ] 48 sample2 hours (0.0799537) sample1 (0.0929787)[ max 2 (0.100258) ] CEM 1 Aurka 86.9 858.6 3069.9 P ( S | Z, I ) = 1.00 Bub1 27.1 1647.8 4482.9 Mean Corr = 0.90679 Plk1 97.1 1090.5 4123.4 Cdc20 119.2 2264.0 5924.1 Ccnb2 82.0 1887.6 5488.8 Sgol1 3.2 754.6 1606.8 Espl1 49.4 457.8 1460.7 Fbxo5 107.6 1039.5 3793.8 Cdc25c 5.0 160.7 507.9 Ccne2 35.5 431.2 2261.2 Ccne1 54.1 116.5 866.8 Pkmyt1 20.4 527.2 1385.3 Smc1a 1291.0 3161.7 5794.1 Ccnb1 3.7 101.9 201.2 Smc3 568.1 2059.3 3096.4 Anapc1 1004.1 2280.1 2739.0 Anapc5 2947.9 6285.1 9543.1 Ccna2 59.4 2370.2 8322.5 Cdk1 120.1 2010.1 10509.1 Birc5 51.2 2596.6 6815.6 Kif20a 14.2 514.4 1454.9 Tpx2 141.9 1184.9 3696.3 CEM 1 + Ncapg 30.4 806.2 2185.9 Top 10 Genes Ube2c 2.5 2724.9 6429.8 Nusap1 35.7 2071.9 5193.8 Shcbp1 5.7 1017.8 4113.0 Kif11 2.1 460.3 2035.6

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE26290" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 12 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26290 Status: Public on Feb 01 2011 Title: Expression data from control and Phospholipid dependent kinase 1 (PDK1) null cytotoxic T-lymphocytes (CTL) and from control and Akt inhibitor treated CTL Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21295499 Summary & Design: Summary: In cytotoxic T cells (CTL), Protein Kinase B /Akt is activated by the T cell antigen receptor (TCR) and the cytokine Interleukin 2 (IL2), in part by phosophorylation of Akt by Phospholipid dependent kinase 1 (PDK1).

The role of PDK1 and Akt in CTL has however not been fully defined.

In order to explore the relative roles of these kinases in CTL we used microarrays to profile the gene expression of control and PDK1 null CTL.

In separate experiments we compared the gene expression profiles of control and Akt inhibitor treated CTL.

Overall design: The gene expression patterns of the AktI treated and the untreated CTL were then compared by microarray.

Background corr dist: KL-Divergence = 0.0257, L1-Distance = 0.0736, L2-Distance = 0.0070, Normal std = 0.8329

0.479 Kernel fit Pairwise Correlations Normal fit

Density 0.239

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

TamoxifenTamoxifen Cre TamoxifenControl Cre PDK1Control CTL, Cre nullbiological PDK1Control CTL, CTL, nullbiologicalPDK1 biologicalCTL, replicate CTL, nullbiologicalwild biological replicate CTL, 1replicate type (0.0916563)wild biological replicateCTL, 2replicate type (0.0936012)1 biological(0.0748455)wild CTL+AktI, 3replicate type (0.0849996)2 (0.0750301)wild CTL, replicate type biological3 biological(0.0944645)wild CTL+AktI, type1 (0.0783846)wild replicate CTL, replicate typebiological biological CTL+AktI,1 (0.0777448)2 (0.0802235) replicate replicate biological 2 (0.0842711)3 (0.0857857) [replicate min 3 (0.0789932)] [ medium ] [ max ] CEM 1 Aurka 927.5 2030.9 2597.5 P ( S | Z, I ) = 1.00 Bub1 933.6 2185.1 2529.6 Mean Corr = 0.90649 Plk1 1274.9 2128.3 2721.2 Cdc20 2366.2 5382.0 5942.3 Ccnb2 1691.5 5369.2 6231.7 Sgol1 879.5 1566.9 1744.5 Espl1 537.0 1112.1 1329.7 Fbxo5 1762.4 3888.8 4179.2 Cdc25c 156.7 217.3 248.5 Ccne2 906.4 1577.4 2173.8 Ccne1 688.2 1023.4 1162.1 Pkmyt1 712.1 1027.6 1085.8 Smc1a 2749.6 3525.6 4247.9 Ccnb1 80.1 233.9 291.6 Smc3 867.5 1280.0 1583.8 Anapc1 2055.0 2257.0 2473.7 Anapc5 6415.6 8789.4 9506.0 Ccna2 2302.2 6018.2 6792.0 Cdk1 2663.6 5941.3 6931.1 Birc5 2692.1 7526.1 8145.8 Kif20a 758.4 1756.6 2093.6 Tpx2 1107.3 2893.6 3135.8 CEM 1 + Ncapg 493.3 1096.3 1240.4 Top 10 Genes Ube2c 3877.2 10525.3 11870.2 Nusap1 1700.8 4347.3 5270.9 Shcbp1 1201.6 2724.7 3068.5 Kif11 659.9 1505.2 1724.6

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE30192" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 6 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30192 Status: Public on Jan 01 2012 Title: Effect of 5-azacytidine on gene expression in C2C12 myoblasts Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21795504 Summary & Design: Summary: Mesenchymal progenitor cells can be differentiated in vitro into myotubes that exhibit many characteristic features of primary mammalian skeletal muscle fibers. However, in general, they do not show the functional excitation-contraction coupling or the striated sarcomere arrangement typical of mature myofibers. Epigenetic modifications have been shown to play a key role in regulating the progressional changes in transcription necessary for muscle differentiation. In this study, we demonstrate that treatment of murine C2C12 mesenchymal progenitor cells with 10 ´M of the DNA methylation inhibitor 5-azacytidine (5AC) promotes myogenesis, resulting in myotubes with enhanced maturity as compared to untreated myotubes. Specifically, 5AC treatment resulted in the upregulation of muscle genes at the myoblast stage while at later stages nearly 50 % of the 5AC-treated myotubes displayed a mature, well-defined sarcomere organization as well as spontaneous contractions that coincided with action potentials and intracellular calcium transients. Both the percentage of striated myotubes and their contractile activity could be inhibited by 20 nM TTX, 10 ´M ryanodine and 100 ´M nifedipine, suggesting that action potential-induced calcium transients are responsible for these characteristics. Our data suggest that genomic demethylation induced by 5AC overcomes an epigenetic barrier that prevents untreated C2C12 myotubes from reaching full maturity.

Overall design: C2C12 cells were plated at 1500 cells/cm2 (day -1), cultured for 1 day in DMEM 10%NCS, then treated (d0) with or without 10uM 5-azacytidine (5AC) for an additional 3 days. RNA was extracted on day 3 and hybridized to GeneChip Mouse Genome 430 2.0 array (Affymetrix).

Background corr dist: KL-Divergence = 0.0286, L1-Distance = 0.0590, L2-Distance = 0.0044, Normal std = 0.7900

0.581 Kernel fit Pairwise Correlations Normal fit

Density 0.290

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

C2C12 untreatedC2C12 untreatedC2C12 day3 untreated C2C12rep1 day3 (0.151338) 5AC C2C12rep2 day3 treated (0.139284) 5AC C2C12rep3 treatedday3 (0.195194) 5AC rep1 treatedday3 (0.152284) rep2 day3 (0.183381) rep3 [(0.17852) min ] [ medium ] [ max ] CEM 1 Aurka 2468.8 3570.0 3656.0 P ( S | Z, I ) = 1.00 Bub1 1869.0 3356.2 3398.4 Mean Corr = 0.90580 Plk1 1562.4 2598.2 2723.8 Cdc20 3691.3 5161.0 5365.4 Ccnb2 1414.6 3914.4 4004.6 Sgol1 1122.4 1673.4 1748.9 Espl1 915.1 1128.7 1177.1 Fbxo5 860.3 2113.3 2163.7 Cdc25c 229.1 652.3 731.7 Ccne2 1085.7 1699.0 1880.2 Ccne1 460.1 658.9 733.2 Pkmyt1 458.8 575.9 632.1 Smc1a 1911.3 3074.1 3322.8 Ccnb1 288.6 434.7 523.5 Smc3 1881.7 2283.1 2340.3 Anapc1 2490.8 2554.6 2729.5 Anapc5 4696.3 7061.1 7314.7 Ccna2 2766.4 4722.1 5085.5 Cdk1 7036.8 11109.5 11712.4 Birc5 4128.0 7338.8 7475.9 Kif20a 2169.2 3605.2 3727.7 Tpx2 1673.2 2656.3 2773.3 CEM 1 + Ncapg 2084.9 2788.5 3058.0 Top 10 Genes Ube2c 4538.4 7741.0 7909.0 Nusap1 1335.2 2179.6 2335.0 Shcbp1 1839.9 3281.6 3612.1 Kif11 601.5 1108.9 1180.3

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE51883" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 30 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE51883 Status: Public on Jan 28 2014 Title: Effect of Mirn378 overexpression on gene expression during C2C12 myogenic and BMP2-induced osteogenic differentiation Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: Background: MicroRNAs (miRNAs) are a family of small, non-coding single-stranded RNA molecules involved in post-transcriptional regulation of gene expression. As such, they are believed to play a role in regulating the step-wise changes in gene expression patterns that occur during cell fate specification of multipotent stem cells. Here, we have studied whether terminal differentiation of C2C12 myoblasts is indeed controlled by lineage-specific changes in miRNA expression.

Results: Using a previously generated RNA polymerase II (Pol-II) ChIP-on-chip dataset, we show differential Pol-II occupancy at the promoter regions of six miRNAs during C2C12 myogenic versus BMP2-induced osteogenic differentiation. Overexpression of one of these miRNAs, miR-378, enhances Alp activity, calcium deposition and mRNA expression of osteogenic marker genes in the presence of BMP2.

Conclusions: Our results demonstrate a previously unknown role for miR-378 in promoting BMP2-induced osteogenic differentiation. #!#

Overall design: Stable C2C12 cell lines C2C12-pMirn0 and C2C12-pMirn378 were generated by lentiviral transduction of C2C12 myoblasts with a Mirn378-overexpression construct and its parent vector, respectively. C2C12-pMirn0 and C2C12-pMirn378 cells were plated at 2.5 x 10^4 cells/cm2 (day -1), cultured for 1 day in DMEM 10%NCS, then (d0) treated with or without 300 ng/ml bone morphogenetic protein 2 (BMP2) for 6 days. RNA was extracted on d0, d3 and d6 and hybridized to GeneChip Mouse Genome 430 2.0 array (Affymetrix).

Background corr dist: KL-Divergence = 0.1521, L1-Distance = 0.0728, L2-Distance = 0.0106, Normal std = 0.4058

1.104 Kernel fit Pairwise Correlations Normal fit

Density 0.552

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

C2C12-pMirn0_d0_rep1C2C12-pMirn0_d0_rep2C2C12-pMirn0_d0_rep3C2C12-pMirn0_day (0.0556574)C2C12-pMirn0_day (0.0524405)C2C12-pMirn0_day (0.0547337) 3_untreated_rep1C2C12-pMirn0_day 3_untreated_rep2C2C12-pMirn0_day 3_untreated_rep3 C2C12-pMirn0_day(0.0266606) 6_untreated_rep1 C2C12-pMirn0_day(0.0223079) 6_untreated_rep2 C2C12-pMirn0_day(0.0306046) 6_untreated_rep3 C2C12-pMirn0_day(0.0341104) 3_BMP2 C2C12-pMirn0_day(0.0356158) 3_BMP2 treated_rep1 C2C12-pMirn0_day(0.0343305) 3_BMP2 treated_rep2C2C12-pMirn0_day (0.0226238)6_BMP2 treated_rep3C2C12-pMirn378_d0_rep1 (0.0251664)6_BMP2 treated_rep1C2C12-pMirn378_d0_rep2 (0.0212612)6_BMP2 treated_rep2C2C12-pMirn378_d0_rep3 (0.0308509) treated_rep3C2C12-pMirn378_day (0.0534754)(0.0310764)C2C12-pMirn378_day (0.0529434)(0.0271687)C2C12-pMirn378_day (0.0530906) 3_untreated_rep1C2C12-pMirn378_day 3_untreated_rep2C2C12-pMirn378_day 3_untreated_rep3C2C12-pMirn378_day (0.0313202) 6_untreated_rep1C2C12-pMirn378_day (0.0258906) 6_untreated_rep2C2C12-pMirn378_day (0.0217726) 6_untreated_rep3C2C12-pMirn378_day (0.0294198) 3_BMP2C2C12-pMirn378_day (0.0245533) 3_BMP2C2C12-pMirn378_day treated_rep1 (0.025673) 3_BMP2C2C12-pMirn378_day treated_rep2 (0.0329275)6_BMP2 treated_rep3 (0.0387549)6_BMP2 treated_rep1 (0.0279709)6_BMP2 treated_rep2 (0.0244521)[ treated_rep3 min (0.0245513) ] (0.0285958)[ medium ] [ max ] CEM 1 Aurka 116.8 290.3 3190.7 P ( S | Z, I ) = 1.00 Bub1 95.3 345.6 3643.2 Mean Corr = 0.90510 Plk1 108.7 230.5 2328.6 Cdc20 250.8 595.5 4683.2 Ccnb2 166.2 545.6 3126.0 Sgol1 51.7 162.4 1427.0 Espl1 64.2 129.7 1240.0 Fbxo5 102.8 236.9 3150.1 Cdc25c 23.8 89.7 646.7 Ccne2 144.6 260.2 2162.2 Ccne1 96.5 168.5 934.9 Pkmyt1 29.5 145.8 447.4 Smc1a 1916.0 2506.5 3571.7 Ccnb1 3.9 31.8 176.3 Smc3 824.2 1173.8 1625.8 Anapc1 506.0 695.6 1339.2 Anapc5 3931.5 4460.0 5660.1 Ccna2 239.5 556.8 5259.4 Cdk1 632.3 1170.1 8837.8 Birc5 195.0 482.4 6672.6 Kif20a 104.7 324.9 3579.2 Tpx2 192.9 388.0 2316.9 CEM 1 + Ncapg 51.2 131.6 1339.5 Top 10 Genes Ube2c 371.3 984.2 9670.0 Nusap1 208.2 455.4 2540.4 Shcbp1 93.4 290.9 2985.9 Kif11 66.9 203.1 1070.4

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE20954" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 14 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20954 Status: Public on Aug 17 2010 Title: mRNA expression profile in mouse lung development Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 20520778 Summary & Design: Summary: We performed miRNA and mRNA profiling over a 7-point time course, encompassing all recognized stages of lung development and explore dynamically regulated miRNAs and potential miRNA-mRNA interaction networks specific to mouse lung development

Overall design: replicated time course of mouse lung development in 7 time points

Background corr dist: KL-Divergence = 0.0229, L1-Distance = 0.0372, L2-Distance = 0.0026, Normal std = 0.7245

0.551 Kernel fit Pairwise Correlations Normal fit

Density 0.275

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

Mouse lung-embryoMouse lung-embryoMouse day lung-embryoMouse 12-rep1 day lung-embryoMouse 12-rep2 (0.0963314) day lung-embryoMouse 14-rep1 (0.105244) day lung-embryoMouse 14-rep2 (0.0767159) day lung-embryoMouse 16-rep1 (0.0801288) day lung-embryoMouse 16-rep2 (0.0472333) day lung-postnatalMouse 18-rep1 (0.0516324) day lung-postnatalMouse 18-rep2 (0.0773197) lung-postnatalMouseday (0.0440162) 2-rep1 lung-postnatalMouseday (0.0342983)2-rep2 lung-postnatalMouseday (0.0402593)10-rep1 lung-postnatalday 10-rep2 (0.0573686) day 30-rep1 (0.0518313) day 30-rep2 (0.113525)[ min (0.124096) ] [ medium ] [ max ] CEM 1 Aurka 98.8 459.8 3079.4 P ( S | Z, I ) = 1.00 Bub1 95.3 623.0 4385.5 Mean Corr = 0.90427 Plk1 163.6 372.4 2272.1 Cdc20 254.5 1208.8 5821.7 Ccnb2 169.5 1104.5 4459.4 Sgol1 160.6 326.6 1445.7 Espl1 139.4 346.0 1528.8 Fbxo5 188.6 468.8 1806.3 Cdc25c 65.1 108.9 513.9 Ccne2 50.1 279.1 1417.8 Ccne1 158.8 218.9 1127.8 Pkmyt1 328.2 435.5 890.4 Smc1a 2942.0 3459.9 5048.9 Ccnb1 36.2 54.0 91.2 Smc3 1268.9 1864.9 2690.3 Anapc1 1052.2 1420.8 2624.9 Anapc5 5580.1 7786.3 8994.7 Ccna2 154.9 954.3 3800.4 Cdk1 138.5 1288.7 5556.8 Birc5 91.1 620.8 4548.7 Kif20a 49.9 395.3 3391.5 Tpx2 90.4 384.0 2807.2 CEM 1 + Ncapg 30.7 185.4 1324.1 Top 10 Genes Ube2c 161.7 1329.0 7298.2 Nusap1 145.1 1010.0 4012.9 Shcbp1 79.5 486.6 3056.0 Kif11 69.9 248.7 1351.8

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE54490" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 12 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54490 Status: Public on Feb 16 2014 Title: FoxA1 directs the lineage and immunosuppressive properties of FoxA1+ regulatory T cells in EAE and MS Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 24531377 Summary & Design: Summary: Affymetrix gene expression analysis was carried out to investigate the differences in gene profile of MBP89-101-reactive encephalitogenic T cells before and after co-culture with cerebellar granular neurons (CGNs). Co-culture of MBP89-101-reactive encephalitogenic T cells with CGNs leads to generation of T cells with regulatory T cells phenotype (CD4+CD25+membrane bound TGF-b+ T cells) or a new regulatory phenotype (CD4highPD-L1high T cells). CGN-induced CD4+CD25+membrane bound TGF-b+ T regulatory cells, CD4highPD-L1high T cells were purified by FACSAria. IFN-beta induced T lymphocytes (CD4highPD-L1high T cells) were also FACSAria purified. All these populations were compared to MBP89-101-reactive encephalitogenic T cells. Samples were prepared from biological triplicates for each FACSAria sorted population.

Overall design: There are four different cell types, as determined by cell surface markers, in triplicate in the experiment.

Background corr dist: KL-Divergence = 0.0239, L1-Distance = 0.0546, L2-Distance = 0.0040, Normal std = 0.7910

0.572 Kernel fit Pairwise Correlations Normal fit

Density 0.286

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

EncephalitogenicEncephalitogenicEncephalitogenic Tcellsneuron rep1 Tcells (0.0468226)neuroninduced rep2 Tcells (0.0574115)neuroninduced FoxA1Treg rep3 (0.0496224)Treginduced FoxA1Treg rep1rep1Treg FoxA1Treg (0.0377805)(0.0525598) rep2rep2Treg (0.0592158)(0.049369) rep3rep3IFN-beta (0.0442699)(0.0620225)IFN-beta inducedIFN-beta induced FoxA1Treg induced FoxA1Treg rep1 FoxA1Treg (0.175855) rep2 (0.174401) rep3[ min (0.190671) ] [ medium ] [ max ] CEM 1 Aurka 563.5 3108.4 3911.0 P ( S | Z, I ) = 1.00 Bub1 918.6 2726.7 3144.4 Mean Corr = 0.90321 Plk1 633.2 2811.9 3387.0 Cdc20 1081.7 5640.4 6882.2 Ccnb2 1294.2 9387.6 10284.0 Sgol1 352.7 1595.7 1990.8 Espl1 427.8 2587.8 2884.4 Fbxo5 1126.2 4402.6 4800.5 Cdc25c 59.1 380.4 448.5 Ccne2 401.8 1425.2 1708.0 Ccne1 377.7 594.5 682.0 Pkmyt1 102.8 1440.3 1781.8 Smc1a 2202.6 5898.8 6718.8 Ccnb1 42.2 112.6 167.1 Smc3 1978.5 2827.3 3183.9 Anapc1 2187.0 3098.6 3303.0 Anapc5 3223.0 6731.0 7604.8 Ccna2 1812.5 8025.1 9258.6 Cdk1 1993.8 8078.6 9259.9 Birc5 1489.5 9772.4 10897.0 Kif20a 320.1 2197.9 2991.6 Tpx2 504.9 3320.4 3920.2 CEM 1 + Ncapg 654.6 3672.3 3952.1 Top 10 Genes Ube2c 2119.0 8582.9 11162.0 Nusap1 1699.9 7820.7 9691.1 Shcbp1 998.8 3703.1 4264.8 Kif11 330.0 1942.4 2448.7

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE51243" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 7 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE51243 Status: Public on Sep 28 2013 Title: Comparison of the transcriptome of TEL-JAK2- versus activated NOTCH1 (ICN1)-induced T cell acute lymphoblastic leukemias (mouse) Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 24268771 Summary & Design: Summary: The TEL-JAK2 fusion oncogene and the ICN1 activated allele of NOTCH1 are the result of specific chromosomal translocations in T cell acute lymphoblastic leukemia (T-ALL). Mouse models of these diseases (TEL-JAK2 transgenic mice; Carron C. et al. Blood (2000); a bone marrow transplantation model for ICN1-induced T-ALL) were used to compare the transcriptional program specific to each oncoprotein in mouse models of these leukemias. Tumor load was >50% leukemic cells in all selected organs.

Overall design: Leukemic cells were collected from the thymus of terminally-ill TEL-JAK2 leukemic mice and bone marrow of terminally-ill ICN1 leukemic mice. RNA was extracted from each sample and processed for hybridization to Affymetrix arrays.

Background corr dist: KL-Divergence = 0.0331, L1-Distance = 0.0151, L2-Distance = 0.0003, Normal std = 0.6426

0.621 Kernel fit Pairwise Correlations Normal fit

Density 0.310

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

ICN1_1701ICN1_1840 leukemiaICN1_24306 leukemia (0.141718)TJ2_1192 leukemia (0.198033)TJ2_1209 leukemia (0.180681)TJ2_1210 leukemia (0.109072)TJ2_1261 leukemia (0.134144) leukemia (0.145446) (0.0909065)[ min ] [ medium ] [ max ] CEM 1 Aurka 579.1 944.9 3042.5 P ( S | Z, I ) = 1.00 Bub1 485.4 1044.7 3644.9 Mean Corr = 0.90162 Plk1 602.1 1003.1 2493.1 Cdc20 1165.8 2113.2 5203.1 Ccnb2 1613.4 3168.7 11728.4 Sgol1 355.6 662.4 2352.0 Espl1 264.7 587.6 2047.7 Fbxo5 696.1 1015.6 3069.9 Cdc25c 108.1 192.7 640.3 Ccne2 91.5 254.3 1555.1 Ccne1 160.0 257.4 867.0 Pkmyt1 370.9 618.7 1290.4 Smc1a 4237.8 5533.2 8345.6 Ccnb1 70.2 79.1 204.3 Smc3 1801.5 2074.0 3039.3 Anapc1 1301.1 1556.6 2647.3 Anapc5 8843.1 11982.8 12799.7 Ccna2 928.0 2050.9 7761.2 Cdk1 879.5 1921.4 5671.9 Birc5 1257.9 2545.1 10895.4 Kif20a 267.1 567.5 1997.6 Tpx2 614.3 1226.6 4243.2 CEM 1 + Ncapg 239.2 593.0 2134.7 Top 10 Genes Ube2c 2371.2 4667.0 20248.8 Nusap1 1194.5 2372.5 7954.5 Shcbp1 392.5 995.3 2867.8 Kif11 389.0 714.1 2965.1

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE39449" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 6 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39449 Status: Public on Feb 25 2014 Title: Differentially activated CD8 T cells in liver and gut Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 19265543 Summary & Design: Summary: NaÃ¯ve, liver- and gut-activated CD8 OT-I T cells show differential migration behaviour. To analyze which genes could be responsible for different migration patterns, naÃ¯ve, liver-activated and gut-activated CD8 T cells were isolated and compared for their gene expression profile.

Overall design: After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 ´g cRNA hybridized in duplicates for each of the three groups to the GeneChip arrays. Group1: naÃ¯ve, Group2: liver-activated Group3: gut-activated. Lists of differentially regulated genes were created using High Performance Chip Data Analysis (HPCDA) with Bioretis database (http://www.bioretis-analysis.de). Worldwide data sharing is possible via Bioretis, please ask the authors.

Background corr dist: KL-Divergence = 0.0358, L1-Distance = 0.0497, L2-Distance = 0.0032, Normal std = 0.6979

0.630 Kernel fit Pairwise Correlations Normal fit

Density 0.315

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

DifferentiallyDifferentially activatedDifferentially activatedDifferentially CD8 Tactivated cellsDifferentially CD8 in Tactivated cellsDifferentially liverCD8 andin Tactivated cells liverCD8 gut: andin Tactivated Liver-activated cells liverCD8 gut: andinT Liver-activated cells liverCD8 gut: andinT Gut-activated CD8cells[liver gut:min OT-I andin Gut-activated CD8liver Tgut: cells OT-I ]and CD8 NaÃ¯ve (liver)Tgut: OT-I cells CD8 NaÃ¯veCD8 ChipT (liver) cells [OT-I OT-I 1medium CD8 (0.149814)(mes)ChipT T cells cells OT-I 2 Chip (0.158457)(mes) (naÃ¯ve)T cells 1 (0.102918)Chip (naÃ¯ve)] Chip 2 (0.152935) 1 (0.187734)Chip[ 2 (0.248143)max ] CEM 1 Aurka 218.0 2334.9 2536.1 P ( S | Z, I ) = 1.00 Bub1 271.5 4114.7 4302.7 Mean Corr = 0.90099 Plk1 260.0 2521.8 2628.1 Cdc20 552.7 5077.2 6021.3 Ccnb2 291.6 7057.4 8003.8 Sgol1 227.1 1452.5 1718.0 Espl1 146.2 1479.4 1958.8 Fbxo5 1053.1 4404.0 5322.7 Cdc25c 38.6 444.7 544.4 Ccne2 250.4 1285.1 1670.5 Ccne1 709.7 1471.5 1855.4 Pkmyt1 370.5 867.6 1151.1 Smc1a 4085.3 7270.3 8920.7 Ccnb1 56.6 166.7 212.2 Smc3 1880.6 2140.9 2392.9 Anapc1 1734.0 2245.1 2505.3 Anapc5 3758.5 5831.3 6319.6 Ccna2 704.6 7106.8 7564.9 Cdk1 291.8 5475.9 7348.8 Birc5 644.8 10529.1 11186.7 Kif20a 158.6 2256.8 2318.5 Tpx2 169.4 2664.4 2780.2 CEM 1 + Ncapg 198.7 2588.9 3117.0 Top 10 Genes Ube2c 592.6 10359.2 13538.1 Nusap1 537.5 6318.6 8728.1 Shcbp1 324.1 3678.6 4170.0 Kif11 134.2 1696.4 2367.4

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE7875" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 16 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7875 Status: Public on Oct 03 2007 Title: Deletion of PKBalpha/Akt1 affects thymic development Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 17912369 Summary & Design: Summary: The thymus constitutes the primary lymphoid organ for the majority of T cells. The phosphatidyl-inositol 3 kinase (PI3K) signaling pathway is involved in lymphoid development. Defects in single components of this pathway prevent thymocytes from progressing beyond early T cell developmental stages. Protein kinase B (PKB) is the main effector of the PI3K pathway. To determine whether PKB mediates PI3K signaling in early T cell development, we characterized PKB knockout thymi. Our results reveal a significant thymic hypocellularity in PKBalpha-/- neonates and an accumulation of early thymocyte subsets in PKBalpha-/- adult mice. The latter finding is specifically attributed to the lack of PKBalpha within the lymphoid component of the thymus. Microarray analyses show that the absence of PKBalpha in early thymocyte subsets modifies the expression of genes known to be involved in pre-TCR signaling, in T cell activation, and in the transduction of interferon-mediated signals. This report highlights the specific requirements of PKBalpha for thymic development.

Keywords: Genetic modification

Overall design: Early thymocyte subsets (DN3 and ISP8) were sorted by FACS from 4 PKBalpha-/- / PKBalpha+/+ mouse littermate pairs. The same number of DN3 or ISP8 cells was sorted (7 000 to 25 000 cells) within a PKBalpha-/- / PKBalpha+/+ pair. Four replicates per condition were then analysed (4xPKBalpha-/- DN3, 4xPKBalpha+/+ DN3, 4xPKBalpha-/- ISP8, 4xPKBalpha+/+ ISP8). Total RNA was extracted using PicoPureTM RNA isolation kit (Arcturus, Sunnyvale, CA, USA) and RNA quality was controlled using the 2100 Bioanalyser (Agilent Technologies, Santa Clara, CA, USA). Total RNA was amplified and labeled using the Affymetrix 2-cycle 3 labelling kit according to manufacturers instructions. After fragmentation, 10 ug cRNA was hybridised to mouse genome 430 2.0 GeneChips (Affymetrix, Santa Clara, CA). The supplementary file represents the expression values estimated using the GC-RMA function provided by Refiner 3.1 (Genedata, Basel, Switzerland) for each of the samples.

Background corr dist: KL-Divergence = 0.1420, L1-Distance = 0.0394, L2-Distance = 0.0024, Normal std = 0.3992

1.035 Kernel fit Pairwise Correlations Normal fit

Density 0.518

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

bh20061128m430v2_A_16_pTN3-PKBa-2435bh20061128m430v2_A_15_pTN3-PKBa-2432bh20061128m430v2_A_14_pTN3-PKBa-2425bh20061128m430v2_A_13_pTN3-PKBa-2424bh20061128m430v2_A_12_pTN3-PKBa-2420bh20061128m430v2_A_11_pTN3-PKBa-2416 (0.0534878)bh20061128m430v2_A_10_pTN3-PKBa-2402 (0.0672096)bh20061128m430v2_A_09_pTN3-PKBa-2401 (0.048666)bh20061128m430v2_A_08_preDP-PKBa-2435 (0.0548797)bh20061128m430v2_A_07_preDP-PKBa-2432 (0.05195)bh20061128m430v2_A_06_preDP-PKBa-2425 (0.0569686)bh20061128m430v2_A_05_preDP-PKBa-2424 (0.101713)bh20061128m430v2_A_04_preDP-PKBa-2420 (0.0639006)bh20061128m430v2_A_03_preDP-PKBa-2416bh20061128m430v2_A_02_preDP-PKBa-2402 (0.0622598)bh20061128m430v2_A_01_preDP-PKBa-2401 (0.0636455) (0.0718759) (0.0763923) (0.0589286)[ (0.0539272) min (0.0543776) ] (0.0598177)[ medium ] [ max ] CEM 1 Aurka 340.9 2349.5 3190.6 P ( S | Z, I ) = 1.00 Bub1 527.0 3251.7 4223.5 Mean Corr = 0.90079 Plk1 165.1 1372.8 2167.6 Cdc20 453.4 2667.4 3536.0 Ccnb2 1882.8 8366.9 12121.2 Sgol1 476.3 2601.7 3365.0 Espl1 470.5 1695.2 3488.0 Fbxo5 1902.3 10540.7 12893.9 Cdc25c 99.8 579.2 882.5 Ccne2 619.6 2408.9 3798.4 Ccne1 141.9 730.6 1140.9 Pkmyt1 376.0 887.2 1759.3 Smc1a 5146.6 7299.2 9186.0 Ccnb1 38.0 175.0 282.5 Smc3 1759.4 2610.8 4223.4 Anapc1 2711.1 3582.4 4550.6 Anapc5 7485.2 11699.6 13395.2 Ccna2 1683.9 8576.7 9946.0 Cdk1 889.7 5042.3 6984.5 Birc5 511.6 3906.8 6133.5 Kif20a 234.1 1589.2 2168.7 Tpx2 475.0 2620.3 3647.8 CEM 1 + Ncapg 758.6 3276.2 4843.1 Top 10 Genes Ube2c 366.5 2573.9 5312.4 Nusap1 704.5 6675.2 9764.7 Shcbp1 1490.3 6239.7 8179.0 Kif11 266.0 2411.3 3427.0

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE34839" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 6 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34839 Status: Public on Feb 28 2012 Title: Pten loss and RAS/MAPK activation cooperate to promote EMT and prostate cancer metastasis initiated from stem/progenitor cells Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 22350410 Summary & Design: Summary: PTEN loss or PI3K/AKT signaling pathway activation correlates with human prostate cancer progression and metastasis. However, in preclinical murine models, deletion of Pten alone fails to mimic the significant metastatic burden that frequently accompanies the end stage of human disease. To identify additional pathway alterations that cooperate with PTEN loss in prostate cancer progression, we surveyed human prostate cancer tissue microarrays and found that the RAS/MAPK pathway is significantly elevated both in primary and metastatic lesions. In an attempt to model this event, we crossed conditional activatable K-rasG12D/WT mice with the prostate conditional Pten deletion model we previously generated. Although RAS activation alone cannot initiate prostate cancer development, it significantly accelerated progression caused by PTEN loss, accompanied by epithelial-to-mesenchymal transition (EMT) and macrometastasis with 100% penitence. A novel stem/progenitor subpopulation with mesenchymal characteristics was isolated from the compound mutant prostates, which was highly metastatic upon orthotopic transplantation. Importantly, inhibition of RAS/MAPK signaling by PD325901, a MEK inhibitor, significantly reduced the metastatic progression initiated from transplanted stem/progenitor cells. Collectively, these data indicate that activation of RAS/MAPK signaling serves as a potentiating second hit to alteration of the PTEN/PI3K/AKT axis and co-targeting both pathways is highly effective in preventing the development of metastatic prostate cancers.

Overall design: Murine mutants with prostate specific loss of Pten and K-ras activation (K-rasG12D) under regulation of the probasin promoter developed high grade, invasive prostate cancer. RNA was extracted from dissected prostate lobes from individual mutants with pathology thought to closely mimic human disease. Prostate tissue was subject to RNA extraction and hybridization on Affymetrix cDNA microarrays.

Background corr dist: KL-Divergence = 0.0408, L1-Distance = 0.0392, L2-Distance = 0.0022, Normal std = 0.6408

0.647 Kernel fit Pairwise Correlations Normal fit

Density 0.323

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

Pb-Cre+;PtenL/W;K-rasG12D/W,Pb-Cre+;PtenL/W;K-rasG12D/W,Pb-Cre+;PtenL/W;K-rasG12D/W,Pten null,Pten biological null,Pten biological null,rep1 biological(0.111384)(0.113518) rep2 (0.173689)(0.352512) rep3 (0.137495)(0.111402)[ min ] [ medium ] [ max ] CEM 1 Aurka 164.1 229.6 923.2 P ( S | Z, I ) = 1.00 Bub1 128.3 244.4 1342.3 Mean Corr = 0.89094 Plk1 203.6 263.8 686.0 Cdc20 357.0 432.9 1475.0 Ccnb2 185.4 309.2 1150.4 Sgol1 144.0 190.3 550.8 Espl1 104.7 219.6 444.7 Fbxo5 163.1 173.2 696.4 Cdc25c 58.2 76.4 194.2 Ccne2 56.8 131.6 288.4 Ccne1 122.8 152.7 211.7 Pkmyt1 297.8 359.9 469.7 Smc1a 1477.5 1516.7 2003.3 Ccnb1 32.3 42.3 109.8 Smc3 792.9 962.7 1179.0 Anapc1 884.1 1065.2 1315.6 Anapc5 2539.8 2948.2 3762.7 Ccna2 259.3 417.3 1532.5 Cdk1 391.7 487.0 2271.0 Birc5 168.1 370.1 1603.7 Kif20a 74.3 110.9 614.2 Tpx2 95.6 129.1 575.0 CEM 1 + Ncapg 31.6 50.4 232.5 Top 10 Genes Ube2c 428.2 744.9 3238.7 Nusap1 258.1 405.3 1413.7 Shcbp1 171.3 230.4 1199.3 Kif11 103.1 141.9 607.5

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE25257" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 6 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25257 Status: Public on Nov 11 2010 Title: Expression data from wild-type and Zmpste24-/- mouse embryonic fibroblasts (MEFs) at an early passage (passage 3, P3) Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: Zmpste24 is a metalloproteinase processing prelamin A into mature lamin A, a nuclear structure protein. Zmpste24-/- mice which accumulate prelamin A in cells recapitulate accelerated aging phenotypes observed in human premature aging disorder, Hutchinson Gilford progeria sydrome (HGPS). Zmpste24-/- mouse embryonic fibroblasts (MEFs) exhibited genomic instabiliy and accelerated aging at cellular level, which is premature senescence.

We performed microarray analysis on Zmpste24-/- MEFs, compared to wild-type littermates' MEFs, at an early passage (P3), which is a pre-symptom stage before cellular senescence occurs in the mutant MEFs, in order to examine gene expression profile and figure out the underneath mechanism triggering the premature aging process.

Overall design: Early passage wild-type and Zmpste24-/- MEFs were collected for RNA extraction, the quality of RNAs were determinded by Electrophoresis Assay (2100 Bioanalyzer, Agilent) and RNA extractions were used for hybridization on Affymetrix microarrays.

Background corr dist: KL-Divergence = 0.0217, L1-Distance = 0.0450, L2-Distance = 0.0023, Normal std = 0.8008

0.542 Kernel fit Pairwise Correlations Normal fit

Density 0.271

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

WT1 (0.186007)WT2 (0.135673)WT3 (0.111769)NT1 (0.266464)NT2 (0.14331)NT3 (0.156777) [ min ] [ medium ] [ max ] CEM 1 Aurka 468.2 2176.5 2681.2 P ( S | Z, I ) = 1.00 Bub1 170.4 1141.0 1260.9 Mean Corr = 0.89083 Plk1 308.9 1854.0 2107.5 Cdc20 1020.7 4571.8 5219.5 Ccnb2 622.8 2402.0 2812.5 Sgol1 99.2 709.6 909.9 Espl1 77.7 404.0 530.3 Fbxo5 246.3 1122.3 1264.4 Cdc25c 72.4 295.1 321.8 Ccne2 204.8 718.0 797.8 Ccne1 910.8 1206.9 1370.0 Pkmyt1 125.4 496.8 560.9 Smc1a 1257.1 1953.1 2301.4 Ccnb1 86.7 478.6 521.6 Smc3 953.9 1067.2 1134.8 Anapc1 402.8 904.1 983.1 Anapc5 3561.2 6040.4 6394.5 Ccna2 572.3 3162.4 3659.3 Cdk1 2663.4 6330.7 7261.0 Birc5 788.0 5474.8 6149.9 Kif20a 474.4 2074.3 2286.9 Tpx2 348.9 1561.9 2104.0 CEM 1 + Ncapg 117.9 502.8 668.9 Top 10 Genes Ube2c 2015.9 8458.5 9327.8 Nusap1 288.1 1343.8 1642.3 Shcbp1 319.6 2493.9 2765.3 Kif11 92.9 296.8 366.3

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE27786" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 20 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27786 Status: Public on May 19 2011 Title: Gene expression profile of mouse hematopoietic cells Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21540074 Summary & Design: Summary: Each fraction of mouse hematopoietic cells was purified by cell sorting from bone marrow of 8-week-old C57BL/6 mice, and its gene expression was analyzed.

Overall design: Two biological replicates of each fraction were analyzed using a Mouse Genome 430 2.0 array (Affymetrix).

Background corr dist: KL-Divergence = 0.1762, L1-Distance = 0.0498, L2-Distance = 0.0060, Normal std = 0.3706

1.098 Kernel fit Pairwise Correlations Normal fit

Density 0.549

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

KSL cells,KSL biological cells,Lineage biological replicateLineage marker(-) replicate B220(+) 1marker(-) (0.0351634) cells, B220(+)2B biological(0.0336882) lymphocytes,cells,CD4(+) B biological lymphocytes, replicate TCD4(+) lymphocytes,biological replicate 1 TCD8(+) (0.0335286) lymphocytes,biological replicate 2 TCD8(+) (0.0276063)biological lymphocytes, replicate 1 TNK1.1+ biological(0.0282883) lymphocytes, replicate 2 NK1.1+NK biological(0.0373539) cells,replicate 1 CD3˛(+)NK1.1(+)(0.0279237)NK biological biological cells,replicate 2 CD3˛(+)NK1.1(+)(0.0431025) biological replicate replicate1 Ter119(+)(0.0347038) NKT replicate2 1cells,Ter119(+)(0.034949) (0.0227929) NKTerythroblasts, biological 2cells,Gr-1(+) (0.0228829) erythroblasts, biological Gr-1(+)neutrophils, replicate biological Mac-1(+)neutrophils, replicate biological 1 (0.0444572)replicatebiologicalMac-1(+) monocytes/macrophages, 2 (0.0476576)replicatebiological 1 replicate (0.159884)monocytes/macrophages, 2 replicate(0.144357) 1 (0.0667585) 2 (0.0752182) biological[ min biological replicate ] replicate 1 (0.0472839) [2 (0.0323999)medium ] [ max ] CEM 1 Aurka 100.3 860.4 14049.3 P ( S | Z, I ) = 1.00 Bub1 36.8 488.2 5259.7 Mean Corr = 0.88863 Plk1 104.1 488.5 5024.6 Cdc20 298.4 787.7 9289.0 Ccnb2 295.5 2679.3 37549.1 Sgol1 22.7 668.7 10151.5 Espl1 22.1 382.9 3437.4 Fbxo5 536.7 1111.1 19700.2 Cdc25c 7.7 104.1 1944.2 Ccne2 109.8 461.6 11649.7 Ccne1 150.7 357.4 3868.2 Pkmyt1 65.8 279.2 1290.1 Smc1a 1694.6 2614.1 7916.8 Ccnb1 9.8 80.5 984.9 Smc3 874.5 1602.7 4965.0 Anapc1 541.6 1555.5 3701.4 Anapc5 2553.4 4797.2 14042.7 Ccna2 216.0 1255.5 21578.6 Cdk1 197.7 983.2 28254.7 Birc5 294.2 843.9 25789.4 Kif20a 21.2 203.2 2457.4 Tpx2 71.5 609.3 13624.9 CEM 1 + Ncapg 28.1 245.2 5878.8 Top 10 Genes Ube2c 57.2 1116.8 45632.8 Nusap1 69.0 1317.7 22270.6 Shcbp1 117.6 1073.5 5504.3 Kif11 83.3 583.8 11931.7

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE21299" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 12 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21299 Status: Public on Feb 01 2011 Title: Expression data from murine cell line transduced with epitope tagged forms of Hoxa9 Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 20541477 Summary & Design: Summary: Importantly increasing evidence shows that Hox genes such as Hoxa9 are key regulators of stem cell self-renewal and hematopoiesis. Hoxa9 is expressed in early hematopoietic progenitor cells and promotes stem cell expansion. In contrast Hoxa9 down regulation is associated with hematopoietic differentiation. In addition to its role in development, HOXA9 has been intensively studied because of its central role in human acute leukemias. Despite their obvious biomedical importance, the mechanisms through which Hoxa9 and its partner proteins exert their downstream functions are poorly understood.

Using whole-genome gene expression profiling, we identified direct targets of Hoxa9 in murine MHPs after 4-OHT withdraw, resulting in cell differentiation.

Overall design: Bone marrow cells were harvested from 5-Fluorouracil treated female 6-8 week old C57BL/6 mice and transduced with an MSCV-based retrovirus expressing Hoxa9 fused to a modified estrogen receptor ligand binding domain (Hoxa9-ER). Hoxa9-ER cells were washed 3x and resuspended in IL-3+ media with/without 100 nM 4-OHT (Sigma). At selected intervals, cells were removed for flow cytometric analysis using anti-Gr1 and anti-Mac1 antibodies (BD biosciences), morphologic assessment by cytocentrifugation and staining with Diff-Quick reagents (Intl. Med. Equip.), and RNA collection. For RNA, Pellets were lysed in Trizol reagent (Invitrogen) and RNA was extracted following manufacturer's instructions until phase separation, after which RNeasy columns (Qiagen) were employed for further purification. cRNA probes were synthesized at the University of Michigan microarray core. Probes were hybridized to Affymetrix Mouse 430 2.0 array.

Background corr dist: KL-Divergence = 0.0290, L1-Distance = 0.0372, L2-Distance = 0.0028, Normal std = 0.6739

0.592 Kernel fit Pairwise Correlations Normal fit

Density 0.296

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

Hoxa9-ERHoxa9-ER on dayHoxa9-ER 3,on rep dayHoxa9-ER 1 3,on(0.0582287) rep dayHoxa9-ER 2 3,on(0.0583775) rep dayHoxa9-ER 3 4,on(0.0475706) rep dayHoxa9-ER 1 4,on(0.0645911) rep dayHoxa9-ER 2 4,on(0.0669207) rep dayHoxa9-ER 3 5,on(0.0497358) rep dayHoxa9-ER 1 5,on(0.137207) rep dayHoxa9-ER 2 5,on(0.13487) rep dayHoxa9-ER 3 0,on(0.13832) rep day 1 0,on(0.0743952) rep day 2 0,(0.101469) rep 3 (0.0683138)[ min ] [ medium ] [ max ] CEM 1 Aurka 758.1 1812.0 2005.9 P ( S | Z, I ) = 1.00 Bub1 661.3 2074.6 2298.6 Mean Corr = 0.88835 Plk1 790.6 1949.8 2195.8 Cdc20 1641.7 3171.8 3677.6 Ccnb2 1485.5 3461.3 4313.9 Sgol1 573.4 1099.8 1268.3 Espl1 329.8 948.4 1052.0 Fbxo5 814.3 1590.9 1808.8 Cdc25c 93.9 218.0 246.4 Ccne2 283.6 739.5 972.7 Ccne1 257.0 451.5 526.6 Pkmyt1 741.2 1182.8 1288.4 Smc1a 2832.4 3806.8 3989.3 Ccnb1 85.6 130.1 155.7 Smc3 1430.4 2523.5 2859.8 Anapc1 1122.0 1790.5 1964.1 Anapc5 3839.2 6154.7 6585.8 Ccna2 1662.1 3378.9 3693.0 Cdk1 1267.6 3816.3 4276.7 Birc5 1205.4 3015.7 3462.4 Kif20a 343.3 919.6 1076.4 Tpx2 919.2 2087.6 2361.3 CEM 1 + Ncapg 239.8 610.8 716.6 Top 10 Genes Ube2c 2490.1 4001.2 4338.8 Nusap1 1276.3 2494.0 2721.4 Shcbp1 899.5 2317.2 2628.1 Kif11 497.0 950.7 1171.1

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE51075" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 12 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE51075 Status: Public on Sep 22 2013 Title: Transcriptional responses of murine macrophages to the adenylate cyclase toxin of Bordetella pertussis Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 17890046 Summary & Design: Summary: Three different recombinant forms of CyaA were used to investigate transcriptional responses of murine bone marrow-derived macrophages (BMDMs) using Affymetrix Mouse Genome Genechips. These forms were enzymically active, invasive CyaA, nonenzymically active, invasive CyaA (CyaA*) and non-enzymically active, non-invasive CyaA (proCyaA*). BMMs, treated with 20 ng/ml of CyaA for 24 h, showed over 1000 significant changes in gene transcription compared with control cells. CyaA caused an increase in transcription of many inflammatory genes and genes associated with various signalling cascades such as those involved in cyclic AMP-dependent protein kinase A signalling. Most strikingly, CyaA caused down-regulation of numerous genes involved in cell proliferation. CyaA* at 20 ng/ml significantly up-regulated the transcription of only twelve genes after 24 h whereas proCyaA* at this concentration significantly increased the transcription of only two genes.

Overall design: The effect of administration of three different recombinant forms of pertussis toxin to mouse bone marrow derived macrophages are compared with a vehicle only contol 24 hours after treatment in technical triplicate measurements

Background corr dist: KL-Divergence = 0.0967, L1-Distance = 0.0706, L2-Distance = 0.0078, Normal std = 0.5189

0.873 Kernel fit Pairwise Correlations Normal fit

Density 0.437

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

BMDM_CyaA*_24h_rep1BMDM_CyaA*_24h_rep2BMDM_CyaA*_24h_rep3BMDM_CyaA_24h_rep1 (0.0473004)BMDM_CyaA_24h_rep2 (0.0692583)BMDM_CyaA_24h_rep3 (0.0572057)BMDM_ProCyaA*_24h_rep1 (0.142284)BMDM_ProCyaA*_24h_rep2 (0.131736)BMDM_ProCyaA*_24h_rep3 (0.149932)BMDM_Urea_24h_rep1 (0.0972666)BMDM_Urea_24h_rep2 (0.0651159)BMDM_Urea_24h_rep3 (0.0610555) (0.0585895) (0.0575314) (0.0627248)[ min ] [ medium ] [ max ] CEM 1 Aurka 364.8 1890.6 2125.9 P ( S | Z, I ) = 1.00 Bub1 167.1 2230.1 2308.8 Mean Corr = 0.88740 Plk1 144.7 2098.0 2312.2 Cdc20 583.8 3461.5 4024.8 Ccnb2 656.6 4568.9 5165.8 Sgol1 107.1 667.4 813.0 Espl1 333.6 919.5 1000.2 Fbxo5 185.7 2332.7 2594.5 Cdc25c 92.1 308.5 402.5 Ccne2 37.6 466.5 564.7 Ccne1 87.8 537.2 607.2 Pkmyt1 105.1 845.0 962.4 Smc1a 1770.7 2840.5 3004.6 Ccnb1 52.8 66.5 84.0 Smc3 684.5 1552.1 1778.4 Anapc1 1536.6 2131.7 2292.8 Anapc5 4669.6 8762.8 9002.4 Ccna2 275.9 7120.8 7791.8 Cdk1 965.7 5757.2 6245.3 Birc5 342.7 6132.3 7035.0 Kif20a 130.2 1079.7 1410.2 Tpx2 296.0 2616.0 2997.8 CEM 1 + Ncapg 65.9 912.5 1006.5 Top 10 Genes Ube2c 1507.1 8775.4 9511.9 Nusap1 121.3 3191.8 3449.2 Shcbp1 112.2 2683.1 3022.7 Kif11 70.2 792.2 958.5

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE12454" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 13 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12454 Status: Public on Aug 01 2009 Title: The SWI/SNF protein ATRX co-regulates pseudoautosomal genes that have translocated to autosomes in the mouse genome Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 18842153 Summary & Design: Summary: Pseudoautosomal regions (PAR1 and PAR2) in eutherians retain homologous regions between the X and Y chromosomes that play a critical role in the obligatory X-Y crossover during male meiosis. Genes that reside in the PAR1 are exceptional in that they are rich in repetitive sequences and undergo a very high rate of recombination. Remarkably, murine PAR1 homologs have translocated to various autosomes, reflecting the complex recombination history during the evolution of the mammalian X chromosome. We now report that the SNF2-type chromatin remodeling protein ATRX controls the expression of eutherians ancestral PAR1 genes that have translocated to autosomes in the mouse. In addition, we have identified two potentially novel mouse PAR1 orthologs. We propose that the ancestral PAR1 genes share a common epigenetic environment that allows ATRX to control their expression.

Overall design: At P0.5, n = 4 biological replicates of littermate-matched wt/ko pairs (for pair #2 there is one wt and 2 Atrx-null samples (2A & 2B) and we count this as 2 pairs).

Background corr dist: KL-Divergence = 0.0342, L1-Distance = 0.0308, L2-Distance = 0.0011, Normal std = 0.6463

0.648 Kernel fit Pairwise Correlations Normal fit

Density 0.324

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

E13.5 wildE13.5 type wildE13.5 #1 type(0.0929379) wildE13.5 #2 type(0.0901913) Atrx-nullE13.5 #3 (0.0720623) Atrx-null E13.5#1 (0.104973) Atrx-null P0.5#2 (0.11571) wild P0.5#3 type (0.071861) wild #1P0.5 type(0.0605018) wild #2P0.5 type(0.0720516) Atrx-null #3P0.5 (0.0632534) Atrx-null #1P0.5 (0.0576848) Atrx-null #2AP0.5 (0.0722829) Atrx-null #2B (0.0706561) #3 (0.0558341) [ min ] [ medium ] [ max ] CEM 1 Aurka 219.6 291.6 1812.4 P ( S | Z, I ) = 1.00 Bub1 84.4 153.0 2195.3 Mean Corr = 0.88659 Plk1 171.2 343.8 2139.5 Cdc20 388.6 902.9 4253.5 Ccnb2 192.9 331.6 2522.0 Sgol1 52.5 167.3 1463.9 Espl1 150.6 260.3 1483.2 Fbxo5 190.6 330.3 2181.3 Cdc25c 43.8 82.4 698.8 Ccne2 118.8 196.9 1085.0 Ccne1 60.8 169.7 670.2 Pkmyt1 86.6 264.6 1180.3 Smc1a 1430.4 1674.0 3644.4 Ccnb1 58.9 94.0 161.5 Smc3 785.5 1472.7 2719.9 Anapc1 864.5 1005.4 1717.4 Anapc5 4424.0 5299.2 6280.9 Ccna2 442.4 726.6 3350.3 Cdk1 407.4 731.4 4345.7 Birc5 249.3 380.4 3544.3 Kif20a 59.1 111.1 1178.8 Tpx2 172.5 287.8 2265.6 CEM 1 + Ncapg 34.0 100.8 1078.0 Top 10 Genes Ube2c 284.3 481.2 5944.8 Nusap1 366.9 613.2 4217.7 Shcbp1 117.8 253.1 2589.3 Kif11 192.2 247.7 2015.0

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE6957" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 12 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6957 Status: Public on Jul 19 2007 Title: Transcriptional profiling of bipotential embryonic liver cells to identify liver progenitor cell surface markers (430) Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 17641245 Summary & Design: Summary: The ability to purify to homogeneity a population of hepatic progenitor cells from adult liver is critical for their characterization prior to any therapeutic application. As a step in this direction, we have utilized gene profiling of a bipotential liver cell line from dpc 14 mouse embryonic liver to catalog genes expressed by liver progenitor cells. These cells, known as Bipotential Mouse Embryonic Liver (BMEL) cells, proliferate in an undifferentiated state and are capable of differentiating into hepatocyte-like and cholangiocyte-like cells in vitro. Upon transplantation, BMEL cells are capable of differentiating into hepatocytes and cholangiocytes in vivo. Microarray analysis of gene expression in the 9A1 and 14B3 BMEL cell lines grown under proliferating and differentiating conditions was used to identify cell surface markers preferentially expressed in the bipotential undifferentiated state. This analysis revealed that proliferating BMEL cells express many genes involved in cell cycle regulation whereas differentiation of BMEL cells by cell aggregation causes a switch in gene expression to functions characteristic of mature hepatocytes. In addition, microarray data and protein analysis indicated that the Notch signaling pathway could be involved in maintaining BMEL cells in an undifferentiated stem cell state. Using GO annotation, a list of cell surface markers preferentially expressed on undifferentiated BMEL cells was generated. One marker, Cd24a, is specifically expressed on progenitor oval cells in livers of DDC treated animals. We therefore consider Cd24a expression a candidate molecule for purification of hepatic progenitor cells.

Keywords: cell type comparison

Overall design: RNA was extracted from two independently isolated BMEL cell lines (9A1 and 14B3) after culture under three conditions (basal, aggregate 1 day, and aggregate 5 days). Duplicate biological replicates were collected for each cell line:culture condition combination for a total of 12 samples. Samples were biotin-labeled, hybridized to mouse 430 2.0 chips, and scanned according to established Affymetrix protocols.

Background corr dist: KL-Divergence = 0.0532, L1-Distance = 0.0670, L2-Distance = 0.0087, Normal std = 0.5905

0.722 Kernel fit Pairwise Correlations Normal fit

Density 0.361

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

basal culture,basal culture, 9A1,basal rep culture, 9A1,basal 1 (430) rep culture, 14B3, D1(0.0440782)2 (430) aggregate rep 14B3, D1(0.130139) 1 aggregate(430) rep culture,D1 (0.130827)2 aggregate(430) culture, 9A1,D1 (0.0825502) aggregate rep culture, 9A1,D5 1 (430)aggregate rep culture, 14B3,D5 (0.0758227)2 (430)aggregate repculture, 14B3,D5 (0.178054) 1 aggregate (430) repculture, 9A1,D5 (0.0400197)2 aggregate (430) rep culture, 9A1, 1 (0.0683708) (430) rep culture, 14B3, (0.0680667)2 (430) rep 14B3, (0.0873367) 1 (430) rep[ (0.0451733)2min (430) (0.0495627) ] [ medium ] [ max ] CEM 1 Aurka 98.2 570.9 3591.3 P ( S | Z, I ) = 1.00 Bub1 35.3 473.0 3231.5 Mean Corr = 0.88640 Plk1 173.9 519.3 2982.5 Cdc20 397.3 1434.8 4678.7 Ccnb2 72.7 1159.9 4118.6 Sgol1 212.3 435.3 2687.0 Espl1 102.3 236.5 1184.4 Fbxo5 118.5 239.3 2147.2 Cdc25c 97.7 218.7 774.9 Ccne2 22.7 48.4 638.0 Ccne1 94.7 115.4 321.5 Pkmyt1 400.0 614.3 1128.3 Smc1a 1487.4 2680.6 4293.3 Ccnb1 46.8 57.0 107.7 Smc3 714.7 1508.9 2955.8 Anapc1 990.6 1677.5 2846.7 Anapc5 2271.5 5232.9 6820.5 Ccna2 52.7 1100.4 4698.1 Cdk1 221.6 1571.6 6498.1 Birc5 62.6 990.4 4027.1 Kif20a 74.7 657.4 3413.7 Tpx2 119.2 576.5 3470.8 CEM 1 + Ncapg 35.7 145.7 1476.9 Top 10 Genes Ube2c 83.5 2687.0 12052.8 Nusap1 63.5 901.5 3583.2 Shcbp1 89.6 500.6 3230.4 Kif11 79.0 266.0 1047.1

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE54653" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 6 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54653 Status: Public on May 07 2014 Title: Expression data from quiescent and activated neural stem cells from the adult mouse V-SVZ niche Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: RNA was purified from GFAP::GFP+CD133+ and GFAP::GFP+CD133+EGFR+ cells isolated from the adult mouse V-SVZ niche (GFAP::GFP mice, Jackson Mice Stock number 003257)

Overall design: 6 samples consisting of two conditions of three biological replicates each were analyzed

Background corr dist: KL-Divergence = 0.0262, L1-Distance = 0.0342, L2-Distance = 0.0016, Normal std = 0.7186

0.560 Kernel fit Pairwise Correlations Normal fit

Density 0.280

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

adult V-SVZadult qNSCs V-SVZadult qNSCs,biological V-SVZadult qNSCs, biologicalV-SVZ adultreplicate aNSCs, biologicalV-SVZadult replicate 1 (0.229477) aNSCs,biologicalV-SVZ replicate 2 (0.148545) aNSCs,biological replicate 3 (0.200799) biological replicate 1 (0.151555)[ replicate 2min (0.158244) 3 (0.111379)] [ medium ] [ max ] CEM 1 Aurka 25.5 2765.7 2996.8 P ( S | Z, I ) = 1.00 Bub1 1.0 1632.1 1897.2 Mean Corr = 0.88170 Plk1 17.5 1078.4 1372.7 Cdc20 11.7 1361.5 2582.7 Ccnb2 34.1 1826.3 2542.2 Sgol1 7.1 658.3 1552.6 Espl1 79.1 1693.9 2375.1 Fbxo5 234.5 1472.2 2438.2 Cdc25c 13.0 500.8 859.6 Ccne2 60.2 608.4 919.2 Ccne1 115.3 419.9 1057.2 Pkmyt1 206.9 654.6 931.1 Smc1a 932.6 2560.0 3774.2 Ccnb1 10.8 2864.0 6533.9 Smc3 1215.8 2322.5 2748.6 Anapc1 304.9 951.6 1401.1 Anapc5 1515.4 4320.2 4841.2 Ccna2 132.1 4175.2 4876.1 Cdk1 151.5 2513.3 4350.5 Birc5 158.5 2460.5 4252.8 Kif20a 10.3 1951.7 3959.7 Tpx2 74.9 3851.6 4266.0 CEM 1 + Ncapg 154.0 3023.9 3800.8 Top 10 Genes Ube2c 161.0 11669.4 13600.7 Nusap1 73.4 3417.2 4652.1 Shcbp1 47.4 2069.3 3669.4 Kif11 8.6 1737.2 2056.9

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE9287" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 8 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9287 Status: Public on Dec 15 2009 Title: Differential gene expression in wild-type versus Yaa mutant mouse spleen cells Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: T cells from many patients with systemic lupus erythematosus are hypoproliferative in response to TCR ligation. This defect is mediated, at least in part, through down regulation of the TCR zeta chain. Investigation of this phenomenon in lupus-prone mice revealed that the hypoproliferative T cell phenotype apparent in BXSB males is mediated

in part by the Yaa locus. The BXSB model of lupus is a recombinant inbred strain that was originally derived from a cross between a male SB/LE mouse and a female C57BL/6 mouse. BXSB is unique among lupus-prone mouse strains, in that males carry an autoimmune accelerating factor on the Y chromosome, termed Yaa, which accelerates disease onset in male BXSB mice so that fatal glomerulonephritis occurs around 6 months of age. It was recently reported that the Yaa locus is a translocation of a short stretch of genes including that encoding Toll-like

receptor 7 (Tlr-7) from the X to the Y chromosome, leading to a two-fold over expression of a subset of these genes, including Tlr-7, and hypersensitivity of Yaa+ cells to TLR-7 agonists.

To more fully understand the functional significance of the Yaa gene and how it plays a part in the modulation of CD4+ T cell responses, we performed microarray analysis using Affymetrix 430 2.0 arrays on spleens from B6 male B6.Yaa male samples. The analysis revealed an enhanced signature of innate immunity, including increased expression not only of Tlr7 and Tlr8, in line with reports that the Yaa locus leads to a duplication of the murine Tlr7 and Tlr8 genes , but also of Tlr2, Tlr5, Cd14, Lbp, C2, C3 and genes for several heat-shock proteins. T cells from B6.Yaa mice also displayed decreased TCRÎ¶ expression. Interestingly, cell surface levels of the inhibitory molecule B7-H1 were increased on B6.Yaa B cells and monocytes/macrophages. In line with increased TLR-7 expression reported in B6.Yaa mice, the TLR-7 agonist imiquimod increased B7-H1 expression on normal B cells. Restoration of proliferation in co-cultures of B6 T cells and B6.Yaa APC with B7-H1 blocking Ab demonstrated a mechanistic contribution of B7-H1 up-regulation to Yaa-mediated APC-dependent T cell hypoproliferation. In addition, T cell hypoproliferation was induced in normal B6 T cells in vitro by the application of imiquimod. However, this defect was not mediated by B7-H1 or secreted factors but was independent of APC and mediated through direct imiquimod stimulation of T cells themselves. We postulate that excessive TLR-7 stimulation in Yaa+ mice mediates T cell hypoproliferation in part through up-regulation of B7-H1 and possibly also through direct T cell-mediated effects.

Keywords: differential gene expression, RNA, spleen, C57Bl/6J, B6.SB-Yaa/J, male, wild type, Yaa

Overall design: RNA was separately extracted, labeled, and hybridized from each animal.

Background corr dist: KL-Divergence = 0.0581, L1-Distance = 0.0301, L2-Distance = 0.0011, Normal std = 0.5502

0.749 Kernel fit Pairwise Correlations Normal fit

Density 0.374

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

spleen_WT_rep1spleen_WT_rep2spleen_WT_rep3 (0.119207)spleen_WT_rep4 (0.0666164)spleen_Yaa_rep1 (0.0743988)spleen_Yaa_rep2 (0.0577724)spleen_Yaa_rep3 (0.0649457)spleen_Yaa_rep4 (0.272899) (0.261071) (0.0830893) [ min ] [ medium ] [ max ] CEM 1 Aurka 960.0 3327.4 5203.0 P ( S | Z, I ) = 1.00 Bub1 782.5 2583.0 3347.0 Mean Corr = 0.87760 Plk1 671.3 1780.8 2967.3 Cdc20 1256.0 4552.1 7254.6 Ccnb2 2989.3 10856.8 16015.8 Sgol1 491.8 2009.9 2990.3 Espl1 549.6 1313.4 2102.6 Fbxo5 1613.6 4107.5 6623.0 Cdc25c 94.0 457.7 531.8 Ccne2 996.9 3271.8 3625.6 Ccne1 493.8 1285.1 2622.5 Pkmyt1 594.3 1105.4 1482.2 Smc1a 3700.0 5951.2 7941.2 Ccnb1 117.5 199.6 273.4 Smc3 1861.6 3406.5 4109.3 Anapc1 1934.4 2717.8 3466.4 Anapc5 6183.1 9175.5 14218.1 Ccna2 3665.4 11815.4 17720.3 Cdk1 1412.8 5064.9 7811.7 Birc5 3221.0 10958.0 14736.2 Kif20a 523.2 1645.6 2537.1 Tpx2 891.7 3948.4 5861.4 CEM 1 + Ncapg 874.8 3461.3 4217.1 Top 10 Genes Ube2c 4352.8 16185.2 23136.0 Nusap1 2558.1 8345.9 10997.5 Shcbp1 658.7 2263.5 2803.7 Kif11 589.3 2255.2 3149.0

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE29241" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 6 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29241 Status: Public on Nov 13 2011 Title: Dendritic cell lineage commitment is instructed by distinct cytokine signals Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 22078373 Summary & Design: Summary: Dendritic cells (DC) develop from hematopoietic stem cells, which is guided by instructive signals through cytokines. DC development progresses from multipotent progenitors (MPP) via common DC progenitors (CDP) into DC. Flt3 ligand (Flt3L) signaling via the Flt3/Stat3 pathway is of pivotal importance for DC development under steady state conditions. Additional factors produced during steady state or inflammation, such as TGF-beta1 or GM-CSF, also influence the differentiation potential of MPP and CDP. Here, we studied how gp130, GM-CSF and TGF-beta1 signaling influence DC lineage commitment from MPP to CDP and further into DC. We observed that activation of gp130 signaling promotes expansion of MPP. Additionally, gp130 signaling inhibited Flt3L-driven DC differentiation, but had little effect on GM-CSF-driven DC development. The inflammatory cytokine GM-CSF induces differentiation of MPP into inflammatory DC and blocks steady state DC development. Global transcriptome analysis revealed a GM-CSF-driven gene expression repertoire that primes MPP for differentiation into inflammatory DC. Finally, TGF-beta1 induces expression of DC-lineage affiliated genes in MPP, including Flt3, Irf-4 and Irf-8. Under inflammatory conditions, however, the effect of TGF- beta1 is altered: Flt3 is not upregulated, indicating that an inflammatory environment inhibits steady state DC development. Altogether, our data indicate that distinct cytokine signals produced during steady state or inflammation have a different outcome on DC lineage commitment and differentiation.

Overall design: - GM-TNFa-DC_2

Background corr dist: KL-Divergence = 0.0220, L1-Distance = 0.0160, L2-Distance = 0.0003, Normal std = 0.7247

0.550 Kernel fit Pairwise Correlations Normal fit

Density 0.275

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

MultipotentMultipotent progenitorDendritic progenitorDendritic sample cell sampleDendritic sample1 cell (GM-MPP_1) sample1Dendritic (GM-DC_1)2 cell (GM-MPP_2) plus2 (0.264517)(GM-DC_2) cell TNFa (0.154437) plus (0.17231) sample TNFa (0.0971003) sample1 (GM-TNFa-DC_1)[ 2min (GM-TNFa-DC_2) ] (0.169266) (0.14237)[ medium ] [ max ] CEM 1 Aurka 226.4 1079.7 3051.7 P ( S | Z, I ) = 1.00 Bub1 215.4 1563.3 2449.8 Mean Corr = 0.87718 Plk1 354.3 943.8 3712.0 Cdc20 500.3 1221.5 4877.9 Ccnb2 481.7 1747.8 4640.6 Sgol1 115.8 572.7 1476.7 Espl1 184.5 403.9 1216.2 Fbxo5 213.4 1050.5 1369.3 Cdc25c 63.9 160.6 413.1 Ccne2 89.8 617.7 920.6 Ccne1 363.8 638.4 1120.4 Pkmyt1 306.1 538.1 1158.4 Smc1a 1612.0 2636.0 4443.9 Ccnb1 62.6 79.0 110.1 Smc3 1074.9 1345.7 2908.5 Anapc1 1267.2 1630.7 2766.5 Anapc5 3715.3 5209.2 8507.6 Ccna2 550.7 2380.9 5390.4 Cdk1 516.3 2050.4 4048.8 Birc5 297.3 1796.8 4348.5 Kif20a 203.4 801.8 2107.8 Tpx2 277.7 1324.2 3041.0 CEM 1 + Ncapg 59.1 617.6 1476.9 Top 10 Genes Ube2c 743.0 2898.9 7680.6 Nusap1 417.8 2312.5 3491.3 Shcbp1 217.3 1520.0 3042.5 Kif11 93.4 496.4 1537.7

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE33308" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 10 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE33308 Status: Public on Jan 01 2013 Title: Keratinocyte Growth Factor and Dexamethasone Plus Elevated cAMP Levels Synergistically Support Pluripotent Stem Cell Differentiation into Alveolar Epithelial Type II Cells. Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 23176317 Summary & Design: Summary: Alveolar epithelial type II (ATII)-like cells can be generated from murine embryonic stem cells (ESCs), although to date, no robust protocols applying specific differentiation factors are established. We hypothesized that the keratinocyte growth factor (KGF), an important mediator of lung organogenesis and primary ATII cell maturation and proliferation, together with dexamethasone, 8-bromoadenosine-cAMP, and isobutylmethylxanthine (DCI), which induce maturation of primary fetal ATII cells, also support the alveolar differentiation of murine ESCs. Here we demonstrate that the above stimuli synergistically potentiate the alveolar differentiation of ESCs as indicated by increased expression of the surfactant proteins (SP-) C and SP-B. This effect is most profound if KGF is supplied not only in the late stage, but at least also during the intermediate stage of differentiation. Our results indicate that KGF most likely does not enhance the generation of (mes)endodermal or NK2 homeobox 1 (Nkx2.1) expressing progenitor cells but rather, supported by DCI, accelerates further differentiation/maturation of respiratory progeny in the intermediate phase and maturation/proliferation of emerging ATII cells in the late stage of differentiation. Ultrastructural analyses confirmed the presence of ATII-like cells with intracellular composite and lamellar bodies. Finally, induced pluripotent stem cells (iPSCs) were generated from transgenic mice with ATII cell-specific lacZ reporter expression. Again, KGF and DCI synergistically increased SP-C and SP-B expression in iPSC cultures, and lacZ expressing ATII-like cells developed. In conclusion, ATII cell-specific reporter expression enabled the first reliable proof for the generation of murine iPSC-derived ATII cells. In addition, we have shown KGF and DCI to synergistically support the generation of ATII-like cells from ESCs and iPSCs. Combined application of these factors will facilitate more efficient generation of stem cell-derived ATII cells for future basic research and potential therapeutic application.

Overall design: mESCs at d24 of differentiation with KGF and DCI treatment

Background corr dist: KL-Divergence = 0.0344, L1-Distance = 0.0193, L2-Distance = 0.0005, Normal std = 0.6401

0.623 Kernel fit Pairwise Correlations Normal fit

Density 0.312

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

mESCs mESCsat d8 of mESCsat differentiation d8 of mESCsat differentiation d17 of mESCs at(Control) differentiation d17 of mESCs atwith differentiation (0.229626)d17 KGF of mESCsat (Control)differentiation d17treatment of mESCsat withdifferentiation d24 (0.043257) (0.222979) KGFof mESCsat withdifferentiation d24 treatment DCIof mESCsat withdifferentiation d24 treatment KGF(0.0461441)of at (Control)differentiation d24 and (0.0513098) of DCI withdifferentiation (0.0946196) treatment KGF with treatment DCI[ (0.035874) withmin treatment KGF(0.0758463) and] (0.0993209) DCI treatment[ medium (0.101024) ] [ max ] CEM 1 Aurka 341.3 813.1 1725.7 P ( S | Z, I ) = 1.00 Bub1 400.5 1626.6 4064.9 Mean Corr = 0.87450 Plk1 261.2 823.7 2288.5 Cdc20 671.5 1699.1 3722.4 Ccnb2 394.3 1385.3 2865.3 Sgol1 199.1 572.5 1312.9 Espl1 136.2 401.1 1202.0 Fbxo5 230.4 661.9 1701.4 Cdc25c 105.6 193.1 508.1 Ccne2 257.8 564.6 991.7 Ccne1 434.6 630.5 761.6 Pkmyt1 272.9 309.9 494.6 Smc1a 1333.7 1862.5 3000.5 Ccnb1 63.6 83.4 149.8 Smc3 968.7 1536.2 2016.5 Anapc1 1463.1 1656.5 2311.4 Anapc5 4308.0 5252.5 5940.2 Ccna2 491.9 1601.8 3245.9 Cdk1 1144.7 3137.0 5440.3 Birc5 456.6 1683.7 4107.4 Kif20a 245.1 789.3 2017.5 Tpx2 339.6 892.8 2309.9 CEM 1 + Ncapg 102.3 378.8 876.6 Top 10 Genes Ube2c 1236.9 3469.3 7189.8 Nusap1 390.0 1379.7 2385.3 Shcbp1 239.1 968.3 2126.3 Kif11 101.4 412.6 713.8

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE15741" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 6 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15741 Status: Public on Nov 10 2009 Title: Gene expression profiles of forced miR-200 expression in 344SQ lung adenocarcinoma cells with high metastatic potential Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 19759262 Summary & Design: Summary: Metastatic disease is a primary cause of cancer-related death, and factors governing tumor cell metastasis have not been fully elucidated. Here we addressed this question by using tumor cell lines derived from mice that develop metastatic lung adenocarcinoma owing to expression of mutant K-ras and p53. A feature of metastasis-prone tumor cells that distinguished them from metastasis-incompetent tumor cells was plasticity in response to changes in their microenvironment. They transited reversibly between epithelial and mesenchymal states, forming highly polarized epithelial spheres in 3-dimensional culture that underwent epithelial-mesenchymal transition (EMT) following treatment with transforming growth factor-beta or injection into syngeneic mice. This plasticity was entirely dependent upon the microRNA-200 family, which decreased during EMT. Forced expression of miR-200 abrogated the capacity of these tumor cells to undergo EMT, invade, and metastasize and conferred transcriptional features of metastasis-incompetent tumor cells. We conclude that microenvironmental cues direct tumor metastasis by regulating miR-200 expression.

Overall design: Cell lines from p53R172Hg/+ K-rasLA1/+ mice were derived from tumor tissues removed at autopsy from two different mice (#344 and #393). The tissues were minced, placed in culture, and passed serially in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), which yielded mass populations of tumor cells derived from primary lung tumors (344P and 393P), mediastinal lymph nodes (344LN and 393LN), and a subcutaneous site (344SQ). Stable 344SQ cell lines expressing the miR-200b-200a-429 cluster or control vector were generated by transduction with lentivirus vectors. GFP positive transfectant pools were selected by growth in RPMI 1640 with 10% FBS and puromycin. RNA samples of miR-200b-200a-429 knockup versus control (from triplicate cultures of each) were processed and analyzed on Affymetrix Mouse Expression Array 430A 2.0 chips.

Background corr dist: KL-Divergence = 0.0327, L1-Distance = 0.0246, L2-Distance = 0.0007, Normal std = 0.6647

0.624 Kernel fit Pairwise Correlations Normal fit

Density 0.312

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

ControlControl A (0.132333)Control B (0.223129)429 C (0.107443) B (0.135153)429 A (0.214261)429 C (0.18768) [ min ] [ medium ] [ max ] CEM 1 Aurka 282.7 1694.7 2347.6 P ( S | Z, I ) = 1.00 Bub1 241.4 2063.7 2386.9 Mean Corr = 0.87376 Plk1 137.5 1518.9 2452.1 Cdc20 680.4 4635.3 5168.2 Ccnb2 169.5 3275.7 3531.8 Sgol1 192.9 1760.0 1871.3 Espl1 19.8 272.9 391.1 Fbxo5 262.6 2094.9 2351.7 Cdc25c 18.8 385.4 443.5 Ccne2 469.8 1440.6 1573.7 Ccne1 117.4 225.9 258.1 Pkmyt1 266.8 356.2 408.6 Smc1a 1433.2 1993.9 2585.6 Ccnb1 154.8 336.1 402.9 Smc3 1097.7 2093.3 2859.6 Anapc1 1138.7 2061.4 2380.6 Anapc5 1622.5 3397.3 4032.8 Ccna2 595.2 6334.9 6724.1 Cdk1 1511.0 5817.1 8028.5 Birc5 167.9 4736.0 4758.2 Kif20a 45.4 774.1 1108.8 Tpx2 197.9 1065.9 1097.9 CEM 1 + Ncapg 149.8 1697.7 2114.2 Top 10 Genes Ube2c 874.4 6494.6 6899.1 Nusap1 273.2 3023.8 3104.5 Shcbp1 287.1 4173.1 5932.9 Kif11 58.5 484.3 746.7

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE46185" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 6 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE46185 Status: Public on Apr 19 2013 Title: Genome-wide gene expression profiling revealed a critical role for GATA3 in the maintenance of the Th2 cell identity Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 23824597 Summary & Design: Summary: Functionally polarized CD4+ T helper (Th) cells such as Th1, Th2 and Th17 cells are central to the regulation of acquired immunity. However, the molecular mechanisms governing the maintenance of the polarized functions of Th cells remain unclear. GATA3, a master regulator of Th2 cell differentiation, initiates the expressions of Th2 cytokine genes and other Th2-specific genes. GATA3 also plays important roles in maintaining Th2 cell function and in continuous chromatin remodeling of Th2 cytokine gene loci. However, it is unclear whether continuous expression of GATA3 is required to maintain the expression of various other Th2-specific genes. In this report, genome-wide DNA gene expression profiling revealed that GATA3 expression is critical for the expression of a certain set of Th2-specific genes. We demonstrated that GATA3 dependency is reduced for some Th2-specific genes in fully developed Th2 cells compared to that observed in effector Th2 cells, whereas it is unchanged for other genes. Moreover, effects of a loss of GATA3 expression in Th2 cells on the expression of cytokine and cytokine receptor genes were examined in detail. A critical role of GATA3 in the regulation of Th2-specific gene expression is confirmed in in vivo generated antigen-specific memory Th2 cells. Therefore, GATA3 is required for the continuous expression of the majority of Th2-specific genes involved in maintaining the Th2 cell identity.

Overall design: Mock-transfected and GATA3 siRNA-transfected Th2 and Th2-4th cells are profiled for mRNA expression

Background corr dist: KL-Divergence = 0.0332, L1-Distance = 0.0373, L2-Distance = 0.0018, Normal std = 0.6839

0.604 Kernel fit Pairwise Correlations Normal fit

Density 0.302

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

Th2 (controlTh2 (control siRNA)Th2 (Gata3 siRNA)(0.224029)Th2-4th siRNA) a-TCRTh2-4th (control a-TCR stimTh2-4th (control siRNA)(0.123069) stim (Gata3(0.108977) siRNA)(0.219739) siRNA) a-TCR a-TCR stim (0.175875) stim[ min (0.14831) ] [ medium ] [ max ] CEM 1 Aurka 575.0 2532.1 3199.6 P ( S | Z, I ) = 1.00 Bub1 515.9 2403.5 4406.4 Mean Corr = 0.87013 Plk1 389.4 1479.2 1896.3 Cdc20 1429.3 5302.3 5379.5 Ccnb2 838.3 3345.5 7664.0 Sgol1 454.5 1533.1 2828.7 Espl1 184.2 899.8 1453.2 Fbxo5 776.1 2705.6 5979.7 Cdc25c 70.0 183.1 329.3 Ccne2 922.2 1938.6 3244.5 Ccne1 306.3 703.1 1356.8 Pkmyt1 204.7 703.3 753.9 Smc1a 3049.2 4926.8 5356.0 Ccnb1 78.9 137.8 150.1 Smc3 963.2 1579.0 2121.5 Anapc1 1043.7 1867.6 2338.6 Anapc5 1609.2 3603.1 4257.1 Ccna2 640.4 3780.8 7079.0 Cdk1 1548.1 7696.7 8955.5 Birc5 1034.5 5884.7 11526.5 Kif20a 301.9 2017.4 3092.2 Tpx2 374.7 1349.9 2314.7 CEM 1 + Ncapg 251.5 1286.4 2871.8 Top 10 Genes Ube2c 2102.1 10114.8 14189.9 Nusap1 716.7 2981.7 10039.3 Shcbp1 361.1 2094.3 4861.4 Kif11 276.1 905.3 2012.4

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE6837" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 8 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6837 Status: Public on Jan 31 2007 Title: Expression data from wild type (wt) and Ikbke knockout (Ikke) embryonic fibroblasts (EF) Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 17332413 Summary & Design: Summary: WT and Ikbke-/- EF cells were stimulated with recombinant interferon beta for 6 hours. Cells lacking IKKe kinase show a defect in a subset of interferon stimulated gene transcription

Keywords: comparative study

Overall design: WT and Ikbke cells were either stimulated and left untreated to compare their response to interferon.

Background corr dist: KL-Divergence = 0.0231, L1-Distance = 0.0545, L2-Distance = 0.0038, Normal std = 0.8315

0.536 Kernel fit Pairwise Correlations Normal fit

Density 0.268

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

unstimulatedunstimulated embryonicstimulated embryonicstimulated fibroblasts embryonicstimulated fibroblasts embryonic WT, stimulatedfibroblasts biologicalembryonic KO, stimulatedfibroblasts biologicalembryonicWT, rep1 stimulatedfibroblasts biological embryonicWT,(0.102363) rep1 fibroblasts biological embryonicrep1WT,(0.0807693) fibroblasts biological(0.0740989) rep2KO, fibroblasts biological (0.0702236) rep3KO,[ biological (0.0788668) min rep1KO, biological(0.25925) rep2] (0.0771988) rep3 (0.25723)[ medium ] [ max ] CEM 1 Aurka 86.6 3528.9 4028.8 P ( S | Z, I ) = 1.00 Bub1 49.1 2906.1 3167.5 Mean Corr = 0.86763 Plk1 81.1 2511.7 3235.6 Cdc20 188.5 5555.7 6407.2 Ccnb2 155.2 2958.9 3930.4 Sgol1 11.9 1208.8 1491.2 Espl1 133.8 1100.9 1585.8 Fbxo5 161.3 2228.8 2353.9 Cdc25c 7.0 481.8 561.3 Ccne2 79.4 1802.2 1923.6 Ccne1 121.3 736.3 903.3 Pkmyt1 39.8 614.4 871.4 Smc1a 1909.9 3569.9 3916.1 Ccnb1 18.1 70.5 79.9 Smc3 976.8 2621.8 3367.4 Anapc1 1251.9 4516.0 4894.7 Anapc5 5208.7 6510.7 6845.2 Ccna2 171.9 3633.6 4723.9 Cdk1 218.2 9389.5 13256.5 Birc5 187.3 8632.1 9347.2 Kif20a 11.7 2677.0 4504.1 Tpx2 128.1 3040.1 3673.8 CEM 1 + Ncapg 78.0 1734.2 2132.1 Top 10 Genes Ube2c 206.8 10550.2 11429.9 Nusap1 140.5 1792.6 2206.1 Shcbp1 46.1 2698.8 2850.5 Kif11 3.8 1272.5 1581.1

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE23845" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 15 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23845 Status: Public on Aug 28 2010 Title: Time course for bladder UCC development in UPII-SV40Tag mice Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 20501863 Summary & Design: Summary: We have identified genes that are differentially expressed between the bladders of UPII-SV40Tag mice and their age-matched wild-type littermates at 3, 6, 20, and 30 weeks of age. These are ages that correspond to premalignant, carcinoma in situ, and early-stage and later stage invasive UCC, respectively

Analysis of the microarray data sets has revealed …1,900 unique genes differentially expressed (¥3-fold difference at one or more time points) between wild-type and UPII-SV40Tag urothelium during the time course of tumor development.

Overall design: RNA from the urothelium of duplicate UPII-SV40Tag hemizygous and age-matched wild type littermate mice was isolated at 3, 6, 20, and 30 weeks of age and gene expression profiles were obtained.

Background corr dist: KL-Divergence = 0.1356, L1-Distance = 0.0293, L2-Distance = 0.0013, Normal std = 0.3985

1.002 Kernel fit Pairwise Correlations Normal fit

Density 0.501

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

3wk Wild3wk type Wild biological3wk type UPII-SV40Tag biological3wk rep UPII-SV40Tag #16wk (0.0697146) rep biological Wild #26wk (0.0638333)type biological UPII-SV40Tag repbiological6wk #1 UPII-SV40Tag (0.0481612) rep20wk rep #2 biological Wild(0.0562346)#120wk (0.0893662) type biological Wild rep20wk biological type#1 UPII-SV40Tag(0.050778) rep20wk biological #2rep UPII-SV40Tag(0.0613668) 30wk#1 (0.0589066) rep biological Wild 30wk#2 (0.0560804)type biological Wild30wk repbiological type #1 UPII-SV40Tag (0.0709029)30wk repbiological rep #2 UPII-SV40Tag (0.0426597)#1 (0.0590881) rep biological #2 (0.0474157) biological rep #1 (0.152935) [rep min #2 (0.0725569) ] [ medium ] [ max ] CEM 1 Aurka 64.3 1661.1 3126.8 P ( S | Z, I ) = 1.00 Bub1 3.5 1953.6 2795.0 Mean Corr = 0.86661 Plk1 26.8 1163.6 1957.4 Cdc20 85.5 3567.7 7187.4 Ccnb2 3.9 2944.7 4492.8 Sgol1 26.0 1207.2 2216.1 Espl1 6.0 643.0 1073.1 Fbxo5 85.7 1340.3 2237.7 Cdc25c 3.3 282.4 492.8 Ccne2 3.2 1253.6 2572.8 Ccne1 10.6 400.7 1045.4 Pkmyt1 29.7 686.4 1068.5 Smc1a 1600.8 3984.0 5061.7 Ccnb1 4.2 23.1 183.6 Smc3 696.6 2003.9 2613.7 Anapc1 843.3 1144.4 1511.6 Anapc5 2959.1 5007.6 6929.3 Ccna2 6.9 4376.2 9257.7 Cdk1 13.0 6716.5 8841.8 Birc5 4.4 3844.9 5856.6 Kif20a 3.5 1020.8 1989.6 Tpx2 137.2 2280.2 3021.6 CEM 1 + Ncapg 2.0 1119.2 2199.4 Top 10 Genes Ube2c 3.0 4007.7 10707.2 Nusap1 64.8 2842.3 4594.9 Shcbp1 2.7 2168.6 4586.5 Kif11 4.3 658.3 1036.3

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE26616" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 6 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26616 Status: Public on Jun 09 2011 Title: EZH1 and EZH2 Co-Govern Histone H3-K27 Trimethylation and Are Essential for Hair Follicle Homeostasis and Wound Repair Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21317239 Summary & Design: Summary: Polycomb protein group (PcG)-dependent trimethylation on H3-K27(H3K27me3) regulates identity of embryonic stem cells (SCs). How H3K27me3 governs adult SCs and tissue development is unclear. Here, we conditionally target H3-K27-methyltransferases Ezh2 and Ezh1 to address their roles in mouse skin homeostasis. Postnatal phenotypes appear only in doubly-targeted skin, where H3K27me3 is abolished, revealing functional redundancy in EZH1/2 proteins. Surprisingly, while Ezh1/2-null hair follicles (HFs) arrest morphogenesis and degenerate due to defective proliferation and increased apoptosis, epidermis hyperproliferates and survives engraftment. mRNA-microarray studies reveal that despite these striking phenotypic differences, similar genes are upregulated in HF and epidermal Ezh1/2-null progenitors. Featured prominently are a) PcG-controlled non-skin lineage genes, whose expression is still significantly lower than in native tissues, and b) the PcG-regulated Ink4a/Inkb/Arf locus. Interestingly, even though Ink4a/Arf/Ink4b genes are fully activated in HF cells, they only partially so in epidermal-progenitors. Importantly, transduction of Ink4b/Ink4a/Arf shRNAs restores proliferation/survival of Ezh1/2-null HF progenitors in vitro, pointing towards the relevance of this locus to the observed HF phenotypes. Our findings reveal new insights into Polycomb-dependent tissue control and provide a new twist to how different progenitors within one tissue respond to loss of H3K27me3.

Overall design: RNAs from FACS-purified WT and Ezh1/2 2KO ORS, matrix and epidermal cells (Rendl et al., 2005) were provided to the Genomics Core Facility, MSKCC for quality control, quantification, reverse transcription, labeling and hybridization to MOE430A 2.0 microarray chips (Affymetrix). Arrays were scanned per the manufacturers specifications for the Affymetrix MOE430v2 chip. Images were background-subtracted. Probesets were identified as differentially expressed when the absolute fold change was ¥2. Probesets selected for visualization were log2 transformed and were analyzed with hierarchical clustering (Pearson correlation, average linkage), and visualized with heatmaps to assist in interpretation.

Background corr dist: KL-Divergence = 0.0410, L1-Distance = 0.0331, L2-Distance = 0.0015, Normal std = 0.6238

0.652 Kernel fit Pairwise Correlations Normal fit

Density 0.326

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

Ezh1/2 2KOEzh1/2 FACS 2KOEzh1/2 purified FACS 2KOEzh1/2 purified basalFACS WTEzh1/2 epidermal purifiedFACS matrix WTEzh1/2 purified FACS cellsORS cells WT (0.171952) cellspurified basalFACS(0.12744) (0.156449) epidermal purified matrix cellsORS cells [ (0.284367)cells (0.150489)min (0.109303) ] [ medium ] [ max ] CEM 1 Aurka 365.6 498.7 1422.8 P ( S | Z, I ) = 1.00 Bub1 515.8 1022.4 2422.3 Mean Corr = 0.86298 Plk1 383.8 694.3 1415.2 Cdc20 1575.1 2922.5 4404.1 Ccnb2 1110.4 2083.7 3863.5 Sgol1 238.7 413.0 882.7 Espl1 308.4 378.6 1026.0 Fbxo5 177.7 234.9 890.4 Cdc25c 162.8 235.8 535.9 Ccne2 227.8 377.7 826.5 Ccne1 178.3 438.0 567.7 Pkmyt1 761.2 909.1 1028.3 Smc1a 3945.7 4631.6 5064.6 Ccnb1 44.3 81.1 109.7 Smc3 1196.8 1427.2 2198.6 Anapc1 1177.2 1392.7 2219.1 Anapc5 3584.7 4060.1 6404.4 Ccna2 1236.0 1814.8 4410.0 Cdk1 1482.1 3379.4 4032.3 Birc5 1282.0 3815.0 5135.4 Kif20a 405.3 614.1 1332.7 Tpx2 556.0 769.2 1649.3 CEM 1 + Ncapg 262.5 474.9 1088.0 Top 10 Genes Ube2c 2754.8 8157.9 8750.3 Nusap1 1032.6 1356.9 2629.0 Shcbp1 1040.8 1610.9 2655.8 Kif11 384.9 541.0 1295.8

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE12498" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 12 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12498 Status: Public on Nov 21 2008 Title: Gene expression profiles regulated by Tead2 mutants, Yap, and cell density in NIH3T3 cells Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 19004856 Summary & Design: Summary: Regulation of organ size is important for development and tissue homeostasis. In Drosophila, Hippo signaling controls organ size by regulating the activity of a TEAD transcription factor, Scalloped, through modulation of its coactivator protein Yki. The role of mammalian Tead proteins in growth regulation, however, remains unknown. Here we examined the role of mouse Tead proteins in growth regulation. In NIH3T3 cells, cell density and Hippo signaling regulated the activity of Tead proteins by modulating nuclear localization of a Yki homologue, Yap, and the resulting change in Tead activity altered cell proliferation. Tead2-VP16 mimicked Yap overexpression, including increased cell proliferation, reduced cell death, promotion of EMT, lack of cell contact inhibition, and promotion of tumor formation. Growth promoting activities of various Yap mutants correlated with their Tead-coactivator activities. Tead2-VP16 and Yap regulated largely overlapping sets of genes. However, only a few of the Tead/Yapregulated genes in NIH3T3 cells were affected in Tead1-/-;Tead2-/- or Yap-/- embryos. Most of the previously identified Yap-regulated genes were not affected in NIH3T3 cells or mutant mice. In embryos, levels of nuclear Yap and Tead1 varied depending on cell types. Strong nuclear accumulation of Yap and Tead1 were seen in myocardium, correlating with requirements of Tead1 for proliferation. However, their distribution did not always correlate with proliferation. Taken together, mammalian Tead proteins regulate cell proliferation and contact inhibition as a transcriptional mediator of Hippo signaling, but the mechanisms by which Tead/Yap regulate cell proliferation differ depending on cell types, and Tead, Yap and Hippo signaling may play multiple roles in mouse embryos.

We used microarrays to know the gene expression profiles regurated by Tead2-VP16, Tead2-EnR, Yap, and cell density in NIH3T3 cells.

Keywords: Cell density, genetic modification

Overall design: Tead2-VP16-, Tead2-EnR-, Yap- and control vector-expressing cells were cultured at low or high density for RNA extraction and hybridization on Affymetrix microarrays.

Background corr dist: KL-Divergence = 0.0711, L1-Distance = 0.0551, L2-Distance = 0.0045, Normal std = 0.5445

0.805 Kernel fit Pairwise Correlations Normal fit

Density 0.402

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

ctrl-low-1ctrl-low-2 (0.14789)tead2VP16-conf-1 (0.164029)tead2VP16-conf-2yap-conf-1 (0.0604907)yap-conf-2 (0.0524933)(0.0535206)tead2EnR-low-1 (0.0494945)tead2EnR-low-2ctrl-over-1 (0.0872665)ctrl-over-2 (0.0843067) (0.0668414)tead2VP16-over-1 (0.0618501)tead2VP16-over-2 (0.0799768) (0.0918407) [ min ] [ medium ] [ max ] CEM 1 Aurka 286.0 521.3 3256.7 P ( S | Z, I ) = 1.00 Bub1 277.3 359.7 3430.2 Mean Corr = 0.86037 Plk1 323.0 447.5 3085.2 Cdc20 1105.2 2033.0 9415.6 Ccnb2 120.6 176.3 651.7 Sgol1 210.8 327.6 1546.1 Espl1 153.6 225.2 1343.5 Fbxo5 242.2 306.4 1873.9 Cdc25c 138.7 158.7 723.5 Ccne2 90.2 200.6 923.3 Ccne1 299.4 347.3 861.0 Pkmyt1 503.4 599.1 1104.2 Smc1a 2411.2 2999.7 3973.9 Ccnb1 36.8 46.6 85.8 Smc3 1954.3 2264.2 2852.1 Anapc1 1741.7 1975.2 2808.2 Anapc5 6608.5 7020.0 7789.1 Ccna2 439.7 606.3 3852.8 Cdk1 1012.3 1230.8 6611.2 Birc5 404.9 721.0 5213.2 Kif20a 250.3 339.7 2331.6 Tpx2 405.0 483.0 3263.9 CEM 1 + Ncapg 120.9 147.5 1230.3 Top 10 Genes Ube2c 508.2 888.4 5856.1 Nusap1 368.5 570.9 2887.0 Shcbp1 249.1 374.1 2391.5 Kif11 166.4 251.6 1265.9

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE21716" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 28 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21716 Status: Public on Oct 01 2010 Title: Hepatic xenobiotic metabolizing enzyme gene expression through the life stages of the mouse Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: Using full-genome arrays, the expression of all XMEs was examined during fetal (gestation day (GD) 19), neonatal (postnatal day (PND) 7), prepubescent (PND30), middle age (12 mon), and old age (18 and 24 mon) in the C57Bl6/J mouse liver and compared to young adults. Fetal and neonatal life stages had a dramatic effect on XME expression compared to the relatively minor effects of old age. At all life stages except PND30 down-regulated genes outnumbered up-regulated genes. The altered XMEs included those in all of the major metabolic phases including phase I (alcohol and aldehyde dehydrogenase and Cyp genes), phase II (aldo-keto reductase, glutathione-S-transferases, sulfotransferases and UDP-glucuronosyl transferases) and phase III (transporters). We have generated a comprehensive catalog of XME hepatic gene changes through the life stages of the mouse that can be used to predict chemicals and chemical classes different life stages are more sensitive to. Some CEL files used in this study have been submitted through GSE21224.

Keywords: gene expression/microarray

Overall design: We characterized gene expression changes in the developing mouse liver at gestational days (GD) 19), neonatal (postnatal day (PND) 7), prepubescent (PND30), middle age (12 mon), and old age (18 and 24 mon) in the C57Bl6/J mouse liver using full-genome microarrays and compared these changes to that in the adult liver.. We also compared results to GD19, PND32, and PND67 C3H mice. Total RNA was isolated from liver samples and gene expression analyzed using Affymetrix Mouse 430 2.0 GeneChips. Data from 28 samples, four mice in each of the age groups for C57BL/6 and C3H, were analyzed.

Background corr dist: KL-Divergence = 0.1189, L1-Distance = 0.0776, L2-Distance = 0.0143, Normal std = 0.4578

1.037 Kernel fit Pairwise Correlations Normal fit

Density 0.519

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

Mouse liver_6month_2Mouse liver_6month_11Mouse liver_6month_16Mouse (0.0149492) liver_6month_21Mouse (0.0143029) liver_12month_3Mouse (0.0191542) liver_12month_6Mouse (0.00989318) liver_12month_13Mouse (0.014656) liver_12month_17Mouse (0.0108684) liver_18month_4Mouse (0.0144844) liver_18month_9Mouse (0.0118134) liver_18month_14Mouse (0.0119715) liver_18month_19Mouse (0.013557) liver_24month_25Mouse (0.0162802) liver_24month_29Mouse (0.0115305) liver_24month_33Mouse (0.0333448) liver_24month_34Mouse (0.0126839) liver_C3H_GD19_1Mouse (0.0215573) liver_C3H_GD19_2Mouse (0.0139165) liver_C3H_GD19_3Mouse (0.10262) liver_C3H_GD19_4Mouse (0.105285) liver_C3H_PD32_1Mouse (0.175904) liver_C3H_PD32_2Mouse (0.180322) liver_C3H_PD32_3Mouse (0.01606) liver_C3H_PD32_4Mouse (0.0141476) liver_C3H_PD67_1Mouse (0.0230573) liver_C3H_PD67_2Mouse (0.0208106) liver_C3H_PD67_3Mouse (0.0371263) liver_C3H_PD67_4 (0.0248454) (0.0203532) (0.0345054)[ min ] [ medium ] [ max ] CEM 1 Aurka 25.2 68.2 2638.6 P ( S | Z, I ) = 1.00 Bub1 2.8 7.5 1652.8 Mean Corr = 0.85366 Plk1 2.9 99.0 1792.9 Cdc20 65.2 157.4 3392.4 Ccnb2 2.7 27.3 3873.3 Sgol1 2.7 4.2 1126.5 Espl1 3.9 40.5 962.2 Fbxo5 2.7 28.0 3147.5 Cdc25c 2.7 4.2 286.9 Ccne2 18.9 72.6 2031.4 Ccne1 6.0 91.6 832.5 Pkmyt1 2.7 4.2 496.8 Smc1a 1415.7 1610.4 2334.0 Ccnb1 3.1 28.5 123.9 Smc3 501.8 639.5 2304.3 Anapc1 918.8 1083.1 2130.5 Anapc5 1705.1 2162.3 6765.1 Ccna2 2.9 28.6 6544.8 Cdk1 15.0 136.6 6377.6 Birc5 2.8 14.2 5187.0 Kif20a 3.7 37.5 912.4 Tpx2 26.6 79.0 1820.1 CEM 1 + Ncapg 3.2 21.1 1563.1 Top 10 Genes Ube2c 2.9 62.3 11801.9 Nusap1 3.2 48.7 5148.3 Shcbp1 2.9 37.3 1383.7 Kif11 3.6 50.0 1176.8

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE6875" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 8 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6875 Status: Public on Jan 26 2007 Title: Development of Regulatory T cell Precursors in the Absence of a Functional Foxp3 Protein Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 17273171 Summary & Design: Summary: To analyze gene expression in in regulatory T cell precursors that develop in the absence of a functional Foxp3 protein as compared to that of normal regulatory T cells

Keywords: Cell type comparison

Overall design: Murine wild-type and mutant (delta) Foxp3 alleles were tagged with EGFP reporters. CD4 positive T cells expressing the respective tagged Foxp3 allele (Foxp3/EGFP and delta Foxp3/EGFP) were isolated from hemizygous male mice by cell sorting using FACS. CD4 positive cells that did not express the EGFP tag were a isolated. Total RNA was prepared and used in the array studies.

Background corr dist: KL-Divergence = 0.0619, L1-Distance = 0.0225, L2-Distance = 0.0006, Normal std = 0.5327

0.758 Kernel fit Pairwise Correlations Normal fit

Density 0.379

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

76090_CD4+,76091_CD4+, FoxP3(EGFP-)76092_CD4+, FoxP3(EGFP+)76093_CD4+, mouse(delta)FoxP3(EGFP-)82428_CD4+, cells (delta)FoxP3(EGFP+)mouse82430_CD4+, (0.143133) FoxP3(EGFP+)cells85382_CD4+, (0.129124) mouse (delta)FoxP3(EGFP+)85384_CD4+, cells mouse FoxP3(EGFP+)mouse (0.0978209) cells (delta)FoxP3(EGFP+)cells.txt (0.135875) mouse mouse (0.119732) cells cells[ min(0.108775) (0.111996) mouse ] cells (0.153543)[ medium ] [ max ] CEM 1 Aurka 127.8 701.1 1410.7 P ( S | Z, I ) = 1.00 Bub1 68.0 785.2 1553.1 Mean Corr = 0.85363 Plk1 195.5 1016.7 2463.4 Cdc20 429.6 2152.0 4481.4 Ccnb2 267.9 2673.3 5439.3 Sgol1 163.2 596.1 1333.6 Espl1 90.7 277.4 615.5 Fbxo5 511.6 1485.5 2324.6 Cdc25c 60.0 133.2 242.1 Ccne2 44.3 242.3 408.0 Ccne1 234.7 727.9 1468.7 Pkmyt1 570.8 868.8 1332.3 Smc1a 2717.5 3269.6 3716.1 Ccnb1 47.9 70.4 100.9 Smc3 2145.4 2484.6 2651.2 Anapc1 1939.1 2213.3 2480.6 Anapc5 4878.7 5590.2 6731.8 Ccna2 172.5 1878.4 3178.0 Cdk1 210.5 1876.0 4938.6 Birc5 282.3 2560.3 5492.1 Kif20a 64.0 568.3 1218.7 Tpx2 96.7 791.1 1519.3 CEM 1 + Ncapg 102.9 813.2 1737.5 Top 10 Genes Ube2c 212.0 1915.5 4307.0 Nusap1 238.6 2735.8 5053.4 Shcbp1 165.5 1334.8 2813.3 Kif11 113.6 632.4 1360.4

Null module Anapc2 Ppp2r1a Ywhah Ywhaz Rps6ka1 Itpr1 Itpr3 Btrc Ppp2ca Rps6ka2 Cpeb1 Adcy4 Adcy6 Anapc7 Adcy9 Calml3 Adcy8 Rec8 Igf1 Pttg1 Prkacb Ywhag Ywhaq Ywhab Adcy7 Pgr Itpr2 Ppp3r1 Ppp2cb Adcy3 Ins2 Plcz1 Camk2d Ar Ppp2r5a Anapc4 Camk2g Cdc26 Prkx Fbxw11 Cdc27 Ppp1cb Ywhae Ppp3ca Ppp2r5b Rps6ka3 Fbxo43 Ppp3cb Ppp2r1b Ppp2r5e Anapc10 Spdya Rps6ka6 Ppp3cc Chp2 Cdc16 Slk Camk2a Ppp3r2 Adcy5 Cdc23 Adcy1 Cdk2 Camk2b Smc1b Mapk12 Prkaca Ppp2r5d Calm4 Mos Anapc13 Adcy2 Anapc11 Ppp1ca Stag3 Mad2l2 GEO Series "GSE12881" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 6 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12881 Status: Public on Jan 26 2009 Title: Loss of Caveolin-3 Induces the Development of a Lactogenic Microenvironment Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 19164602 Summary & Design: Summary: Here, we show that functional loss of a single gene is sufficient to confer constitutive milk protein production and protection against mammary tumor formation. Caveolin-3 (Cav-3), a muscle-specific caveolin-related gene, is highly expressed in striated and smooth muscle cells. We demonstrate that Cav-3 is also expressed in myoepithelial cells within the mammary gland. To determine if genetic ablation of Cav-3 expression affects adult mammary gland development, we next studied the phenotype(s) of Cav-3 (-/-) null mice. Interestingly, detailed analysis of Cav-3 (-/-) virgin mammary glands shows dramatic increases in ductal thickness, side-branching, and the development of extensive lobulo-alveolar hyperplasia, akin to the changes normally observed during pregnancy and lactation. Analysis by genome-wide expression profiling reveals the upregulation of gene transcripts associated with pregnancy/lactation, mammary stem cells, and human breast cancers, consistent with a constitutive lactogenic phenotype. The expression levels of three key transcriptional regulators of lactation, namely Elf5, Stat5a, and c-Myc are also significantly elevated. Experiments with pregnant mice directly show that Cav-3 (-/-) mice undergo precocious lactation. Finally, using orthotopic implantation of a transformed mammary cell line (known as Met-1), we demonstrate that virgin Cav-3 (-/-) mice are dramatically protected against mammary tumor formation. Interestingly, Cav-3 (+/-) mice also show similar protection, indicating that even reductions in Cav-3 levels are sufficient to render these mice resistant to tumorigenesis. Thus, Cav-3 (-/-) mice are a novel preclinical model to study the protective effects of a constitutive lactogenic microenviroment on mammary tumor onset and progression. Our current studies have broad implications for using the lactogenic micro-environment as a paradigm to discover new therapies for the prevention and/or treatment of human breast cancers. Most importantly, a lactation-based therapeutic strategy would provide a more natural and nontoxic approach to the development of novel anti-cancer therapies.

Overall design: All WT and Cav-3 knockout (KO) mice used in this study were in the FVB/N genetic background. 4-month old virgin female mice were utilized in a micro array study between 3 wildtype and 3 Caveolin-3 knock-out mammary glands.

Background corr dist: KL-Divergence = 0.0260, L1-Distance = 0.0141, L2-Distance = 0.0002, Normal std = 0.6931

0.576 Kernel fit Pairwise Correlations Normal fit

Density 0.288

0.000 CEM 1

Z-score -5.0 -4.0 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 5.0 Correlation -1.00 -1.00 -1.00 -0.96 -0.76 0.00 0.76 0.96 1.00 1.00 1.00

Pre-normalization Quantiles

MammaryMammary Gland_WT_rep1Mammary Gland_WT_rep3Mammary Gland_WT_rep2 (0.101322)Mammary Gland_Cav-3KO_rep1 (0.162675)Mammary Gland_Cav-3KO_rep2 (0.17792) Gland_Cav-3KO_rep3 (0.135203) (0.163624)[ (0.259257)min ] [ medium ] [ max ] CEM 1 Aurka 150.1 243.8 731.7 P ( S | Z, I ) = 1.00 Bub1 70.7 207.8 1066.6 Mean Corr = 0.85077 Plk1 133.9 217.4 539.3 Cdc20 316.6 529.8 2118.4 Ccnb2 211.6 509.5 1900.1 Sgol1 82.8 161.7 401.5 Espl1 230.7 338.5 711.8 Fbxo5 210.0 256.8 576.0 Cdc25c 78.6 98.6 270.9 Ccne2 20.0 37.0 71.6 Ccne1 117.4 152.7 236.2 Pkmyt1 762.8 956.9 1750.8 Smc1a 3228.5 4342.4 4844.3 Ccnb1 35.4 40.1 56.4 Smc3 689.8 925.9 1169.5 Anapc1 1679.9 1905.2 2010.8 Anapc5 4546.3 5425.1 6142.0 Ccna2 169.4 343.5 1296.1 Cdk1 197.2 663.8 2356.8 Birc5 115.9 264.6 1202.2 Kif20a 34.7 50.5 131.8 Tpx2 99.7 182.6 677.7 CEM 1 + Ncapg 43.7 99.5 364.5 Top 10 Genes Ube2c 178.8 324.5 967.2 Nusap1 126.7 257.7 1166.7 Shcbp1 120.6 297.9 938.1 Kif11 49.4 76.1 266.8