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: 7 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. Wdr61 Cdc73 Num ofGenesinQueryGeneset:7.CEMs:1. Overview ofCo-ExpressionModules(CEMs) with DatasetWeighting Pex2 Leo1 Paf1 Ctr9 Rtf1

Ctr9 Rtf1 Paf1 Cdc73 Leo1 Wdr61 Pex2 CEM 1(15datasets) 0.0 Scale ofaveragePearsoncorrelations 0.2 0.4 0.6 0.8 1.0 Symbol Num ofCEMGenes:7.Predicted585.SelectedDatasets:15.Strength:0.0 CEM 1,Geneset"[G]Cdc73/Paf1complex",Page1 Hsp90aa1 Trappc11 Fam221a Ccdc115 Pak1ip1 Slc30a6 Ctnnbl1 Cbfa2t2 Fbxo45 Zmym1 Morc2a Mettl14 Trmt13 Ppm1d Lemd3 Gtf3c4 Ythdf2 Wdr70 Wdr61 Adck5 Senp5 Cd320 Klhl12 Ddx42 Cdc73 Zc3h8 Tex30 Jade3 Aggf1 Abcf1 Taf1b Taf1a Prpf3 Actr6 Diexf Coa7 Phax Sde2 Tefm Pex2 Ints2 Leo1 Mtif2 Drg1 Clp1 Clpx Paf1 Taf7 Ctr9 Rtf1 0.0 1.0

GSE13692 [8] GSE30160 [6]

GSE26299 [108] Only showingfirst200datasets-Seetxtoutputforfulldetails. GSE11222 [42] GSE9247 [15] GSE11220 [44] GSE16679 [8] GSE17886 [16] GSE13235 [9] GSE3296 [16] GSE39458 [6] GSE21033 [12] GSE13753 [10] GSE51483 [45] GSE48790 [8] GSE35825 [9] GSE33308 [10] GSE13707 [20] GSE20696 [8] GSE29241 [6] GSE20954 [14] GSE42601 [6] GSE13874 [14] GSE16266 [6] GSE26668 [6] GSE40296 [6] GSE21379 [10] GSE52220 [6] GSE38831 [7] GSE14012 [24] GSE48204 [6] GSE24061 [88] GSE18308 [6] GSE4288 [36] GSE36513 [8] GSE12748 [7] GSE10989 [6] GSE17794 [44] GSE39770 [10] GSE30176 [12] GSE2527 [6] GSE54490 [12] GSE38031 [8] GSE55809 [8] GSE54207 [9] GSE8488 [15] GSE39082 [6] GSE15767 [6] GSE31792 [18] GSE21041 [6] GSE46443 [12] GSE7342 [12] GSE5976 [12] GSE26745 [24] GSE27708 [9] GSE17266 [59] GSE54349 [6] GSE7141 [6] GSE6903 [6] GSE19286 [6] GSE19204 [6] GSE26568 [6] GSE11148 [6] GSE31598 [12] GSE35543 [6] GSE13408 [14] GSE4308 [16] GSE21299 [12] GSE14243 [6] GSE34324 [12] GSE22527 [6] GSE15069 [15] GSE31313 [22] GSE14478 [7] GSE28830 [9] GSE10273 [9] GSE18993 [13] GSE24289 [6] GSE40685 [11] GSE42688 [8] GSE7069 [8] GSE11201 [18] GSE52101 [17] GSE35366 [78] GSE51108 [6] GSE40286 [10] GSE17817 [6] GSE38257 [14] GSE18660 [10] GSE32265 [6] GSE26023 [6] GSE32093 [6] GSE40284 [6] GSE8039 [32] GSE5497 [6] GSE38001 [12] GSE50865 [12] GSE11679 [25] GSE38335 [9] GSE15173 [6] GSE20372 [6] GSE8715 [6] GSE13805 [7] GSE30684 [6] GSE22381 [12] GSE5232 [6] GSE6837 [8] GSE45143 [6] GSE39034 [9] GSE53916 [6] GSE37676 [6] GSE53946 [6] GSE17553 [16] GSE27092 [6] GSE30192 [6] GSE14753 [6] GSE32598 [11] GSE32963 [6] GSE9044 [6] GSE21018 [6] GSE15541 [12] GSE13635 [6] GSE37431 [6] GSE6933 [15] GSE8091 [16] GSE9316 [12] GSE6813 [12] GSE7676 [10] GSE56345 [9] GSE11677 [8] GSE38304 [8] GSE4189 [14] GSE49237 [8] GSE9441 [36] GSE13547 [12] GSE22824 [24] GSE21054 [8] GSE36665 [6] GSE31359 [8] GSE20325 [6] GSE7863 [16] GSE44025 [6] GSE19979 [6] GSE7683 [12] GSE14415 [31] GSE6210 [12] GSE36530 [6] GSE47719 [6] GSE13873 [27] GSE7705 [10] GSE6116 [70] GSE12499 [10] GSE35785 [10] GSE18135 [18] CEM+ CEM GSE48932 [12] GSE34618 [7] GSE4041 [6] GSE27114 [6] GSE13224 [6] GSE46723 [6] 0.0 GSE42238 [9] GSE32102 [49]

GSE22371 [6] Scale ofaveragePearsoncorrelations GSE10556 [6] GSE21716 [28] GSE19073 [6] GSE6867 [6] GSE51608 [6] GSE8156 [6] 0.2 GSE53299 [6] GSE10071 [10] GSE46869 [6] GSE53077 [8] GSE25768 [6] GSE39897 [36] GSE43197 [27] GSE23002 [8] GSE43419 [20] 0.4 GSE11149 [8] GSE21996 [14] GSE39375 [10] GSE2557 [6] GSE52075 [9] GSE55607 [18] GSE3463 [12] GSE11973 [6] GSE54581 [21] 0.6 GSE43145 [12] GSE33156 [18] GSE35219 [6] GSE12986 [10] GSE13259 [10] GSE4718 [6] GSE31972 [6] GSE21944 [6] GSE23908 [31] 0.8 GSE33942 [12] GSE27972 [6] GSE23600 [10] GSE36437 [6] Score 5.70 5.79 5.81 5.94 5.98 5.98 6.02 6.09 6.15 6.20 6.26 6.35 6.46 6.51 6.53 6.65 6.77 6.84 6.92 6.95 6.95 6.96 7.01 7.07 7.17 7.18 7.38 7.45 7.53 7.82 7.83 7.94 8.01 8.12 8.13 8.23 8.27 8.46 8.50 8.54 9.02 9.04 9.72 1.0 Notes 1110038F14Rik Symbol Num ofCEMGenes:7.Predicted585.SelectedDatasets:15.Strength:0.0 CEM 1,Geneset"[G]Cdc73/Paf1complex",Page2 Smarcad1 Rnaseh1 Ankrd17 Ppp2r5e Smndc1 Smchd1 Sec24a Dnttip2 Htatsf1 Alkbh8 Rbm12 Trim44 Zfp408 Zfp566 Zfp868 Zfp568 Zfp869 Slc5a6 Tma16 Prpf4b Prdm2 Gtf2e1 Med19 Knop1 Sbno1 Ddx27 Ddx10 Ddx46 Ylpm1 Cep63 Tfb2m Tex10 Dyrk2 Bms1 Snip1 Riok2 Smc3 Fbxl6 Vwa9 Plrg1 Crls1 Noa1 Urb2 Sirt1 Taf2 Gtl3 Tfrc Zfx Ik 0.0 1.0

GSE13692 [8] GSE30160 [6]

GSE22371 [6] Scale ofaveragePearsoncorrelations GSE10556 [6] GSE21716 [28] GSE19073 [6] GSE6867 [6] GSE51608 [6] GSE8156 [6] 0.2 GSE53299 [6] GSE10071 [10] GSE46869 [6] GSE53077 [8] GSE25768 [6] GSE39897 [36] GSE43197 [27] GSE23002 [8] GSE43419 [20] 0.4 GSE11149 [8] GSE21996 [14] GSE39375 [10] GSE2557 [6] GSE52075 [9] GSE55607 [18] GSE3463 [12] GSE11973 [6] GSE54581 [21] 0.6 GSE43145 [12] GSE33156 [18] GSE35219 [6] GSE12986 [10] GSE13259 [10] GSE4718 [6] GSE31972 [6] GSE21944 [6] GSE23908 [31] 0.8 GSE33942 [12] GSE27972 [6] GSE23600 [10] GSE36437 [6] Score 4.39 4.43 4.44 4.46 4.49 4.52 4.54 4.56 4.58 4.61 4.62 4.63 4.64 4.67 4.67 4.70 4.71 4.72 4.72 4.72 4.73 4.83 4.84 4.84 4.91 4.93 4.99 4.99 5.00 5.00 5.04 5.07 5.09 5.11 5.14 5.16 5.19 5.20 5.22 5.22 5.25 5.27 5.28 5.35 5.47 5.50 5.61 5.64 5.64 5.68 1.0 Notes 2410018M08Rik D15Ertd621e Symbol Num ofCEMGenes:7.Predicted585.SelectedDatasets:15.Strength:0.0 CEM 1,Geneset"[G]Cdc73/Paf1complex",Page3 Tomm70a Cdkn2aip Thumpd1 Dcun1d2 Zdhhc16 Zcchc11 Fastkd5 Slc19a2 Slc16a1 Ndufaf1 Map4k5 Cenpc1 Snapc1 Mrps22 Osgin2 Cnot11 Spata5 Zfp451 Zfp639 Cwc27 Polrmt Wdr73 Nop14 Eif2b3 Haus1 Ddx47 Chtop Cnot7 Hars2 Trmt6 Trmt5 Nif3l1 Mrpl2 Taf11 Rnmt Bdp1 Coq5 Pogz Drg2 Ofd1 Rnf8 Aptx Iws1 Pigg Elp5 Nifk Aqr Ivd 0.0 1.0

GSE13692 [8] GSE30160 [6]

GSE22371 [6] Scale ofaveragePearsoncorrelations GSE10556 [6] GSE21716 [28] GSE19073 [6] GSE6867 [6] GSE51608 [6] GSE8156 [6] 0.2 GSE53299 [6] GSE10071 [10] GSE46869 [6] GSE53077 [8] GSE25768 [6] GSE39897 [36] GSE43197 [27] GSE23002 [8] GSE43419 [20] 0.4 GSE11149 [8] GSE21996 [14] GSE39375 [10] GSE2557 [6] GSE52075 [9] GSE55607 [18] GSE3463 [12] GSE11973 [6] GSE54581 [21] 0.6 GSE43145 [12] GSE33156 [18] GSE35219 [6] GSE12986 [10] GSE13259 [10] GSE4718 [6] GSE31972 [6] GSE21944 [6] GSE23908 [31] 0.8 GSE33942 [12] GSE27972 [6] GSE23600 [10] GSE36437 [6] Score 3.48 3.48 3.49 3.51 3.52 3.57 3.57 3.57 3.58 3.59 3.60 3.61 3.62 3.62 3.63 3.63 3.64 3.65 3.65 3.68 3.68 3.74 3.77 3.78 3.78 3.79 3.81 3.83 3.84 3.84 3.87 3.87 3.92 3.96 3.97 3.97 4.00 4.00 4.03 4.05 4.06 4.08 4.08 4.15 4.21 4.23 4.27 4.28 4.31 4.36 1.0 Notes 2700097O09Rik Symbol Num ofCEMGenes:7.Predicted585.SelectedDatasets:15.Strength:0.0 CEM 1,Geneset"[G]Cdc73/Paf1complex",Page4 AU019823 Trp53bp1 Vkorc1l1 Zfp518a Ranbp2 Cd3eap Rprd1b Csrnp2 Dhrs13 Srp54b Ndufv1 Psmg3 Mrpl49 Zfp647 Cwc22 Rbbp5 Qsox2 Ncbp1 Rnpc3 Nup43 Senp3 Ddx20 Dhx33 Caap1 Pex10 Prmt6 Nars2 Ercc3 Smu1 Clcn3 Emc6 Luc7l Strap Pdhb Chd2 Fmr1 Edc3 Faim Lsg1 Taf5l Ints4 Mfn1 Mina Gle1 Kat7 Ei24 Ttc4 Kri1 Dld 0.0 1.0

GSE13692 [8] GSE30160 [6]

GSE22371 [6] Scale ofaveragePearsoncorrelations GSE10556 [6] GSE21716 [28] GSE19073 [6] GSE6867 [6] GSE51608 [6] GSE8156 [6] 0.2 GSE53299 [6] GSE10071 [10] GSE46869 [6] GSE53077 [8] GSE25768 [6] GSE39897 [36] GSE43197 [27] GSE23002 [8] GSE43419 [20] 0.4 GSE11149 [8] GSE21996 [14] GSE39375 [10] GSE2557 [6] GSE52075 [9] GSE55607 [18] GSE3463 [12] GSE11973 [6] GSE54581 [21] 0.6 GSE43145 [12] GSE33156 [18] GSE35219 [6] GSE12986 [10] GSE13259 [10] GSE4718 [6] GSE31972 [6] GSE21944 [6] GSE23908 [31] 0.8 GSE33942 [12] GSE27972 [6] GSE23600 [10] GSE36437 [6] Score 2.88 2.89 2.90 2.90 2.91 2.91 2.94 2.94 3.03 3.04 3.04 3.04 3.05 3.06 3.07 3.07 3.09 3.09 3.10 3.11 3.11 3.12 3.13 3.14 3.14 3.16 3.16 3.20 3.20 3.20 3.21 3.23 3.23 3.24 3.27 3.27 3.30 3.30 3.34 3.34 3.36 3.38 3.38 3.39 3.41 3.41 3.44 3.44 3.46 3.46 1.0 Notes 2310057M21Rik 1600002H07Rik 0610009D07Rik D3Ertd751e Symbol Num ofCEMGenes:7.Predicted585.SelectedDatasets:15.Strength:0.0 CEM 1,Geneset"[G]Cdc73/Paf1complex",Page5 Tmem201 Pafah1b2 Wbscr22 Traf3ip1 Rsl24d1 Timm22 Enoph1 Ccdc51 H2-Ke2 Mettl18 Ppp1r8 Kdm5a Kdm1a Rbm34 Trim33 Cbwd1 Yeats2 Zfp655 Zfp593 Zfp113 Gtf2h3 Polr2b Med23 Aasdh Ap1g1 Stmn1 Kpna1 Rpap3 Rad17 Spsb3 Fubp3 Zmat2 Mettl2 Bpnt1 Lactb Tmx2 Med4 Adnp Tfam Cry2 Rars Gnl2 Glce Lars Lias Aatf 0.0 1.0

GSE13692 [8] GSE30160 [6]

GSE22371 [6] Scale ofaveragePearsoncorrelations GSE10556 [6] GSE21716 [28] GSE19073 [6] GSE6867 [6] GSE51608 [6] GSE8156 [6] 0.2 GSE53299 [6] GSE10071 [10] GSE46869 [6] GSE53077 [8] GSE25768 [6] GSE39897 [36] GSE43197 [27] GSE23002 [8] GSE43419 [20] 0.4 GSE11149 [8] GSE21996 [14] GSE39375 [10] GSE2557 [6] GSE52075 [9] GSE55607 [18] GSE3463 [12] GSE11973 [6] GSE54581 [21] 0.6 GSE43145 [12] GSE33156 [18] GSE35219 [6] GSE12986 [10] GSE13259 [10] GSE4718 [6] GSE31972 [6] GSE21944 [6] GSE23908 [31] 0.8 GSE33942 [12] GSE27972 [6] GSE23600 [10] GSE36437 [6] Score 2.33 2.33 2.34 2.35 2.36 2.36 2.37 2.37 2.38 2.39 2.39 2.43 2.43 2.44 2.45 2.46 2.48 2.48 2.50 2.51 2.53 2.56 2.57 2.58 2.59 2.60 2.61 2.64 2.64 2.65 2.66 2.67 2.67 2.69 2.70 2.70 2.71 2.74 2.74 2.75 2.76 2.77 2.77 2.77 2.81 2.82 2.85 2.85 2.87 2.88 1.0 Notes Symbol Num ofCEMGenes:7.Predicted585.SelectedDatasets:15.Strength:0.0 CEM 1,Geneset"[G]Cdc73/Paf1complex",Page6 Tmem136 Nsmce4a Zscan21 Trmt10a Zswim1 Katnbl1 Anapc4 L2hgdh Mterfd3 Pdcd11 Cdc123 Tuba4a Mettl13 Metap2 Gnb2l1 Pard6b Pih1d2 Gtf2h2 Polr3g Pbrm1 Apitd1 Cdan1 Nop10 Ubxn8 Wdr74 Dhx29 Cox11 Klhl23 Cox15 Rps13 Cebpz Znhit3 Lcmt2 Pex19 Mark3 Mars2 Gtf2f1 Ajuba Aifm1 Nosip Ptch1 Smg7 Fitm2 Rngtt Tyw5 Trnt1 Ss18 Prcc Srr Ilf2 0.0 1.0

GSE13692 [8] GSE30160 [6]

GSE22371 [6] Scale ofaveragePearsoncorrelations GSE10556 [6] GSE21716 [28] GSE19073 [6] GSE6867 [6] GSE51608 [6] GSE8156 [6] 0.2 GSE53299 [6] GSE10071 [10] GSE46869 [6] GSE53077 [8] GSE25768 [6] GSE39897 [36] GSE43197 [27] GSE23002 [8] GSE43419 [20] 0.4 GSE11149 [8] GSE21996 [14] GSE39375 [10] GSE2557 [6] GSE52075 [9] GSE55607 [18] GSE3463 [12] GSE11973 [6] GSE54581 [21] 0.6 GSE43145 [12] GSE33156 [18] GSE35219 [6] GSE12986 [10] GSE13259 [10] GSE4718 [6] GSE31972 [6] GSE21944 [6] GSE23908 [31] 0.8 GSE33942 [12] GSE27972 [6] GSE23600 [10] GSE36437 [6] Score 1.91 1.91 1.92 1.93 1.93 1.93 1.96 1.97 1.97 1.99 2.00 2.00 2.00 2.01 2.01 2.01 2.04 2.06 2.07 2.08 2.09 2.11 2.12 2.12 2.14 2.14 2.14 2.14 2.14 2.16 2.16 2.20 2.21 2.23 2.23 2.23 2.24 2.24 2.25 2.25 2.27 2.28 2.29 2.31 2.32 2.32 2.32 2.32 2.32 2.33 1.0 Notes A830080D01Rik 1810026J23Rik Symbol Num ofCEMGenes:7.Predicted585.SelectedDatasets:15.Strength:0.0 CEM 1,Geneset"[G]Cdc73/Paf1complex",Page7 AW209491 Suv39h1 Ccdc117 Sh3bp5l Eps15l1 Slco4a1 Adprhl2 Zswim3 Poldip2 Hnrnpu Fbxo31 Mrps17 Ndufs1 Rbm15 Atp5a1 Dcaf13 Slc7a5 Nufip1 Wdr77 Senp2 Jarid2 Pex26 Pex12 Gtf2f2 Tssc1 Upf3b Atad5 Cpsf3 Utp15 Cpsf7 U2af2 Uspl1 Nol11 Trap1 Uchl5 Acin1 Zfp11 Pwp1 Msh2 Ccnh Klhl7 Dgke Rev1 Tdp2 Abt1 Cct4 Tsr3 Srl 0.0 1.0

GSE13692 [8] GSE30160 [6]

GSE22371 [6] Scale ofaveragePearsoncorrelations GSE10556 [6] GSE21716 [28] GSE19073 [6] GSE6867 [6] GSE51608 [6] GSE8156 [6] 0.2 GSE53299 [6] GSE10071 [10] GSE46869 [6] GSE53077 [8] GSE25768 [6] GSE39897 [36] GSE43197 [27] GSE23002 [8] GSE43419 [20] 0.4 GSE11149 [8] GSE21996 [14] GSE39375 [10] GSE2557 [6] GSE52075 [9] GSE55607 [18] GSE3463 [12] GSE11973 [6] GSE54581 [21] 0.6 GSE43145 [12] GSE33156 [18] GSE35219 [6] GSE12986 [10] GSE13259 [10] GSE4718 [6] GSE31972 [6] GSE21944 [6] GSE23908 [31] 0.8 GSE33942 [12] GSE27972 [6] GSE23600 [10] GSE36437 [6] Score 1.51 1.52 1.52 1.52 1.53 1.53 1.53 1.54 1.54 1.56 1.57 1.57 1.58 1.59 1.62 1.62 1.63 1.63 1.64 1.66 1.66 1.67 1.67 1.68 1.69 1.70 1.70 1.70 1.71 1.71 1.71 1.72 1.74 1.74 1.74 1.74 1.74 1.76 1.78 1.79 1.79 1.82 1.83 1.84 1.88 1.88 1.88 1.89 1.89 1.91 1.0 Notes Symbol Num ofCEMGenes:7.Predicted585.SelectedDatasets:15.Strength:0.0 CEM 1,Geneset"[G]Cdc73/Paf1complex",Page8 Rps19bp1 Xrcc6bp1 Tubgcp6 Hnrnph1 Hnrnph3 Snrnp25 Trmt10c Fgfr1op Mrps12 Otud6b Gtpbp4 Tada2a U2surp Snrpd3 Cnot10 Nudt15 Rbm48 Dnaaf2 Trmt11 Zfp184 Slc7a6 Qrich1 Mplkip Polr1c Cited2 Rnps1 Cep44 Nsfl1c Fubp1 Xxylt1 Tsen2 Prim2 Cpsf1 Dimt1 Ptcd3 Sppl3 Patz1 Nfrkb Bzw2 Srsf5 Wdr3 Eif3g Rbak Uba2 Uba6 Xpo1 Ints7 Utp6 Ppat Tbl2 0.0 1.0

GSE13692 [8] GSE30160 [6]

GSE22371 [6] Scale ofaveragePearsoncorrelations GSE10556 [6] GSE21716 [28] GSE19073 [6] GSE6867 [6] GSE51608 [6] GSE8156 [6] 0.2 GSE53299 [6] GSE10071 [10] GSE46869 [6] GSE53077 [8] GSE25768 [6] GSE39897 [36] GSE43197 [27] GSE23002 [8] GSE43419 [20] 0.4 GSE11149 [8] GSE21996 [14] GSE39375 [10] GSE2557 [6] GSE52075 [9] GSE55607 [18] GSE3463 [12] GSE11973 [6] GSE54581 [21] 0.6 GSE43145 [12] GSE33156 [18] GSE35219 [6] GSE12986 [10] GSE13259 [10] GSE4718 [6] GSE31972 [6] GSE21944 [6] GSE23908 [31] 0.8 GSE33942 [12] GSE27972 [6] GSE23600 [10] GSE36437 [6] Score 1.19 1.19 1.19 1.19 1.21 1.23 1.23 1.24 1.25 1.25 1.25 1.28 1.28 1.28 1.29 1.31 1.31 1.31 1.32 1.33 1.33 1.33 1.34 1.36 1.36 1.36 1.37 1.38 1.39 1.39 1.39 1.40 1.40 1.41 1.42 1.43 1.43 1.44 1.44 1.44 1.45 1.47 1.47 1.48 1.48 1.48 1.48 1.48 1.49 1.50 1.0 Notes 1110004F10Rik 1110037F02Rik 3110001I22Rik D11Wsu47e Symbol Num ofCEMGenes:7.Predicted585.SelectedDatasets:15.Strength:0.0 CEM 1,Geneset"[G]Cdc73/Paf1complex",Page9 Tmem199 Rabgef1 Pom121 Fam57b Slc16a4 Fam98a Rbmxl1 Nup133 Ccdc77 Hnrnpk Tsen54 Alkbh1 Setdb2 Tcerg1 Pmpca Mrpl41 Zfp281 Med31 Nubp2 Ap1s3 Rps24 Elovl4 Magi3 Myef2 Gpam Ccar1 Rsrc2 Prkdc Ciao1 Cct6a Pms2 Birc2 Hagh Sdha Eif4b Rad1 Hus1 Bex1 Ppil1 Blzf1 Yrdc Rnf4 Tprn Rtcb Mtor Ltv1 0.0 1.0

GSE13692 [8] GSE30160 [6]

GSE22371 [6] Scale ofaveragePearsoncorrelations GSE10556 [6] GSE21716 [28] GSE19073 [6] GSE6867 [6] GSE51608 [6] GSE8156 [6] 0.2 GSE53299 [6] GSE10071 [10] GSE46869 [6] GSE53077 [8] GSE25768 [6] GSE39897 [36] GSE43197 [27] GSE23002 [8] GSE43419 [20] 0.4 GSE11149 [8] GSE21996 [14] GSE39375 [10] GSE2557 [6] GSE52075 [9] GSE55607 [18] GSE3463 [12] GSE11973 [6] GSE54581 [21] 0.6 GSE43145 [12] GSE33156 [18] GSE35219 [6] GSE12986 [10] GSE13259 [10] GSE4718 [6] GSE31972 [6] GSE21944 [6] GSE23908 [31] 0.8 GSE33942 [12] GSE27972 [6] GSE23600 [10] GSE36437 [6] Score 0.83 0.83 0.84 0.84 0.86 0.86 0.88 0.90 0.90 0.91 0.91 0.92 0.93 0.93 0.93 0.94 0.94 0.94 0.94 0.96 0.97 0.98 1.00 1.01 1.02 1.03 1.03 1.05 1.06 1.06 1.06 1.07 1.08 1.08 1.08 1.08 1.08 1.09 1.09 1.10 1.10 1.11 1.12 1.13 1.13 1.15 1.15 1.16 1.16 1.17 1.0 Notes Symbol Num ofCEMGenes:7.Predicted585.SelectedDatasets:15.Strength:0.0 CEM 1,Geneset"[G]Cdc73/Paf1complex",Page10 Tmem245 Slc25a17 Ccdc107 Timm44 Skiv2l2 Zc3hc1 Rmdn3 Psmb2 Dnajc9 Mrpl50 Gtf3c3 Heatr3 Polr1e Mak16 Ubxn7 Cdcp1 Abcb6 Rpp14 Afg3l1 Pdcd2 Usp14 Pmm1 Apex2 Qtrtd1 Fahd1 Rrp1b Oxsr1 Cenpt Ptpn2 Amd1 Sf3b4 Noc3l Emc4 Prpf6 Gnl3l Nop2 Coa3 Sos1 Pask Swt1 Dbr1 Parg Arv1 Erc1 Kat8 Xylb Nkrf Coil Eed Fh1 0.0 1.0

GSE13692 [8] GSE30160 [6]

GSE22371 [6] Scale ofaveragePearsoncorrelations GSE10556 [6] GSE21716 [28] GSE19073 [6] GSE6867 [6] GSE51608 [6] GSE8156 [6] 0.2 GSE53299 [6] GSE10071 [10] GSE46869 [6] GSE53077 [8] GSE25768 [6] GSE39897 [36] GSE43197 [27] GSE23002 [8] GSE43419 [20] 0.4 GSE11149 [8] GSE21996 [14] GSE39375 [10] GSE2557 [6] GSE52075 [9] GSE55607 [18] GSE3463 [12] GSE11973 [6] GSE54581 [21] 0.6 GSE43145 [12] GSE33156 [18] GSE35219 [6] GSE12986 [10] GSE13259 [10] GSE4718 [6] GSE31972 [6] GSE21944 [6] GSE23908 [31] 0.8 GSE33942 [12] GSE27972 [6] GSE23600 [10] GSE36437 [6] Score 0.57 0.57 0.57 0.58 0.58 0.58 0.59 0.60 0.61 0.61 0.61 0.62 0.62 0.62 0.63 0.64 0.65 0.65 0.66 0.66 0.68 0.68 0.68 0.68 0.68 0.69 0.69 0.69 0.70 0.71 0.73 0.74 0.74 0.74 0.74 0.75 0.75 0.76 0.76 0.78 0.79 0.79 0.79 0.80 0.81 0.81 0.81 0.82 0.82 0.83 1.0 Notes A130010J15Rik Symbol Num ofCEMGenes:7.Predicted585.SelectedDatasets:15.Strength:0.0 CEM 1,Geneset"[G]Cdc73/Paf1complex",Page11 Casp8ap2 Tmem11 Mmachc Ndufa12 Smim12 Swsap1 Prpf38a B3galt6 Ddrgk1 Chrac1 Rnmtl1 Supt16 Psmd6 Zfp458 Zfp623 Slc1a5 Gmcl1 Nup35 Wdr36 Spint2 Cops3 Usp10 Actl6a Tasp1 Lclat1 Tdrkh Asf1a Recql Zgpat Bcs1l Pwp2 Prpf4 Pop1 Cbx7 Cdv3 Ints9 Ints1 Toe1 Uros Yars Adsl Pigo Tars Zfp7 Brf1 Lzic Yy1 Dr1 Ipp 0.0 1.0

GSE13692 [8] GSE30160 [6]

GSE22371 [6] Scale ofaveragePearsoncorrelations GSE10556 [6] GSE21716 [28] GSE19073 [6] GSE6867 [6] GSE51608 [6] GSE8156 [6] 0.2 GSE53299 [6] GSE10071 [10] GSE46869 [6] GSE53077 [8] GSE25768 [6] GSE39897 [36] GSE43197 [27] GSE23002 [8] GSE43419 [20] 0.4 GSE11149 [8] GSE21996 [14] GSE39375 [10] GSE2557 [6] GSE52075 [9] GSE55607 [18] GSE3463 [12] GSE11973 [6] GSE54581 [21] 0.6 GSE43145 [12] GSE33156 [18] GSE35219 [6] GSE12986 [10] GSE13259 [10] GSE4718 [6] GSE31972 [6] GSE21944 [6] GSE23908 [31] 0.8 GSE33942 [12] GSE27972 [6] GSE23600 [10] GSE36437 [6] Score 0.27 0.27 0.28 0.29 0.29 0.29 0.30 0.30 0.30 0.31 0.31 0.32 0.32 0.33 0.33 0.33 0.34 0.34 0.35 0.36 0.36 0.36 0.36 0.37 0.37 0.39 0.39 0.40 0.41 0.41 0.41 0.42 0.42 0.42 0.44 0.44 0.44 0.45 0.45 0.46 0.47 0.48 0.50 0.54 0.54 0.55 0.55 0.55 0.56 0.56 1.0 Notes Symbol Num ofCEMGenes:7.Predicted585.SelectedDatasets:15.Strength:0.0 CEM 1,Geneset"[G]Cdc73/Paf1complex",Page12 Sec61a2 Snrnp40 Hdgfrp2 Slc30a9 Trp53rk Prpf40a Nup107 Uqcrc1 Rbm14 Psmd9 Pgam5 Psmc1 Mrpl22 Zfp446 Luc7l2 Mocs3 Wdr33 Cand1 Ddx31 Cep78 Rccd1 Hspa4 Fnbp4 Thoc6 Thoc5 Fkbp3 Prmt5 Kctd5 Ccbl2 Puf60 Cse1l Taf1c Tyw3 Srsf1 Frat2 Coa6 Stam Ftsj3 Mib1 Ssr2 Cct2 Pigl 0.0 1.0

GSE13692 [8] GSE30160 [6]

GSE22371 [6] Scale ofaveragePearsoncorrelations GSE10556 [6] GSE21716 [28] GSE19073 [6] GSE6867 [6] GSE51608 [6] GSE8156 [6] 0.2 GSE53299 [6] GSE10071 [10] GSE46869 [6] GSE53077 [8] GSE25768 [6] GSE39897 [36] GSE43197 [27] GSE23002 [8] GSE43419 [20] 0.4 GSE11149 [8] GSE21996 [14] GSE39375 [10] GSE2557 [6] GSE52075 [9] GSE55607 [18] GSE3463 [12] GSE11973 [6] GSE54581 [21] 0.6 GSE43145 [12] GSE33156 [18] GSE35219 [6] GSE12986 [10] GSE13259 [10] GSE4718 [6] GSE31972 [6] GSE21944 [6] GSE23908 [31] 0.8 GSE33942 [12] GSE27972 [6] GSE23600 [10] GSE36437 [6] Score 0.02 0.04 0.04 0.04 0.04 0.04 0.07 0.08 0.08 0.08 0.08 0.09 0.09 0.09 0.09 0.09 0.09 0.10 0.10 0.11 0.11 0.12 0.13 0.13 0.14 0.14 0.14 0.15 0.16 0.16 0.16 0.17 0.18 0.19 0.20 0.20 0.23 0.24 0.25 0.25 0.25 0.26 1.0 Notes GEO Series "GSE13692" 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=GSE13692 Status: Public on Feb 06 2009 Title: Expression profiling of MLL-AF10 myeloid leukemia cellular subsets Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 19200802 Summary & Design: Summary: Leukemia cells from mice with MLL-AF10 AML were fractionated into separate sub-populations on the basis of c-kit expression, which correlates with MLL LSC frequency (Somervaille and Cleary, 2006). The sorted AML sub-populations exhibited substantial differences in their frequencies of AML CFCs/LSCs (mean 14-fold) and morphologic features, consistent with a leukemia cell hierarchy with maturation through to terminally differentiated neutrophils.

Overall design: Leukemic splenocytes from four mice with MLL-AF10 AML were sub-fractionated in to c-kit high and c-kit negative sub-populations by FACS.

Background corr dist: KL-Divergence = 0.0464, L1-Distance = 0.0346, L2-Distance = 0.0017, Normal std = 0.6099

0.681 Kernel fit Pairwise Correlations Normal fit

Density 0.341

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

MLL-AF10MLL-AF10 LEUKEMICMLL-AF10 LEUKEMIC MLL-AF10SPLENOCYTES_CD117NEG_948 LEUKEMIC MLL-AF10SPLENOCYTES_CD117POS_948 LEUKEMIC MLL-AF10SPLENOCYTES_CD117NEG_951 LEUKEMIC MLL-AF10SPLENOCYTES_CD117POS_951 LEUKEMIC MLL-AF10SPLENOCYTES_CD117NEG_952 LEUKEMIC(0.102863) SPLENOCYTES_CD117POS_952 LEUKEMIC(0.101158) SPLENOCYTES_CD117NEG_953 (0.105693) SPLENOCYTES_CD117POS_953 (0.139052)[ min(0.0857088) (0.158415) ] (0.136271) [(0.170839) medium ] [ max ] CEM 1 Ctr9 197.7 254.3 369.4 P ( S | Z, I ) = 1.00 Rtf1 1109.4 1875.0 2823.2 Mean Corr = 0.68629 Paf1 600.7 808.1 1261.5 Cdc73 1681.7 2428.1 2568.8 Leo1 178.6 308.0 373.3 Wdr61 68.2 105.4 114.5 Pex2 135.9 166.4 200.2 Ddx42 589.6 776.6 1180.3 Morc2a 539.3 683.4 838.3 Taf1a 265.6 374.1 441.4 Aggf1 1790.6 2138.6 2461.3 Taf1b 231.3 333.7 547.8 CEM 1 + Pak1ip1 3724.4 4263.8 4433.0 Top 10 Genes Actr6 1176.8 1627.3 2215.7 Jade3 100.5 220.2 316.9 Cbfa2t2 427.0 522.2 696.9 Clpx 216.5 292.1 545.6

Null module GEO Series "GSE30160" 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=GSE30160 Status: Public on Jul 05 2011 Title: The RANK IVVY Motif-regulated Genes in Osteoclastogenesis Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: By carrying out a systematic structure/function study of the RANK cytoplasmic domain, we previously identified a specific 4-a.a. RANK motif (IVVY535-538) which plays a critical role in osteoclastogenesis by mediating commitment of macrophages to the osteoclast lineage. We have recently validated the role of this IVVY motif in osteoclastogenesis in vivo by generating knockin (KI) mice bearing inactivating mutations in the RANK IVVY motif. This microarray experiment was performed to determine whether the IVVY motif is involved in regulating gene expression in osteoclastogenesis.

We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

Overall design: Bone marrow macrophages isolated from wild-type (WT) or knockin (KI) mice were plated in 60-mm tissue culture dishes and treated with M-CSF (44ng/ml) and RANKL (100ng/ml) for 24 hours. Each genotype has three triplicates. Total RNA was isolated for microarray analysis using mouse chips (type 430.2.0) at the Microarray Shared Facility at the University of Alabama at Birmingham.

Background corr dist: KL-Divergence = 0.0193, L1-Distance = 0.0421, L2-Distance = 0.0019, Normal std = 0.8277

0.522 Kernel fit Pairwise Correlations Normal fit

Density 0.261

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

wild typewild replicate typewild replicate 1 type (0.428994)knockin replicate 2 (0.0509886)knockin replicate 3 (0.161261)knock replicate 1 (0.12514) in replicate 2 (0.124692) 3 (0.108924)[ min ] [ medium ] [ max ] CEM 1 Ctr9 228.8 269.6 301.8 P ( S | Z, I ) = 1.00 Rtf1 851.7 873.2 960.6 Mean Corr = 0.68600 Paf1 510.4 536.0 700.3 Cdc73 845.8 1039.4 1196.1 Leo1 235.6 427.7 511.0 Wdr61 83.5 95.3 109.3 Pex2 133.6 141.1 154.9 Ddx42 662.9 758.5 874.5 Morc2a 593.2 708.5 773.9 Taf1a 116.5 158.8 168.2 Aggf1 1984.8 2263.3 2363.9 Taf1b 562.9 645.9 691.5 CEM 1 + Pak1ip1 1515.0 1758.5 2135.4 Top 10 Genes Actr6 534.0 647.1 697.6 Jade3 101.7 175.7 189.2 Cbfa2t2 474.8 532.4 558.9 Clpx 889.2 1293.2 1459.9

Null module GEO Series "GSE26299" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 108 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

Details of this dataset are not shown due to large number of samples and the page size limit. Find details in http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26299

Background corr dist: KL-Divergence = 0.0440, L1-Distance = 0.0244, L2-Distance = 0.0009, Normal std = 0.5775 GEO Series "GSE11222" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 42 -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=GSE11222 Status: Public on Apr 23 2008 Title: Placental and decidual timecourse samples normalized and modeled with an undissected e17 sample Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 18340042 Summary & Design: Summary: We used full genome microarrays to profile the full lifetime of the mouse placenta from embryonic day 8.5 (e8.5), at the time of chorioallantoic fusion, until postnatal day 0 (P0). For these samples, at each stage the fetal placenta and maternal decidual tissues were dissected and profiled separately (See series 1).

For this experiment (Series 2), placental and decidual timecourse samples were normalized and modeled with two undissected (including placental and decidual tissue) e17 placentas to allow for scaling of values for comparison to the undissected placenta samples used in the publicly available mouse GeneAtlas dataset

Keywords: time course

Overall design: Mouse placentas were obtained from timed pregnant female mice at each timepoint, and fetal tissues were used to confirm embryo staging. For all dissected samples, fetal placenta and maternal decidual tissues were dissected and pooled separately for each litter prior to RNA extraction and hybridization on Affymetrix microarrays.

Background corr dist: KL-Divergence = 0.1507, L1-Distance = 0.0356, L2-Distance = 0.0027, Normal std = 0.3773

1.057 Kernel fit Pairwise Correlations Normal fit

Density 0.529

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

PlacentaPlacenta e8.5, biologicalPlacenta e9.0, biologicalPlacenta e9.0, rep3 biologicalPlacenta(Series e9.0, rep1 biologicalPlacenta(Series2) e10.5, rep2(0.0143128) Placenta(Series 2)biological e10.5, rep3(0.018859) Placenta(Series 2)biological e10.5, (0.0131717) rep1 Placenta 2) biological (Seriese12.0, (0.00982354) rep2Placenta biological (Series2)e12.0, rep3(0.0184346)Placenta biological (Series2)e12.0, rep1(0.00774491)Placenta biological (Series2)e13.5, rep2(0.0103444)Placenta biological (Series2)e13.5, rep3(0.0282726)Placenta biological (Series2)e15.0, rep1(0.0104731)Placenta biological (Series2)e15.0, rep2(0.0170812)Placenta biological (Series2)e15.0, rep1(0.00874222)Placenta biological (Series2)e17.0, rep2(0.00736733)Placenta biological (Series2)e17.0, rep3(0.0329819)Placenta biological (Series2)e17.0, rep1(0.0349135)Placenta biological (Series2)e19.0, rep2(0.0287027)Placenta biological (Series2)e19.0, rep3(0.0610052)Placenta biological (Series2)P0, rep1(0.046476) biologicalDecidua (Series2)P0, rep2(0.0684943) biologicalDecidua rep1e8.5,(Series2) (0.0609796) (SeriesbiologicalDecidua rep2e8.5,2) (0.0291206) (Series2)biologicalDecidua (0.0894753)e8.5, rep1, 2)biological Deciduatechnical (0.0232778)e8.5, rep2, biological Deciduatechnical e9.0, rep1,rep1 biological Decidua(Seriestechnical e9.0, rep2,rep1 biological Decidua(Seriestechnical2) e10.5, rep1rep2(0.014225) (SeriesDecidua(Series2)biological e10.5, rep2rep2(0.0182816) (Series2)Decidua(Series2)biological e12.0, (0.0141386) (0.0185251)rep1 2)Decidua 2)biological (Seriese12.0, (0.013135) (0.0164357)rep2 Decidua biological (Series2)e15.0, rep1(0.014347) Decidua biological (Series2)e15.0, rep2(0.0189415) Decidua biological (Series2)e17.0, rep1(0.0176495) Decidua biological (Series2)e17.0, rep2(0.0204095) Decidua biological (Series2)e19.0, rep1(0.0175975) Decidua biological (Series2)e19.0, rep2(0.0225007) Decidua biological (Series2)P0, rep1(0.0148527) biologicalPlacenta (Series2)P0, rep2(0.0203764) biologicalPlacenta rep1(Series2) and (0.0184985) (SeriesDecidua rep22) and (0.0158797) (Series2)Decidua e17.0, (0.00922801) 2) biological e17.0, (0.014197) biological[ repmin 1 (Series rep ] 2 (Series2) (0.0115574) 2) (0.0491694)[ medium ] [ max ] CEM 1 Ctr9 221.9 625.0 2208.5 P ( S | Z, I ) = 1.00 Rtf1 373.9 547.3 1905.3 Mean Corr = 0.52355 Paf1 267.8 413.6 731.7 Cdc73 537.8 1841.0 4701.3 Leo1 192.0 485.8 878.2 Wdr61 145.1 216.6 391.1 Pex2 227.6 307.5 552.5 Ddx42 342.5 534.7 921.6 Morc2a 569.4 869.5 1329.8 Taf1a 192.0 251.1 410.5 Aggf1 735.9 1039.1 1551.2 Taf1b 234.1 348.8 780.2 CEM 1 + Pak1ip1 884.8 2090.1 4825.0 Top 10 Genes Actr6 183.7 400.7 922.2 Jade3 184.8 1417.9 3681.3 Cbfa2t2 417.9 547.8 1128.6 Clpx 246.3 646.9 1053.3

Null module GEO Series "GSE9247" 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=GSE9247 Status: Public on Oct 06 2007 Title: Effect of histone deacetylase inhibitors on osteoblast gene expression Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 17925016 Summary & Design: Summary: Background:

Osteoblast differentiation requires the coordinated stepwise expression of multiple genes. Histone deacetylase inhibitors (HDIs) accelerate the osteoblast differentiation process by blocking the activity of histone deacetylases (HDACs), which alter gene expression by modifying chromatin structure. We previously demonstrated that HDIs and HDAC3 shRNAs accelerate matrix mineralization and the expression of osteoblast maturation genes (e.g. alkaline phosphatase, osteocalcin). Identifying other genes that are differentially regulated by HDIs might identify new pathways that contribute to osteoblast differentiation.

Results:

To identify other osteoblast genes that are altered early by HDIs, we incubated MC3T3-E1 preosteoblasts with HDIs (trichostatin A, MS-275, or valproic acid) for 18 hours in osteogenic conditions. The promotion of osteoblast differentiation by HDIs in this experiment was confirmed by osteogenic assays. Gene expression profiles relative to vehicle-treated cells were assessed by microarray analysis with Affymetrix GeneChip 430 2.0 arrays. The regulation of several genes by HDIs in MC3T3-E1 cells and primary osteoblasts was verified by quantitative real-time PCR. Nine genes were differentially regulated by at least two-fold after exposure to each of the three HDIs and six were verified by PCR in osteoblasts. Four of the verified genes (solute carrier family 9 isoform 3 regulator 1 (Slc9a3r1), sorbitol dehydrogenase 1, a kinase anchor protein, and glutathione S-transferase alpha 4) were induced. Two genes (proteasome subunit, beta type 10 and adaptor-related protein complex AP-4 sigma 1) were suppressed. We also identified eight growth factors and growth factor receptor genes that are significantly altered by each of the HDIs, including Frizzled related proteins 1 and 4, which modulate the Wnt signaling pathway.

Conclusions: This study identifies osteoblast genes that are regulated early by HDIs and indicates pathways that might promote osteoblast maturation following HDI exposure. One gene whose upregulation following HDI treatment is consistent with this notion is Slc9a3r1. Also known as NHERF1, Slc9a3r1 is required for optimal bone density. Similarly, the regulation of Wnt receptor genes indicates that this crucial pathway in osteoblast development is also affected by HDIs. These data support the hypothesis that HDIs regulate the expression of genes that promote osteoblast differentiation and maturation.

Keywords: gene expression

Overall design: To identify other osteoblast genes that are altered early by HDIs, we incubated MC3T3-E1 preosteoblasts with HDIs (trichostatin A, MS-275, or valproic acid) or the vehicle control (DMSO) for 18 hours in osteogenic conditions. Gene expression profiles relative to vehicle-treated cells were assessed in triplicate (in some cases quadruplicate) samples by microarray analysis with Affymetrix GeneChip 430 2.0 arrays.

Background corr dist: KL-Divergence = 0.1049, L1-Distance = 0.0636, L2-Distance = 0.0067, Normal std = 0.4730

0.936 Kernel fit Pairwise Correlations Normal fit

Density 0.468

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

DMSO TreatedDMSO Treated DMSOControl Treated DMSOControl 1 (0.0364245) Treated MS-275Control 2 (0.0402046) MS-275Control Treated3 (0.0661447) MS-275 Treated 4Rep1 (0.0357947) (0.0128703) MS-275Treated Rep2 (0.060923) TSATreated Rep3 Treated (0.0210495)TSA Rep4 Treated Rep (0.0255785)TSA 1 (0.180613)Treated RepVPA 2 (0.271688)Treated RepVPA 3 (0.12861)Treated RepVPA 1 (0.0175432)Treated RepVPA 2 (0.0397214)Treated Rep 3 (0.0194261) Rep 4 (0.0434081)[ min ] [ medium ] [ max ] CEM 1 Ctr9 357.8 571.2 1028.7 P ( S | Z, I ) = 1.00 Rtf1 911.1 1017.8 1562.4 Mean Corr = 0.50301 Paf1 409.0 477.1 873.1 Cdc73 948.1 1097.3 1387.3 Leo1 377.2 471.0 565.5 Wdr61 72.7 82.6 99.3 Pex2 215.8 278.6 438.4 Ddx42 797.8 952.9 1146.1 Morc2a 881.0 1046.7 1513.1 Taf1a 189.7 233.1 266.5 Aggf1 666.8 810.2 1138.1 Taf1b 300.6 335.2 476.1 CEM 1 + Pak1ip1 1099.0 1268.2 1883.8 Top 10 Genes Actr6 369.1 506.2 590.0 Jade3 100.3 130.1 174.3 Cbfa2t2 857.0 962.7 1218.6 Clpx 578.3 636.8 985.6

Null module GEO Series "GSE11220" 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=GSE11220 Status: Public on Apr 23 2008 Title: Timecourse of developing mouse placenta, with placental and decidual tissues profiled separately Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 18340042 Summary & Design: Summary: We used full genome microarrays to profile the full lifetime of the mouse placenta from embryonic day 8.5 (e8.5), at the time of chorioallantoic fusion, until postnatal day 0 (P0).

At each stage, the fetal placenta and maternal decidual tissues were dissected and profiled separately

Keywords: time course

Overall design: Mouse placentas were obtained from timed pregnant female mice at each timepoint, and fetal tissues were used to confirm embryo staging. Fetal placenta and maternal decidual tissues were dissected and pooled separately for each litter prior to RNA extraction and hybridization on Affymetrix microarrays.

Background corr dist: KL-Divergence = 0.1391, L1-Distance = 0.0310, L2-Distance = 0.0019, Normal std = 0.3911

1.020 Kernel fit Pairwise Correlations Normal fit

Density 0.510

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

PlacentaPlacenta e8.5, biologicalPlacenta e8.5, biologicalPlacenta e8.5, rep1, biologicalPlacenta technical e8.5, rep2, biologicalPlacenta technical e8.5, rep1,rep1 biologicalPlacenta (0.010022)technical e9.0, rep2,rep1 biologicalPlacenta (0.0222997)technical e9.0, rep3rep2 biologicalPlacenta (0.0106527)(0.0109779) e9.0, rep1rep2 biologicalPlacenta (0.0148342)(0.0142907) e10.5, rep2 Placenta(0.0101568) biological e10.5, rep3 Placenta(0.00795818) biological e10.5, rep1Placenta biological (0.0169451)e12.0, rep2Placenta biological (0.00559842)e12.0, rep3Placenta biological (0.00789533)e12.0, rep1Placenta biological (0.0254688)e13.5, rep2Placenta biological (0.00786731)e13.5, rep3Placenta biological (0.0134475)e15.0, rep1Placenta biological (0.00731598)e15.0, rep2Placenta biological (0.0110662)e15.0, rep1Placenta biological (0.0364885)e17.0, rep2Placenta biological (0.0328672)e17.0, rep3Placenta biological (0.0290523)e17.0, rep1Placenta biological (0.0712182)e19.0, rep2Placenta biological (0.0473389)e19.0, rep3Placenta biological (0.0733252)P0, rep1 biologicalDecidua (0.0654637)P0, rep2 biologicalDecidua rep1e8.5,(0.0298783) (0.0896344)biologicalDecidua rep2e8.5, (0.0286169)biologicalDecidua e8.5, rep1, biological Deciduatechnical e8.5, rep2, biological Deciduatechnical e9.0, rep1,rep1 biological Decidua(0.0135969)technical e9.0, rep2,rep1 biological Decidua(0.017767)technical e10.5, rep1rep2 (0.0141126)Decidua(0.0170495)biological e10.5, rep2rep2 (0.0141472)Decidua(0.0159683)biological e12.0, rep1 Decidua biological (0.0144507)e12.0, rep2 Decidua biological (0.0195689)e15.0, rep1 Decidua biological (0.0168266)e15.0, rep2 Decidua biological (0.019901)e17.0, rep1 Decidua biological (0.0190059)e17.0, rep2 Decidua biological (0.0222809)e19.0, rep1 Decidua biological (0.0161587)e19.0, rep2 Decidua biological (0.0207305)P0, rep1 biological (0.0191913)P0, rep2 biological rep1(0.015615) (0.00909369) rep2 (0.0138549)[ min ] [ medium ] [ max ] CEM 1 Ctr9 221.0 615.1 2202.9 P ( S | Z, I ) = 1.00 Rtf1 373.3 557.2 1900.6 Mean Corr = 0.51810 Paf1 267.3 415.5 729.6 Cdc73 535.2 2050.4 4698.2 Leo1 191.0 537.6 875.3 Wdr61 144.7 211.5 386.9 Pex2 220.4 301.1 472.9 Ddx42 341.4 583.5 919.2 Morc2a 566.7 932.8 1327.2 Taf1a 191.6 248.5 409.1 Aggf1 735.0 1068.5 1547.8 Taf1b 233.4 376.3 779.0 CEM 1 + Pak1ip1 880.4 2319.5 4812.7 Top 10 Genes Actr6 183.4 402.2 897.9 Jade3 184.2 1503.8 3671.3 Cbfa2t2 415.9 543.1 1126.4 Clpx 245.6 645.5 1051.8

Null module GEO Series "GSE16679" 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=GSE16679 Status: Public on Aug 01 2010 Title: Plag1 overexpression cooperates with Evi1 overexpression and Gata1s mutation in leading to M7 leukemia Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 20679399 Summary & Design: Summary: The goal of this study is to develop a Plag1 signature and determine how its overexpression contributes to leukemogenesis.

To study this, we transduced an immortalized (but not transformed) cell line (derived from Gata1s mutant fetal liver progenitor through insertional mutagenesis) by Plag1-expressing retrovirus. This turned a non-transformed cell line to a leukemogenic cell line. To study whether Plag1 overexpression led to deregulation of signaling pathways that may contribute to leukemic transformation, we generated microarray gene expression profiles of this cell line transduced with either Plag1 or the empty vector.

Overall design: We generated gene expression profiles by microarray from stable cell lines transduced with either the empty vector or the Plag1-expressing vector.

Background corr dist: KL-Divergence = 0.0435, L1-Distance = 0.0264, L2-Distance = 0.0008, Normal std = 0.6089

0.677 Kernel fit Pairwise Correlations Normal fit

Density 0.338

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

cell line2_Plag1_KT_subline1_Acell line2_Plag1_KT_subline2_Acell line2_Vector_KT_subline1_Acell line2_Vector_KT_subline2_Acell (0.127822) line2_Plag1_KT_subline1_Bcell (0.144154) line2_Plag1_KT_subline2_Bcell (0.128557)line2_Vector_KT_subline1_Bcell (0.125184)line2_Vector_KT_subline2_B (0.203724) (0.141194) (0.0428423)[ min (0.0865238) ] [ medium ] [ max ] CEM 1 Ctr9 701.0 1040.3 1425.2 P ( S | Z, I ) = 1.00 Rtf1 595.5 966.7 1067.1 Mean Corr = 0.40287 Paf1 129.6 233.4 309.0 Cdc73 631.2 1068.0 1215.7 Leo1 156.8 333.0 379.2 Wdr61 336.0 480.2 575.4 Pex2 267.5 306.7 329.7 Ddx42 823.2 1073.1 1127.0 Morc2a 713.0 1068.1 1139.1 Taf1a 94.4 131.2 134.6 Aggf1 658.9 1034.1 1125.2 Taf1b 484.5 681.4 742.6 CEM 1 + Pak1ip1 1479.7 2317.5 3294.3 Top 10 Genes Actr6 265.3 355.3 400.2 Jade3 130.5 151.9 364.9 Cbfa2t2 607.0 679.6 713.7 Clpx 440.5 537.0 651.2

Null module GEO Series "GSE17886" 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=GSE17886 Status: Public on Mar 22 2010 Title: Gene expression data of BBB and BCB two-cell embryos Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 20107036 Summary & Design: Summary: We constructed one-cell stage embryos by maternal pronuclear (mPN) transfer having B6 ooplasm, B6 paternal PN (pPN), and either B6 or C3H mPN (BBB and BCB, respectively). We collected embryos of each type that were either treated (BBB+a, BCB+a) or untreated with Î±-amanitin (BBB, BCB) at the two-cell stage for microarray analysis.

Comparison of the transcriptomes of these different kinds of embryos revealed genes for which expression differs according to maternal PN strain of origin, and the Î±-amanitin data revealed which of these differences is due to gene transcription, as opposed to any transcription-independent differences attributable to ooplasm-derived maternal mRNA pools.

Overall design: There are 4 replicates for each kind/treatment two-cell embryos (BBB, BCB, BBB+a, BCB+a).

Background corr dist: KL-Divergence = 0.0287, L1-Distance = 0.0723, L2-Distance = 0.0067, Normal std = 0.7860

0.588 Kernel fit Pairwise Correlations Normal fit

Density 0.294

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

BBB two-cellBBB two-cell embryos,BBB two-cell embryos,BBB Sample1 two-cell embryos,BCB Sample2 (0.109527) two-cell embryos,BCB Sample3 (0.0703853) two-cell embryos,BCB Sample4 (0.0383165) two-cell embryos,BCB Sample1 (0.0603694) two-cell embryos,Î±-amantin-treated Sample2 (0.0820533) embryos,Î±-amantin-treated Sample3 (0.0335848)Î±-amantin-treated Sample4 (0.0961506) BBBÎ±-amantin-treated two-cell (0.056023) BBBÎ±-amantin-treated two-cell embryos, BBBÎ±-amantin-treated two-cell embryos, BBB Sample1Î±-amantin-treated two-cell embryos, BCB Sample2 (0.0538929)Î±-amantin-treated two-cell embryos, BCB Sample3 (0.0545499) two-cell embryos, BCB Sample4 (0.0637775) two-cell embryos, BCB Sample1 (0.0794842) two-cell embryos, Sample2 (0.0369335)[ embryos,min Sample3 (0.0606792) ] Sample4 (0.0324572) (0.0718161)[ medium ] [ max ] CEM 1 Ctr9 350.1 760.4 1291.6 P ( S | Z, I ) = 0.99 Rtf1 3.4 233.1 397.1 Mean Corr = 0.65881 Paf1 46.1 1412.8 2024.8 Cdc73 842.3 2334.5 3251.6 Leo1 14.5 661.6 1210.5 Wdr61 3.4 18.5 42.2 Pex2 64.2 117.0 183.2 Ddx42 115.0 424.1 565.1 Morc2a 851.5 1956.9 2344.2 Taf1a 1665.7 3739.0 6345.0 Aggf1 981.0 3080.4 4035.1 Taf1b 38.3 189.5 355.2 CEM 1 + Pak1ip1 534.9 2101.4 2673.3 Top 10 Genes Actr6 66.6 1424.8 2211.7 Jade3 5.0 448.8 773.0 Cbfa2t2 406.4 1266.4 2312.1 Clpx 196.4 3076.8 4417.5

Null module GEO Series "GSE13235" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 9 -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=GSE13235 Status: Public on Oct 17 2008 Title: Gene expression profile of mouse embryonic stem cells (D3-pOCT-mESC) grown in low concentrations of nitric oxide Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: In order to identify the genes regulated in mouse embryonic stem cells (mESC) by the effect of low concentrations of nitric oxide (NO), we analysed the transcriptome of cells treated with NO and compared it to those of cells cultured in the absence of leukemia inhibitory factor (LIF), and in the presence of LIF. We used the cell line D3-pOct4, which carries the enhanced Green Fluorescence Protein gene (eGFP) under the control of the Oct-4 promotor. This line is continuously maintained in the undifferentiated state in the presence of LIF, in comparison with the wild type line .

Overall design: D3-pOct4 cells cultured in the presence of 1000 U/ml of LIF, in the absence of LIF, and in the absence of LIF supplemented with 2uM of diethylenetriamine nitric oxide adduct (DETA)/NO (Sigma) used as donor of nitric oxide. Treatments were maintained for seven days. RNA was extracted and analyzed by Bioanalyzer of Agilent. The cDNA microarray chip used was Mouse Genome 430_2.0 (Affymetrix) and the data were analyzed with GeneChip Operating System v1.4.0.036 using global scaling as the normalization method.

Background corr dist: KL-Divergence = 0.0684, L1-Distance = 0.0302, L2-Distance = 0.0016, Normal std = 0.5120

0.779 Kernel fit Pairwise Correlations Normal fit

Density 0.390

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

D3-pOct4D3-pOct4 (passD3-pOct4 31) (pass withD3-pOct4 31) LIF(pass without (0.190417)D3-pOct4 31) (pass without LIFD3-pOct4 33)(0.23057) (pass with LIFD3-pOct4 33) plus LIF(pass without (0.0653722) NOD3-pOct4 33) (pass(0.192604) without LIFD3-pOct4 34)(0.0466193) (pass with LIF 34) plus LIF(pass without (0.0208733) NO 34) (0.0423835) without LIF (0.0554894) LIF[ plusmin NO (0.155671) ] [ medium ] [ max ] CEM 1 Ctr9 382.3 512.0 703.2 P ( S | Z, I ) = 1.00 Rtf1 254.8 475.6 1153.1 Mean Corr = 0.27548 Paf1 163.2 521.4 635.8 Cdc73 1040.7 1958.5 3462.4 Leo1 334.7 986.3 1747.4 Wdr61 40.7 67.2 80.7 Pex2 71.3 162.2 410.5 Ddx42 308.0 697.6 906.4 Morc2a 997.0 1356.1 1747.2 Taf1a 55.1 173.6 413.1 Aggf1 427.0 1983.3 3635.1 Taf1b 194.1 425.8 706.4 CEM 1 + Pak1ip1 2124.3 3548.3 5092.4 Top 10 Genes Actr6 413.5 838.8 1607.3 Jade3 347.4 1129.7 1542.2 Cbfa2t2 1237.2 1773.1 2888.1 Clpx 250.1 600.2 1439.8

Null module GEO Series "GSE3296" 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=GSE3296 Status: Public on Oct 24 2005 Title: Gene expression in MEFs in response to treatment with dipyridyl and trichostatin A Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 16237459 Summary & Design: Summary: The CH1 protein interaction domain of the transcriptional coactivators p300 and CBP is thought to interact with HIF-1alpha and this interaction is thought to be critical to the expression of HIF-1alpha target genes in response to hypoxia. Trichostatin A (TSA), an inhibitor of histone deacetylases, has been reported to repress the expression of HIF-1alpha target genes. To test the requirement of the CH1 domain and TSA for gene expression in response to dipyridyl (a hypoxia mimetic), primary mouse embryonic fibroblasts (MEFs) were generated from C57Bl/6x129/Sv F2 e14.5 embryos that contain a deletion in the CH1 domain of three of four alleles of CBP and p300. The remaining allele of p300 or CBP was a conditional knock out allele. Control MEFs with only a single conditional knockout allele of p300 or CBP were also generated. At passage 3 MEFs were infected with Cre Adenovirus and grown until they had expanded at least 100 fold. Subconfluent MEFs were treated with ethanol vehicle or 100ng/ml TSA with 5% carbon dioxide at 37 C in a humid chamber for 30 min., followed by ethanol vehicle or 100 umdipyridyl (DP) for an additional 3hrs. Immediately after treatment, cells were lysed in Trizol for RNA extraction.

Keywords: genetic modification, dose response

Overall design: 16 samples; 4 genotypes [CBP+/flox (flox1), p300 +/flox (flox2), CBP CH1/flox;p300 CH1/CH1 (triCH1flox1),CBP CH1/CH1;p300 CH1/flox (triCH1flox2)] , 4 treatments (EtOH, TSA, dipyridyl (DP) and TSA+DP).

Background corr dist: KL-Divergence = 0.1940, L1-Distance = 0.0378, L2-Distance = 0.0029, Normal std = 0.3381

1.180 Kernel fit Pairwise Correlations Normal fit

Density 0.590

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

flox1_EtOHtriCH1flox1_EtOH (0.114199)flox2_2_EtOHtriCH1flox2_2_EtOH (0.0454722) (0.0421503)flox1_TSAtriCH1flox1_TSA (0.0542312) (0.061747)flox2_2_TSAtriCH1flox2_2_TSA (0.0419464) (0.0575293)flox1_DPtriCH1flox1_DP (0.0292854) (0.100697)flox2_2_DPtriCH1flox2_2_DP (0.0918454) (0.0472727)flox1_TSA_DPtriCH1flox1_TSA_DP (0.0460183) flox2_2_TSA_DP(0.0497573)triCH1flox2_2_TSA_DP (0.10078) (0.0513309) (0.0657373)[ min ] [ medium ] [ max ] CEM 1 Ctr9 227.3 783.5 1506.0 P ( S | Z, I ) = 1.00 Rtf1 432.0 882.3 1283.0 Mean Corr = 0.11723 Paf1 437.7 1236.6 1850.8 Cdc73 936.5 1404.3 1839.0 Leo1 651.9 840.6 1048.4 Wdr61 53.7 133.3 266.3 Pex2 96.7 185.2 282.6 Ddx42 472.3 746.4 854.3 Morc2a 383.1 909.7 1406.5 Taf1a 142.8 261.2 506.8 Aggf1 855.1 1374.0 1770.4 Taf1b 193.2 283.3 403.3 CEM 1 + Pak1ip1 2452.1 3235.6 3804.5 Top 10 Genes Actr6 308.1 861.3 1226.9 Jade3 177.2 330.6 532.6 Cbfa2t2 744.6 1027.0 1309.5 Clpx 426.9 721.6 1362.1

Null module GEO Series "GSE39458" 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=GSE39458 Status: Public on Dec 31 2012 Title: Differential gene expression of Kit+Sca1+Lin- (KSL) cells from arthritic versus control mice Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: The involvement of mature hematopoietic cells in disease pathogenesis is well recognized. However it is not clear how if and how primitive progenitors might contribute to inflammatory disease processes.

This microarray experiment is used together with data from functional assays to determine how primitive progenitors are altered in a mouse model of autoimmune arthritis and how this in turn might contribute to the disease process.

Overall design: All the mice used in this study were C57BL/6 background strain. G7 mice are congenic with C57BL/6 but with MHC II I-Ab replaced with MHC II I-Ag7.

Background corr dist: KL-Divergence = 0.0145, L1-Distance = 0.0305, L2-Distance = 0.0010, Normal std = 0.8466

0.495 Kernel fit Pairwise Correlations Normal fit

Density 0.247

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_B6xG7_sortedKSL cells_KRN_sortedKSL cells_KRNxG7_sortedLin+_B6xG7_sorted (0.112582)Lin+_KRN_sorted (0.122812)Lin+_KRNxG7_sorted (0.20509)(0.167257) (0.190611) (0.201648)[ min ] [ medium ] [ max ] CEM 1 Ctr9 273.1 775.9 895.0 P ( S | Z, I ) = 0.73 Rtf1 2032.5 3001.0 3555.3 Mean Corr = 0.49561 Paf1 493.0 941.8 1275.0 Cdc73 1716.6 1890.0 1935.6 Leo1 182.0 279.7 302.2 Wdr61 56.3 130.6 151.3 Pex2 73.0 90.4 119.5 Ddx42 518.0 884.0 1259.0 Morc2a 609.8 786.8 920.8 Taf1a 291.3 569.7 706.4 Aggf1 1228.4 1420.7 1607.6 Taf1b 218.0 403.1 437.4 CEM 1 + Pak1ip1 3060.4 3672.5 3933.6 Top 10 Genes Actr6 818.2 967.1 1038.3 Jade3 68.2 324.9 432.7 Cbfa2t2 477.5 983.6 1131.1 Clpx 202.9 391.5 479.7

Null module GEO Series "GSE21033" 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=GSE21033 Status: Public on Aug 26 2010 Title: Timecourse analysis of gene expression by murine bone marrow-generated dendritic cells following treatment with Poly I:C Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 20682054 Summary & Design: Summary: BACKGROUND: Dendritic cells (DC) play a central role in primary immune responses and become potent stimulators of the adaptive immune response after undergoing the critical process of maturation. Understanding the dynamics of DC maturation would provide key insights into this important process. Time course microarray experiments can provide unique insights into DC maturation dynamics. Replicate experiments are necessary to address the issues of experimental and biological variability. Statistical methods and averaging are often used to identify significant signals. Here a novel strategy for filtering of replicate time course microarray data, which identifies consistent signals between the replicates, is presented and applied to a DC time course microarray experiment.

RESULTS: The temporal dynamics of DC maturation were studied by stimulating DC with poly(I:C) and following gene expression at 5 time points from 1 to 24 hours. The novel filtering strategy uses standard statistical and fold change techniques, along with the consistency of replicate temporal profiles, to identify those differentially expressed genes that were consistent in two biological replicate experiments. To address the issue of cluster reproducibility a consensus clustering method, which identifies clusters of genes whose expression varies consistently between replicates, was also developed and applied. Analysis of the resulting clusters revealed many known and novel characteristics of DC maturation, such as the up-regulation of specific immune response pathways. Intriguingly, more genes were down-regulated than up-regulated. Results identify a more comprehensive program of down-regulation, including many genes involved in protein synthesis, metabolism, and housekeeping needed for maintenance of cellular integrity and metabolism.

CONCLUSIONS: The new filtering strategy emphasizes the importance of consistent and reproducible results when analyzing microarray data and utilizes consistency between replicate experiments as a criterion in both feature selection and clustering, without averaging or otherwise combining replicate data. Observation of a significant down-regulation program during DC maturation indicates that DC are preparing for cell death and provides a path to better understand the process. This new filtering strategy can be adapted for use in analyzing other large-scale time course data sets with replicates. #!#

Overall design: DC were generated from the bone marrow of C57BL/6 mice using GM-CSF, Treated with poly I:C, and RNA was isolated at 0, 1, 3, 6, 12 and 24 hours, and subjected to microarray analysis. Two independent replicate experiments were performed.

Background corr dist: KL-Divergence = 0.1114, L1-Distance = 0.0281, L2-Distance = 0.0014, Normal std = 0.4266

0.935 Kernel fit Pairwise Correlations Normal fit

Density 0.468

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

MouseDC-0hr-1MouseDC-0hr-2MouseDC-1hr-1 (0.102244)MouseDC-1hr-2 (0.0442189)MouseDC-3hr-1 (0.0858147)MouseDC-3hr-2 (0.068125)MouseDC-6hr-1 (0.0622794)MouseDC-6hr-2 (0.0270755)MouseDC-12hr-1 (0.0326199)MouseDC-12hr-2 (0.0297405)MouseDC-24hr-1 (0.0467891)MouseDC-24hr-2 (0.238005) (0.0495353) (0.213553) [ min ] [ medium ] [ max ] CEM 1 Ctr9 147.8 346.9 493.4 P ( S | Z, I ) = 0.71 Rtf1 286.2 656.1 808.6 Mean Corr = 0.41018 Paf1 298.5 410.1 468.0 Cdc73 556.6 1293.4 1518.6 Leo1 252.4 472.8 603.5 Wdr61 38.5 74.2 100.3 Pex2 121.4 180.0 220.3 Ddx42 341.8 442.1 495.0 Morc2a 102.2 312.5 601.6 Taf1a 24.7 118.9 235.8 Aggf1 697.8 1668.4 2754.8 Taf1b 267.3 335.5 472.0 CEM 1 + Pak1ip1 1157.1 2661.7 2881.8 Top 10 Genes Actr6 252.3 467.0 552.3 Jade3 61.1 142.3 263.5 Cbfa2t2 282.0 383.7 470.0 Clpx 400.7 550.6 684.1

Null module GEO Series "GSE13753" 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=GSE13753 Status: Public on Jun 08 2009 Title: E2F4 cooperates with pRB in the development of extra-embryonic, not embryonic, tissues Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: Homozygous mutation of the murine retinoblastoma tumor suppressor gene, Rb, results in embryonic lethality between E13.5 and E15.5 with defects in cellular proliferation, differentiation and apoptosis. Many of these defects are suppressed by mutation of an activating E2F, E2f1 or E2f3, indicating that they are key downstream targets of the retinoblastoma protein, pRB. In this study, we assess how E2F4 contributes to the developmental consequences of pRb-loss. In stark contrast to the activating E2Fs, the homozygous mutation of E2f4 shortened the lifespan of Rb-/- embryos. This resulted from an exacerbation of the placental defect of the Rb-/- mice indicating that E2F4 and pRB cooperate in the development of this tissue. Further analyses indicated that this defect reflects an increase in trophectoderm-like cells. Under conditions where the placenta was wild-type but the embryo mutant for E2f4 and pRb embryos survived to birth and exhibited all of the defects that were observed in the E2f4 and Rb single mutant embryos. Thus, while pRB and E2F4 cooperate in placental development, they play largely non-overlapping roles the development of many embryonic tissues.

Keywords: genetically modified tissue comparison

Overall design: In one experiment, embryonic Day 13.5 placentas from wild-type and Rb -/- knock-out mice were compared. In the second experiment, embronic day 11.5 placentas from wild-type and Rb -/-;E2f4 -/- double knock-out mice were compared.

Background corr dist: KL-Divergence = 0.0302, L1-Distance = 0.0398, L2-Distance = 0.0027, Normal std = 0.6625

0.602 Kernel fit Pairwise Correlations Normal fit

Density 0.301

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

Day11.5_Placenta_WT_183-1Day11.5_Placenta_WT_150-8Day11.5_Placenta_WT_172-6Day11.5_Placenta_RbE2f4NULL_169-4 (0.0427795)Day11.5_Placenta_RbE2f4NULL_183-6 (0.13555)Day11.5_Placenta_RbE2f4NULL_183-10 (0.100421)Day13.5_Placenta_RbNULL_2Day13.5_Placenta_RbNULL_3Day13.5_Placenta_WT_4 (0.0688309)Day13.5_Placenta_WT_5 (0.107143) (0.0714433) (0.0333406) (0.183679) (0.141762) (0.115052)[ min ] [ medium ] [ max ] CEM 1 Ctr9 2011.5 2537.8 3533.3 P ( S | Z, I ) = 0.52 Rtf1 1195.6 1659.5 1832.9 Mean Corr = 0.65661 Paf1 1139.4 1499.1 1841.7 Cdc73 3967.6 4829.4 5714.6 Leo1 1354.5 1498.5 1636.6 Wdr61 21.9 29.0 78.3 Pex2 12.9 20.7 26.7 Ddx42 772.8 916.4 1113.7 Morc2a 944.6 1067.0 1371.1 Taf1a 76.3 129.8 238.9 Aggf1 1972.2 2435.3 3042.6 Taf1b 502.9 694.8 801.6 CEM 1 + Pak1ip1 6198.2 7066.6 7263.7 Top 10 Genes Actr6 1105.5 1419.4 1722.0 Jade3 6269.1 7987.6 9344.5 Cbfa2t2 506.9 770.6 953.3 Clpx 1365.9 1648.3 1832.9

Null module GEO Series "GSE51483" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 45 -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=GSE51483 Status: Public on May 19 2014 Title: Transcriptional Atlas of Cardiogenesis Maps Congenital Heart Disease Interactome Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 24803680 Summary & Design: Summary: Mammalian heart development is built on highly conserved molecular mechanisms with polygenetic perturbations resulting in a spectrum of congenital heart diseases (CHD). However, the transcriptional landscape of cardiogenic ontogeny that regulates proper cardiogenesis remains largely based on candidate-gene approaches. Herein, we designed a time-course transcriptome analysis to investigate the genome-wide expression profile of innate murine cardiogenesis ranging from embryonic stem cells to adult cardiac structures. This comprehensive analysis generated temporal and spatial expression profiles, prioritized stage-specific gene functions, and mapped the dynamic transcriptome of cardiogenesis to curated pathways. Reconciling the bioinformatics of the congenital heart disease interactome, we deconstructed disease-centric regulatory networks encoded within this cardiogenic atlas to reveal stage-specific developmental disturbances clustered on epithelial-to-mesenchymal transition (EMT), BMP regulation, NF-AT signaling, TGFb-dependent induction, and Notch signaling. Therefore, this cardiogenic transcriptional landscape defines the time-dependent expression of cardiac ontogeny and prioritizes regulatory networks at the interface between health and disease.

Overall design: To interrogate the temporal and spatial expression profiles across the entire genome during mammalian heart development, we designed a time-course microarray experiment using the mouse model at defined stages of cardiogenesis, starting with embryonic stem cells (ESC, R1 stem cell line), early embryonic developmental stages: E7.5 whole embryos, E8.5 heart tubes, left and right ventricle tissues at E9.5, E12.5, E14.5, E18.5 to 3 days after birth (D3) and adult heart (Figure 1A). At each time point, microarray experiments were performed on triplicate biological samples. Starting at E9.5, tissue samples from left ventricles (LV) and right ventricles (RV) were microdissected for RNA purification and microarray analysis to determine spatially differential gene expression between LV and RV during heart development.

Background corr dist: KL-Divergence = 0.0679, L1-Distance = 0.0271, L2-Distance = 0.0013, Normal std = 0.5057

0.789 Kernel fit Pairwise Correlations Normal fit

Density 0.394

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 R1Mouse Stem R1Mouse Cells Stem R1.1R1Mouse Cells Stem (0.039833) R1.2E7.5Mouse Cells (0.109997)whole R1.3E7.5Mouse embryo (0.0392649)whole E7.5Mouse embryo tissuewhole E8.5Mouse E7.1embryo tissuewhole E8.5Mouse (0.0675907) E7.2heart tissuewhole E8.5Mouse (0.0530584) tissue E7.3heart whole E9.5Mouse (0.0852815)(heart tissue heart left E9.5Mousetube) ventricle(heart tissue left E8.1 E9.5Mousetube) ventricle(heart tissue (0.0418968) left E8.2 E9.5Mousetube) ventricle E9L.1 tissue (0.0435055) right E8.3 E9.5Mouse (0.0235218) E9L.2ventricletissue (0.0321551) right E9.5Mouse (0.0160054) E9L.3ventricle tissueright E12.5Mouse (0.0234988) ventricle E9R.1 tissue left E12.5Mouse ventricle(0.00924936) E9R.2 tissue left E12.5Mouse ventricle(0.0157775) E9R.3tissue left E12.5Mouse ventricle(0.0122847) E12L.1 tissue right E12.5Mouse (0.00174257)E12L.2ventricletissue right E12.5Mouse (0.00418559)E12L.3ventricle tissueright E14.5Mouse (0.001131)ventricle E12R.1 tissueleft E14.5Mouse ventricle E12R.2(0.00722366) tissueleft E14.5Mouse ventricle tissue E12R.3(0.0028139) left E14.5Mouse ventricle E14L.1 tissue (0.0052553) right E14.5Mouse (0.00467711)E14L.2ventricletissue right E14.5Mouse (0.0174115)E14L.3ventricle tissueright E18.5Mouse (0.00809632)ventricle E14R.1 tissueleft E18.5Mouse ventricle E14R.2(0.0176716) tissueleft E18.5Mouse ventricle tissue E14R.3(0.00879207) left E18.5Mouse ventricle E18L.1 tissue (0.00804022) right E18.5Mouse (0.0169915)E18L.2ventricletissue right E18.5Mouse (0.0285738)E18L.3ventricle tissueright leftMouse (0.0096194)ventricle E18R.1 tissue leftMouse ventricle E18R.2 (0.00843715)tissue leftMouse ventricle atE18R.3 (0.00576014)tissue 3rightMouse days at (0.00623185)ventricletissue after3rightMouse days birth atventricle aftertissue3rightAdult days D3L.1 birth ventricle mouseat aftertissueAdult 3(0.011263) D3L.2 days birth leftmouseat tissueAdult after3(0.0156088) ventricleD3L.3 days leftbirthmouseatAdult after3(0.0108601) ventricle days D3R.1tissue leftbirthmouseAdult after ventricle (0.0175072) AdltL.1D3R.2tissue rightbirthmouseAdult (0.0178595) AdltL.2(0.0222558)ventricleD3R.3tissue rightmouse (0.0172046) AdltL.3(0.0160018)ventricle tissueright (0.0190094)ventricle AdltR.1 tissue AdltR.2(0.0454069)tissue[ min AdltR.3(0.0150511) ] (0.0163969) [ medium ] [ max ] CEM 1 Ctr9 269.4 493.7 1238.1 P ( S | Z, I ) = 0.51 Rtf1 447.1 821.4 1604.5 Mean Corr = 0.39993 Paf1 318.8 549.0 864.6 Cdc73 961.0 1367.6 3556.3 Leo1 545.3 758.5 1520.5 Wdr61 40.5 58.2 124.3 Pex2 84.5 111.8 164.9 Ddx42 316.8 472.7 1209.6 Morc2a 502.7 905.7 1762.9 Taf1a 131.7 181.5 673.0 Aggf1 1283.4 1603.2 3581.5 Taf1b 137.0 401.7 711.2 CEM 1 + Pak1ip1 1858.8 2351.5 6337.8 Top 10 Genes Actr6 799.6 1093.7 1686.4 Jade3 48.1 194.2 1044.2 Cbfa2t2 608.7 790.1 1133.8 Clpx 740.1 1016.5 3538.7

Null module GEO Series "GSE48790" 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=GSE48790 Status: Public on Jul 12 2013 Title: Expression data from GTF2i mutated ES cells Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 23831514 Summary & Design: Summary: Data present the expression analysis of different mouse ES cell line with altered expression of GTF2I.

Overall design: We used microarrays to detail the global programme of gene expression underlying altered expression of GTF2I and identified distinct classes of deregulated genes

Background corr dist: KL-Divergence = 0.0303, L1-Distance = 0.0391, L2-Distance = 0.0018, Normal std = 0.6989

0.613 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

HPRTKO,HPRTKO, biologicalGTF2iTrap biological rep1GTF2iTrap (0.257973)line, rep2Wild-type, biological (0.23462)line,Wild-type, biological biological rep Gtf2i1 (0.0384415) biological rep Mutant rep1 Gtf2i2 (0.0466261) (0.0781152) Mutantline, rep2 biological (0.0485541) line, biological rep 1 (0.175911) rep[ 2min (0.119759) ] [ medium ] [ max ] CEM 1 Ctr9 346.8 459.7 724.7 P ( S | Z, I ) = 0.50 Rtf1 780.7 1004.6 1068.5 Mean Corr = 0.52146 Paf1 414.5 570.3 723.3 Cdc73 1676.6 1924.2 2336.3 Leo1 1008.7 1180.3 1691.1 Wdr61 89.7 126.7 157.3 Pex2 119.8 131.1 141.9 Ddx42 575.7 697.0 841.1 Morc2a 1129.2 1280.1 1597.4 Taf1a 329.7 414.1 553.4 Aggf1 1572.1 2310.0 2545.9 Taf1b 413.8 553.0 710.7 CEM 1 + Pak1ip1 3578.1 4384.9 5069.7 Top 10 Genes Actr6 995.4 1320.3 1669.3 Jade3 442.0 538.8 1164.7 Cbfa2t2 894.3 1632.6 1810.5 Clpx 661.5 747.8 867.2

Null module GEO Series "GSE35825" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 9 -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=GSE35825 Status: Public on Feb 15 2012 Title: Type I and II Interferon-Stimulated Genes in Murine Primary Bone Marrow Macrophages Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 22371602 Summary & Design: Summary: We used microarrays to compare interferon-alpha (IFNa)- and interferon-gamma (IFNg)-stimulated genes under an equivalent biological input. The goal was to compare IFNa- and IFNg-stimulated genes, as well as to identify common and distinct sets of type I and II ISGs.

Overall design: Bone marrow macrophages derived from mouse bone marrow in M-CSF for 7 days. The cells were stimulated with 62U/mL IFNa and 1U/mL of IFNg for 2.5 hrs in culture. These concentrations induced equivalent STAT1 phosphorylation in BMMs.

Background corr dist: KL-Divergence = 0.0865, L1-Distance = 0.0224, L2-Distance = 0.0007, Normal std = 0.4706

0.848 Kernel fit Pairwise Correlations Normal fit

Density 0.424

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

Media rep1Media (0.0728009) rep2Media (0.296853) rep3IFNa (0.0462691) rep1IFNa (0.120482) rep2IFNa (0.0753381) rep3IFNg (0.177348) rep1IFNg (0.0470509) rep2IFNg (0.0958724) rep3 (0.0679858) [ min ] [ medium ] [ max ] CEM 1 Ctr9 294.4 354.0 457.4 P ( S | Z, I ) = 0.21 Rtf1 672.2 958.3 1030.5 Mean Corr = 0.51698 Paf1 562.7 602.0 654.1 Cdc73 1196.6 1656.0 1810.0 Leo1 195.2 228.8 260.0 Wdr61 15.7 33.2 71.9 Pex2 136.8 159.3 291.2 Ddx42 486.7 572.2 759.0 Morc2a 399.0 525.8 649.0 Taf1a 89.3 107.6 150.5 Aggf1 1886.7 2129.5 2416.6 Taf1b 392.7 436.3 493.0 CEM 1 + Pak1ip1 1876.6 2434.1 2759.0 Top 10 Genes Actr6 492.7 625.4 855.9 Jade3 170.4 227.1 342.4 Cbfa2t2 391.0 455.7 575.1 Clpx 463.0 953.9 1210.5

Null module 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 (0.23822)d17 KGF of mESCsat (Control)differentiation d17treatment of mESCsat withdifferentiation d24 (0.0151079) (0.265202) KGFof mESCsat withdifferentiation d24 treatment DCIof mESCsat withdifferentiation d24 treatment KGF(0.0258698)of at (Control)differentiation d24 and (0.068706) of DCI withdifferentiation (0.0610784) treatment KGF with treatment DCI[ (0.0313082) withmin treatment KGF(0.14346) and] (0.0902752) DCI treatment[ medium (0.0607731) ] [ max ] CEM 1 Ctr9 410.2 450.2 715.1 P ( S | Z, I ) = 0.17 Rtf1 639.2 876.6 1292.9 Mean Corr = 0.59083 Paf1 517.8 623.9 745.7 Cdc73 1493.9 1766.0 2240.2 Leo1 431.6 605.1 1236.8 Wdr61 97.0 124.8 132.9 Pex2 102.2 150.7 199.8 Ddx42 631.5 848.7 1047.7 Morc2a 784.3 1078.8 1486.1 Taf1a 311.7 365.4 414.2 Aggf1 1147.5 1505.4 2079.4 Taf1b 170.8 324.8 394.9 CEM 1 + Pak1ip1 1644.3 1797.6 1851.3 Top 10 Genes Actr6 919.0 980.3 1001.8 Jade3 426.9 561.8 930.4 Cbfa2t2 564.3 753.7 882.2 Clpx 1106.6 1281.5 1548.8

Null module GEO Series "GSE13707" 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=GSE13707 Status: Public on Nov 22 2008 Title: Effect of an anti-myostatin antibody on skeletal muscle gene expression in mice Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 19141683 Summary & Design: Summary: More than 2,000 genes appear to be upregulated or downregulated in skeletal muscle of mice with constitutive knockout of myostatin (Steelman et al., FASEB J 20:580-2, 2006). This study was done to determine whether inhibition of myostatin activity in mature mice has similar effects on the pattern of gene expression.

Keywords: Differential expression in treated and control mice

Overall design: Ten samples from JA16 antibody-treated mice were compared with 10 samples from saline-treated mice

Background corr dist: KL-Divergence = 0.1434, L1-Distance = 0.0544, L2-Distance = 0.0058, Normal std = 0.4029

1.055 Kernel fit Pairwise Correlations Normal fit

Density 0.527

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

Muscle_Saline_01Muscle_Saline_02Muscle_Saline_03 (0.0295037)Muscle_Saline_04 (0.0598543)Muscle_Saline_05 (0.00878008)Muscle_Saline_06 (0.0626291)Muscle_Saline_07 (0.0555476)Muscle_Saline_08 (0.0200228)Muscle_Saline_09 (0.0781958)Muscle_Saline_10 (0.0516153)Muscle_JA16_01 (0.0267788)Muscle_JA16_02 (0.0400551)Muscle_JA16_03 (0.0473804)Muscle_JA16_04 (0.0470179)Muscle_JA16_05 (0.048985)Muscle_JA16_06 (0.0390283)Muscle_JA16_07 (0.0670128)Muscle_JA16_08 (0.0689027)Muscle_JA16_09 (0.0836693)Muscle_JA16_10 (0.0897951) (0.0325516) (0.0426744) [ min ] [ medium ] [ max ] CEM 1 Ctr9 25.2 68.6 155.3 P ( S | Z, I ) = 0.03 Rtf1 323.3 655.3 870.0 Mean Corr = 0.34054 Paf1 646.8 1017.3 1905.8 Cdc73 208.8 457.1 775.4 Leo1 159.7 253.0 737.4 Wdr61 1.8 38.4 112.6 Pex2 8.5 69.2 110.0 Ddx42 1223.7 1927.1 2503.0 Morc2a 503.1 634.6 1247.6 Taf1a 81.6 243.0 369.0 Aggf1 871.1 1286.2 1809.3 Taf1b 87.2 143.3 305.9 CEM 1 + Pak1ip1 1963.5 2573.2 3214.3 Top 10 Genes Actr6 68.0 166.5 237.1 Jade3 12.8 32.0 81.2 Cbfa2t2 709.3 1036.2 1387.8 Clpx 490.7 827.6 1505.2

Null module GEO Series "GSE20696" 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=GSE20696 Status: Public on Sep 30 2010 Title: Expression profiling of 3T3-L1 adipogenesis Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 20887899 Summary & Design: Summary: 3T3-L1 pre-adipocyte cells were grown to confluence and induced to differentiate in adipogeneic media.

Overall design: Two technical replicates from four time points relative to induction of adipogenesis (day 0)

Background corr dist: KL-Divergence = 0.0408, L1-Distance = 0.0317, L2-Distance = 0.0012, Normal std = 0.6378

0.651 Kernel fit Pairwise Correlations Normal fit

Density 0.325

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

3T3-L1_t1_rep13T3-L1_t1_rep23T3-L1_t2_rep1 (0.0485039)3T3-L1_t2_rep2 (0.0376748)3T3-L1_t3_rep1 (0.129067)3T3-L1_t3_rep2 (0.0930742)3T3-L1_t4_rep1 (0.200245)3T3-L1_t4_rep2 (0.23442) (0.150621) (0.106395) [ min ] [ medium ] [ max ] CEM 1 Ctr9 882.7 944.7 1440.0 P ( S | Z, I ) = 0.01 Rtf1 933.9 1211.9 1378.8 Mean Corr = 0.34372 Paf1 236.5 274.4 569.4 Cdc73 1176.2 2422.8 2793.5 Leo1 508.0 660.1 1370.5 Wdr61 54.3 101.3 108.5 Pex2 153.3 208.0 265.8 Ddx42 589.7 749.8 805.3 Morc2a 538.8 705.0 997.0 Taf1a 237.8 398.2 705.8 Aggf1 1201.0 1375.5 1629.4 Taf1b 383.9 506.8 531.2 CEM 1 + Pak1ip1 1326.7 2179.8 2689.8 Top 10 Genes Actr6 511.5 1102.4 1858.5 Jade3 231.2 447.1 609.2 Cbfa2t2 852.7 904.1 1379.9 Clpx 898.5 1612.4 4045.8

Null module 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 (0.36014)(GM-DC_2) cell TNFa (0.105328) plus (0.0910783) sample TNFa (0.141928) sample1 (GM-TNFa-DC_1)[ 2min (GM-TNFa-DC_2) ] (0.155573) (0.145953)[ medium ] [ max ] CEM 1 Ctr9 255.6 325.5 560.0 P ( S | Z, I ) = 0.01 Rtf1 784.7 1103.3 1131.1 Mean Corr = 0.48059 Paf1 534.5 703.1 766.6 Cdc73 719.4 900.5 1432.2 Leo1 345.0 403.0 677.1 Wdr61 69.5 87.2 108.5 Pex2 194.2 249.0 267.0 Ddx42 551.6 588.9 683.9 Morc2a 416.6 479.4 647.1 Taf1a 107.3 146.0 168.6 Aggf1 947.4 1400.5 2070.7 Taf1b 327.4 419.5 542.0 CEM 1 + Pak1ip1 1526.1 1766.3 2399.6 Top 10 Genes Actr6 247.0 451.8 558.5 Jade3 73.7 91.6 100.2 Cbfa2t2 454.3 526.4 553.1 Clpx 610.1 738.4 863.8

Null module 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 (0.136397) day lung-embryoMouse 14-rep1 (0.0610205) day lung-embryoMouse 14-rep2 (0.109618) day lung-embryoMouse 16-rep1 (0.0788546) day lung-embryoMouse 16-rep2 (0.0311263) day lung-postnatalMouse 18-rep1 (0.0220247) day lung-postnatalMouse 18-rep2 (0.0754073) lung-postnatalMouseday (0.0131148) 2-rep1 lung-postnatalMouseday (0.0805343)2-rep2 lung-postnatalMouseday (0.0557408)10-rep1 lung-postnatalday 10-rep2 (0.0328363) day 30-rep1 (0.0679338) day 30-rep2 (0.112783)[ min (0.122608) ] [ medium ] [ max ] CEM 1 Ctr9 288.0 486.2 774.2 P ( S | Z, I ) = 0.00 Rtf1 805.9 885.5 1327.2 Mean Corr = 0.46092 Paf1 398.1 521.7 595.1 Cdc73 850.4 1099.6 1250.2 Leo1 304.3 509.2 978.5 Wdr61 147.8 214.1 252.5 Pex2 229.3 304.9 383.8 Ddx42 559.0 717.6 936.2 Morc2a 705.0 986.5 1411.8 Taf1a 355.2 412.3 472.7 Aggf1 996.6 1165.1 1398.7 Taf1b 294.1 348.8 528.2 CEM 1 + Pak1ip1 1310.6 1497.4 1685.7 Top 10 Genes Actr6 472.6 581.6 970.8 Jade3 239.3 413.4 536.6 Cbfa2t2 656.3 760.6 899.7 Clpx 648.2 789.3 1079.9

Null module GEO Series "GSE42601" 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=GSE42601 Status: Public on Jun 01 2013 Title: Expression data from wild-type and Dazap1 mutant mouse testes Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 23965306 Summary & Design: Summary: Deleted in Azoospermia Associated Protein 1 (DAZAP1) is a ubiquitous RNA-binding protein that is highly expressed in the testis. It is a component of the hnRNP particles and shuttles between the nucleus and the cytoplasm. Mice expressing the DAZAP1-Fn mutant protein manifest both growth retardation and spermatogenic arrest before meiosis I. To elucidate the biological function(s) of DAZAP1 and to search for its natural RNA substrates, we compared the expression profiles of wild-type and Dazap1 mutant testes by cDNA microarrays.

Overall design: We used wild-type and Dazap1 mutant mouse testes. Each genotype has three replicates. 6 total samples were analyzed.

Background corr dist: KL-Divergence = 0.0070, L1-Distance = 0.0271, L2-Distance = 0.0008, Normal std = 0.9770

0.430 Kernel fit Pairwise Correlations Normal fit

Density 0.215

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

Wild-typeMutant testes Wild-typetestes at P21, atMutant P21,biological testes biological Wild-typetestes at P21,rep1 atMutant P21,biological rep1(0.0846238)testes biological(0.173363)testes at P21,rep2 at P21,biologicalrep2(0.172644) biological(0.215701) rep3[ rep3(0.232848)min (0.12082) ] [ medium ] [ max ] CEM 1 Ctr9 1035.2 1045.6 1210.8 P ( S | Z, I ) = 0.00 Rtf1 652.3 1105.9 1189.2 Mean Corr = 0.34144 Paf1 499.1 692.3 741.3 Cdc73 2175.1 3729.1 4106.7 Leo1 894.8 1012.9 1123.7 Wdr61 44.6 70.1 94.1 Pex2 127.1 178.5 196.1 Ddx42 785.7 874.7 1026.3 Morc2a 1666.6 2096.9 2538.8 Taf1a 465.1 804.2 848.3 Aggf1 1201.0 1669.0 1966.4 Taf1b 1170.6 2293.4 2529.2 CEM 1 + Pak1ip1 3162.4 3755.8 4332.8 Top 10 Genes Actr6 2056.0 2381.8 2583.6 Jade3 1028.6 2739.7 2819.3 Cbfa2t2 1211.4 1433.6 1548.4 Clpx 1164.8 1777.0 1984.1

Null module 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 (0.0517461) 3 (Affymetrix)Tg,Calcineurin biological (0.0407877) 4 (Affymetrix)Tg,Calcineurin biological (0.0417521) replicate Tg,Differentiating biological (0.0282927) replicate Tg, 1 (Affymetrix)Differentiating biological replicate 2 P19CL6(Affymetrix)Differentiating replicate (0.0474013) 3 P19CL6(Affymetrix)Differentiating cells (0.0471834) 4at P19CL6(Affymetrix)Differentiating cellsday (0.0431537)6 at afterP19CL6Differentiating cellsday DMSO(0.0597717)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 (0.115581)replicate 3 (Affymetrix) treatment, (0.0813995)replicate [1 (Affymetrix)medium (0.15505)replicate 2 (Affymetrix) (0.0893769) 3 (Affymetrix) ] (0.0953857) (0.103119)[ max ] CEM 1 Ctr9 336.1 412.2 1119.2 P ( S | Z, I ) = 0.00 Rtf1 338.0 616.6 1449.0 Mean Corr = 0.34494 Paf1 320.2 400.2 1073.1 Cdc73 966.4 1136.3 1805.9 Leo1 183.9 228.3 1191.4 Wdr61 127.8 174.3 196.6 Pex2 200.9 245.8 380.3 Ddx42 526.3 614.8 998.5 Morc2a 663.5 764.6 1823.4 Taf1a 325.4 360.6 587.2 Aggf1 707.9 1079.8 1640.8 Taf1b 315.9 387.3 770.7 CEM 1 + Pak1ip1 1333.9 1614.7 2143.9 Top 10 Genes Actr6 603.5 808.5 987.6 Jade3 48.2 83.5 335.1 Cbfa2t2 714.8 847.5 1241.4 Clpx 839.1 2011.5 2256.3

Null module GEO Series "GSE16266" 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=GSE16266 Status: Public on Dec 21 2009 Title: Identification of inflammatory genes suppressed by heat shock Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 20018623 Summary & Design: Summary: To clarify inflammatory genes whose expression is suppressed at high temperatures, we performed comprehensive analysis of gene expression by using a DNA microarray. Two independent primary cultures of mouse embryo fibroblasts (MEF1 and MEF2) were treated with LPS for 4 hours, or treated with LPS for 4 hours after the pretreatment with heat shock at 42¸C for 1 hour, and we identified 100 genes that undergo more than a 3-fold increase with LPS treatment. Remarkably, 86 genes (86%) underwent less than a 2-fold increase after combined treatments with heat shock and LPS in MEF1 and MEF2 cells.

Overall design: Total RNAs were prepared from two primary cultures of mouse embryo fibroblasts (MEF) derived from two independent embryos at embryonic day 15.5 (ICR mice). Cells were maintained at 37¸C (Control), treated with lipopolysaccharide (LPS, E. coli 0127:B8, Sigma, 1 ˛…g/ml) for 4 hours, or treated with LPS for 4 hours after the pretreatment of heat shock at 42¸C for 1 hour. Gene expression was analyzed by using GeneChip Mouse Genome 430 2.0 Array (Affymetrix, Santa Clara, CA).

Background corr dist: KL-Divergence = 0.0404, L1-Distance = 0.0284, L2-Distance = 0.0010, Normal std = 0.6266

0.668 Kernel fit Pairwise Correlations Normal fit

Density 0.334

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

MEF1-ControlMEF1-LPS (0.197181)MEF1-HS+LPS (0.14441)MEF2-Control MEF2-LPS(0.152812) (0.044254)MEF2-HS+LPS (0.162119) (0.299224) [ min ] [ medium ] [ max ] CEM 1 Ctr9 425.3 597.5 656.3 P ( S | Z, I ) = 0.00 Rtf1 389.1 654.0 700.8 Mean Corr = 0.28904 Paf1 217.4 395.2 439.5 Cdc73 1438.7 1774.0 1855.4 Leo1 523.1 641.7 897.8 Wdr61 35.8 60.9 88.5 Pex2 92.0 121.9 179.1 Ddx42 508.7 536.6 548.7 Morc2a 862.9 1011.6 1158.9 Taf1a 97.9 160.8 283.4 Aggf1 1128.9 1376.9 1550.8 Taf1b 128.4 250.8 325.6 CEM 1 + Pak1ip1 1972.8 2485.6 2687.6 Top 10 Genes Actr6 397.6 547.2 570.2 Jade3 122.5 195.3 247.4 Cbfa2t2 591.6 893.0 1039.2 Clpx 531.1 969.9 1117.4

Null module GEO Series "GSE26668" 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=GSE26668 Status: Public on Mar 23 2011 Title: Expression data from E13.5 Fz4-/-Fz8-/- and Fz4+/+Fz8-/- kidneys Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21343368 Summary & Design: Summary: Fz4 and Fz8 cooperate in regulating the branching morhpogenesis of the developing kidney during mouse embryonic development, hence determines the eventual kidney size.

We used microarrays to study the global gene expression profiles regulated by Fz4 and Fz8 signaling during early kidney development, and to understand the collaboration between the signaling events mediated by Fz4 and Fz8

Overall design: Kidney rudiments were dissected from E13.5 mouse embryos for RNA extraction and hybridization on Affymetrix MOE430.2 arrays. Three biological replicates of each genotype were analyzed.

Background corr dist: KL-Divergence = 0.0193, L1-Distance = 0.0128, L2-Distance = 0.0002, Normal std = 0.7424

0.537 Kernel fit Pairwise Correlations Normal fit

Density 0.269

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

Fz4Fz8 Fz4Fz8DKO C1 Fz4Fz8DKO (0.0940979) C2 Fz4Fz8DKO (0.230527) C3 Fz4Fz8DKO (0.133661) M1 Fz4Fz8DKO (0.150136) M2 DKO (0.30984) M3 (0.0817376) [ min ] [ medium ] [ max ] CEM 1 Ctr9 126.6 196.3 265.0 P ( S | Z, I ) = 0.00 Rtf1 634.2 880.2 1113.0 Mean Corr = 0.23482 Paf1 1594.3 2100.4 2508.4 Cdc73 733.4 816.1 983.1 Leo1 544.9 835.0 1019.3 Wdr61 133.9 173.6 195.1 Pex2 167.1 208.2 257.9 Ddx42 2694.6 3145.5 3398.3 Morc2a 1391.7 1841.3 1990.1 Taf1a 401.1 543.5 571.0 Aggf1 1745.4 1884.7 2206.0 Taf1b 337.4 389.1 445.0 CEM 1 + Pak1ip1 1853.3 2117.8 2315.4 Top 10 Genes Actr6 200.2 244.8 264.9 Jade3 423.9 547.5 625.0 Cbfa2t2 690.1 829.9 998.6 Clpx 280.3 298.4 336.2

Null module GEO Series "GSE40296" 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=GSE40296 Status: Public on Aug 23 2012 Title: Essential roles of the histone methyltransferase ESET in the epigenetic control of neural progenitor cells during development Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 22991445 Summary & Design: Summary: In the developing brain, neural progenitor cells (NPCs) switch the differentiation competency via changing gene expression profiles that are governed partly by epigenetic control such as histone modification, although the precise mechanism is unknown. Here we found that ESET/Setdb1/KMT1E, a histone H3 Lys-9 (H3K9) methyltransferase, was highly expressed at early stages of brain development but down-regulated over time, and that ablation of ESET led to decreased H3K9 trimethylation and misregulation of genes, resulting in severe brain defects and early lethality. In the mutant brain, endogenous retrotransposons were derepressed, and non-neural gene expression was activated. Furthermore, early neurogenesis was most severely impaired, while astrocyte formation was enhanced. We conclude that there is an epigenetic role of ESET in temporal and tissue-specific gene regulation in the developing brain.

We used microarrays to identify genes up- or downregulated when ESET is ablated in the dorsal telencephalon.

Overall design: We used 3 WT and 3 cKO male E14.5 embryo for each analysis

Background corr dist: KL-Divergence = 0.0404, L1-Distance = 0.0189, L2-Distance = 0.0004, Normal std = 0.6141

0.656 Kernel fit Pairwise Correlations Normal fit

Density 0.328

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

TelencephalonTelencephalon TelencephalonWT 1 (0.0359763) TelencephalonWT 2 (0.180112) TelencephalonWT 3 (0.173902) TelencephaloncKO 1 (0.214577) cKO 2 (0.0405775) cKO 3 (0.354855)[ min ] [ medium ] [ max ] CEM 1 Ctr9 450.7 565.7 738.0 P ( S | Z, I ) = 0.00 Rtf1 1490.6 1768.8 1862.4 Mean Corr = -0.11581 Paf1 414.7 591.2 634.4 Cdc73 1408.6 1708.4 1952.2 Leo1 572.9 642.0 688.1 Wdr61 175.5 216.1 225.4 Pex2 110.3 184.4 261.1 Ddx42 917.3 1293.3 1321.2 Morc2a 1867.7 2287.6 2808.5 Taf1a 252.5 293.5 311.0 Aggf1 2209.7 2389.5 2576.1 Taf1b 575.4 635.6 686.1 CEM 1 + Pak1ip1 2102.2 2432.2 2796.4 Top 10 Genes Actr6 1479.7 1599.2 1938.4 Jade3 473.7 605.0 708.1 Cbfa2t2 2515.4 3205.3 3573.8 Clpx 797.6 839.1 954.7

Null module GEO Series "GSE21379" 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=GSE21379 Status: Public on Apr 20 2010 Title: Expression Data from WT and Sh2d1a-/- in vivo follicular helper CD4 T cells (TFH) versus non follicular helper CD4 T cells (non-TFH) Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 20525889 Summary & Design: Summary: CD4 T cell help is critical for both the generation and maintenance of germinal centers, and T follicular helper (TFH) cells are the CD4 T cell subset required for this process. SAP (SH2D1A) expression in CD4 T cells is essential for germinal center development. However, SAP-deficient mice have only a moderate defect in TFH differentiation as defined by common TFH surface markers. CXCR5+ TFH cells are found within the germinal center as well as along the boundary regions of T/B cell zones. Here we show that germinal center associated T cells (GC TFH) can be identified by their co-expression of CXCR5 and the GL7 epitope, allowing for phenotypic and functional analysis of TFH and GC TFH populations. Here we show GC TFH are a functionally discrete subset of further polarized TFH cells, with enhanced B cell help capacity and a specialized ability to produce IL-4 in a TH2-independent manner. Strikingly, SAP-deficient mice have an absence of the GC TFH subset and SAP- TFH are defective in IL-4 and IL-21 production. We further demonstrate that SLAM (Slamf1, CD150), a surface receptor that utilizes SAP signaling, is specifically required for IL-4 production by GC TFH. GC TFH cells require IL-4 and IL-21 production for optimal help to B cells. These data illustrate complexities of SAP-dependent SLAM family receptor signaling, revealing a prominent role for SLAM receptor ligation in IL-4 production by germinal center CD4 T cells but not in TFH and GC TFH differentiation.

Overall design: Analysis of in vivo antigen-specific (LCMV-specific, SMARTA TCR transgenic) WT and Sh2d1a-/- follicular helper CD4 T cells (CXCR5high),versus non-follicular helper CD4 T cells (CXCR5low), eight days after viral infection.

Background corr dist: KL-Divergence = 0.0691, L1-Distance = 0.0416, L2-Distance = 0.0025, Normal std = 0.5262

0.800 Kernel fit Pairwise Correlations Normal fit

Density 0.400

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

NaÃ¯ve CXCR5_Negative_Rep1(0.182192)CXCR5_Positive_Rep1CXCR5_Negative_Rep2CXCR5_Positive_Rep2 (0.0666389)SAPKO (0.0454883)SAPKO_CXCR5_Negative_Rep1 NaÃ¯ve (0.0530966)SAPKO_CXCR5_Positive_Rep1 (0.280183)(0.0258498)SAPKO_CXCR5_Negative_Rep2SAPKO_CXCR5_Positive_Rep2 (0.0447936) (0.049443) (0.0882946)[ (0.164021)min ] [ medium ] [ max ] CEM 1 Ctr9 162.9 218.6 253.3 P ( S | Z, I ) = 0.00 Rtf1 1385.5 1504.1 1900.7 Mean Corr = 0.24860 Paf1 2462.1 2904.1 3573.2 Cdc73 708.4 785.3 1025.5 Leo1 628.3 749.5 842.7 Wdr61 45.1 53.8 343.1 Pex2 40.3 64.5 204.7 Ddx42 4154.8 4772.9 4957.6 Morc2a 964.3 1403.8 1835.5 Taf1a 140.6 231.7 438.8 Aggf1 2750.0 3476.6 4042.6 Taf1b 960.0 1238.7 1327.8 CEM 1 + Pak1ip1 3477.5 3776.9 4511.9 Top 10 Genes Actr6 195.8 263.7 491.0 Jade3 173.8 214.7 371.9 Cbfa2t2 357.1 465.5 628.8 Clpx 376.1 434.0 464.3

Null module GEO Series "GSE52220" 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=GSE52220 Status: Public on Nov 09 2013 Title: Expression data from E11.5 mouse branchial arch 1 (BA1) - comparison between Ezh2lox/lox and Wnt1Cre Ezh2lox/lox embryos Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 24496623 Summary & Design: Summary: Conditional ablation of Ezh2 in the neural crest lineage results in loss of the neural crest-derived mesenchymal derivatives. In this data sheet we determine gene expression analysis in Ezh2lox/lox and Wnt1Cre Ezh2lox/lox in E11.5 mouse BA1 cells.

Overall design: Conditional ablation of Ezh2 in the neural crest lineage was achieved by crossing Wnt1creEzh2lox/wt mice with Ezh2lox/lox mouse lines. We analyzed a total of 6 samples including 3 biological replicates from Ezh2lox/lox embryos and 3 biological replicates from Wnt1cre Ezh2lox/lox embryos.

Background corr dist: KL-Divergence = 0.0375, L1-Distance = 0.0159, L2-Distance = 0.0002, Normal std = 0.6257

0.643 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

Ezh2lox/lox,Ezh2lox/lox, BranchialEzh2lox/lox, BranchialWnt1CreEzh2lox/lox, arch Branchial1, Wnt1CreEzh2lox/lox,biologicalarch 1, Wnt1CreEzh2lox/lox,biologicalarch replicate 1, branchial biological replicate 1 branchial(0.128662) arch replicate 2 branchial1,(0.345799) biologicalarch 3 1,(0.160344)[ biologicalarch min replicate 1, biological replicate] 1 (0.0391809) replicate 2 (0.16157)[ medium3 (0.164443) ] [ max ] CEM 1 Ctr9 439.3 578.5 656.0 P ( S | Z, I ) = 0.00 Rtf1 1587.5 1872.1 1978.6 Mean Corr = 0.39462 Paf1 707.5 783.3 830.7 Cdc73 1674.5 1992.4 2106.2 Leo1 1036.4 1123.7 1163.5 Wdr61 148.3 161.3 183.1 Pex2 112.4 133.9 139.1 Ddx42 876.4 970.9 1044.1 Morc2a 1572.1 1734.7 1770.9 Taf1a 471.9 536.8 550.5 Aggf1 2452.6 2647.3 2759.6 Taf1b 276.6 343.8 373.3 CEM 1 + Pak1ip1 1561.9 1645.5 1746.5 Top 10 Genes Actr6 1075.0 1238.4 1349.6 Jade3 473.6 635.3 683.3 Cbfa2t2 1392.6 1499.7 1698.8 Clpx 1185.5 1278.6 1360.7

Null module GEO Series "GSE38831" 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=GSE38831 Status: Public on Dec 22 2013 Title: Deciphering genomic alterations in colorectal cancer through transcriptional subtype-based network analysis Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 24260186 Summary & Design: Summary: High-throughput genomic studies have identified thousands of genetic alterations in colorectal cancer (CRC). Distinguishing driver from passenger mutations is critical for developing rational therapeutic strategies. Because only a few transcriptional subtypes exist in previously studied tumor types, we hypothesize that highly heterogeneous genomic alterations may converge to a limited number of distinct mechanisms that drive unique gene expression patterns in different transcriptional subtypes. In this study, we defined transcriptional subtypes for CRC and identified driver networks/pathways for each subtype, respectively. Applying consensus clustering to a patient cohort with 1173 samples identified three transcriptional subtypes, which were validated in an independent cohort with 485 samples. The three subtypes were characterized by different transcriptional programs related to normal adult colon, early colon embryonic development, and epithelial mesenchymal transition, respectively. They also showed statistically different clinical outcomes. For each subtype, we mapped somatic mutation and copy number variation data onto an integrated signaling network and identified subtype-specific driver networks using a random walk-based strategy. We found that genomic alterations in the Wnt signaling pathway were common among all three subtypes; however, unique combinations of pathway alterations including Wnt, VEGF, Notch and TGF-beta drove distinct molecular and clinical phenotypes in different CRC subtypes. Our results provide a coherent and integrated picture of human CRC that links genomic alterations to molecular and clinical consequences, and which provides insights for the development of personalized therapeutic strategies for different CRC subtypes.

Overall design: To characterize the embryonic development of colon, we conducted a time course microarray study using the inbred C57BL/6 (Jackson Laboratories, Bar Harbor, ME) mice. Seven samples corresponding to the mouse colonic development from E13.5 to E18.5 and adult (eight week post-natal) were collected. RNA samples were submitted to the Vanderbilt Functional Genomics Shared Resource (FSGR, http://array.mc.vanderbilt.edu), where RNA was hybridized to the Affymetrix Mouse Genome 430 2.0 GeneChip Expression Arrays (Santa Clara, CA) according to manufacturers instructions. The RMA algorithm was used for data normalization. Mouse gene symbols were mapped to human gene symbols by the Human and Mouse Orthology list available from the Mouse Genome Informatics (http://www.informatics.jax.org/).

Background corr dist: KL-Divergence = 0.0290, L1-Distance = 0.0333, L2-Distance = 0.0015, Normal std = 0.7069

0.606 Kernel fit Pairwise Correlations Normal fit

Density 0.303

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

C57BL/6JE13.5C57BL/6JE14.5C57BL/6JE15.5 (0.189611)C57BL/6JE16.5 (0.140104)C57BL/6JE17.5 (0.182564)C57BL/6JE18.5 (0.0318712)C57BL/6JADULT (0.0891542) (0.085159) COLON (0.281537)[ min ] [ medium ] [ max ] CEM 1 Ctr9 231.0 275.5 330.1 P ( S | Z, I ) = 0.00 Rtf1 364.1 663.2 795.8 Mean Corr = 0.38525 Paf1 905.3 1030.5 1273.7 Cdc73 562.6 813.5 1103.0 Leo1 199.7 220.9 300.3 Wdr61 71.1 81.7 132.8 Pex2 82.0 103.8 119.5 Ddx42 1070.6 2045.6 2970.1 Morc2a 564.5 1181.7 1638.5 Taf1a 257.5 305.5 342.5 Aggf1 3314.7 3628.1 4123.5 Taf1b 68.5 99.9 173.5 CEM 1 + Pak1ip1 1201.6 1395.1 1474.2 Top 10 Genes Actr6 147.5 305.0 485.1 Jade3 184.5 412.2 825.2 Cbfa2t2 701.0 788.3 1037.3 Clpx 81.4 88.4 128.2

Null module GEO Series "GSE14012" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 24 -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=GSE14012 Status: Public on Jan 28 2009 Title: Role of the reprogramming factors in inducing pluripotency Organism: Mus musculus Experiment type: Genome binding/occupancy profiling by array Platform: GPL1261 Pubmed ID: 19167336 Summary & Design: Summary: Induced pluripotent stem (iPS) cells can be obtained from fibroblasts by expression of Oct4, Sox2, Klf4, and c-Myc. To determine how these factors induce this change in cell identity, we carried out genomewide promoter analysis of their binding in iPS and partially reprogrammed cells. Most targets in iPS cells are shared with ES cells and the factors cooperate to activate the ES-like expression program. In partially reprogrammed cells, genes bound by c-Myc have achieved a more ES-like binding and expression pattern. In contrast, genes that are co-bound by Oct4, Sox2, and Klf4 in ES cells and that encode pluripotency regulators show severe lack of both binding and transcriptional activation. Among the factors, c-Myc has a pivotal effect on the initiation of the ES transcription program, including the repression of fibroblast-specific genes. Our analysis begins to unravel how the four factors function together and suggests a temporal and separable order of their effects during reprogramming.

Overall design: Oct4/Sox2/c-Myc/Klf4 were performed with biological duplicates (2 clonally isolated iPS/partial iPS lines and ES cells were performed with v6.5 and E14 cell lines)

Background corr dist: KL-Divergence = 0.1543, L1-Distance = 0.0420, L2-Distance = 0.0038, Normal std = 0.3796

1.071 Kernel fit Pairwise Correlations Normal fit

Density 0.536

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

10 coloniesSorted from GFP+uninduced 1A2 cells partialv6.5 fromMEFs ES iPSv6.5 cells 1A2 forclone ES #1tetpartialE14 cells -(1A2-col)experiments control ES iPS#2 E14cells - clone control(0.0645324) (0.0205682) ES #1 (0.0453961)1D4 cells (0.0251585)- control (0.0369744) iPS #21D4 clone- control(0.0113493) iPS #12D4 clone (0.0598476)(0.103079) iPS #22D4 clone (0.041555) iPS #1MEFs clone (0.050128) (male) #2MEFs (0.0523836) #1 (male)MEFs (0.0433804) #2 (female)MEFs (0.0156681) (female) #1OCK (0.0169273) Clone #2OCK (0.0295943) 2 Clone - generated1A2 3partial - generated1A2 from iPSpartial 1B3 cloneOct4/c-Myc/Klf4 from iPSpartial #1 tetC cloneOct4/c-Myc/Klf4 (0.0148548) iPS (tetC-Myc) #2 tetKclone (0.0198127)infected (tet-Klf4) #1tetO induced (0.0239247)infected MEFs (tet-Oct4) inducedtetS MEFs(0.0812752) MEFs (tet-Sox2) induced MEFs(0.0513023) (0.0462503) (0.0296433) induced MEFs (0.0405287) MEFs (0.0758663)[ min ] [ medium ] [ max ] CEM 1 Ctr9 396.5 841.4 1547.3 P ( S | Z, I ) = 0.00 Rtf1 590.3 855.5 1289.8 Mean Corr = 0.08917 Paf1 363.0 567.4 762.0 Cdc73 1105.5 2119.6 3293.5 Leo1 397.8 937.5 2048.5 Wdr61 49.9 70.4 118.9 Pex2 72.9 133.9 171.9 Ddx42 627.4 793.1 1174.6 Morc2a 890.3 1296.0 2414.8 Taf1a 135.3 284.3 441.0 Aggf1 1136.7 2362.3 3448.8 Taf1b 235.3 690.0 1716.4 CEM 1 + Pak1ip1 1236.3 4002.8 5602.2 Top 10 Genes Actr6 196.9 881.4 2045.7 Jade3 124.8 278.3 1351.5 Cbfa2t2 581.4 1454.5 3111.7 Clpx 480.0 1066.0 1444.9

Null module GEO Series "GSE48204" 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=GSE48204 Status: Public on Jul 26 2013 Title: Gene expression in epithelial, EMT (epithelial-mesenchymal transition) and MET (mesenchymal-epithelial transition) cells Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 23878399 Summary & Design: Summary: NMuMG is an epithelial cell line that can be induced into EMT by TGF-Î² treatment or MET by TGF-Î² withdrawl. During EMT, several marker genes were downregulated/upregulated, which is consistent with its mesenchymal phenotype.

Transcription factors that are regulated during EMT and its reverse process MET are candidate genes for the regulations of the EMT marker genes.

Overall design: NMuMG cells treated with vehicle, TGF-Î² for 11 days, or 11days of TGF-Î² treatment followed by TGF-Î² withdrawl for another 13 days. RNA from these 3 conditions of NMuMG were extracted and subject to microarray analysis

Background corr dist: KL-Divergence = 0.0249, L1-Distance = 0.0454, L2-Distance = 0.0022, Normal std = 0.8085

0.537 Kernel fit Pairwise Correlations Normal fit

Density 0.269

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 NMuMGNMuMG NMuMG cells, NMuMGreplicate cells cells, treated NMuMGreplicate cells 1 (0.153159) treatedbyNMuMG cells 211 (0.203801) days treatedby cells 11 with days treatedby 4ng/ml 11 with days by TGF-Î²,4ng/ml 11 with days [ TGF-Î²,4ng/mlfollowed minwith TGF-Î²,4ng/mlfollowed by ] TGF-Î² TGF-Î²,replicate by withdrawlTGF-Î² replicate 1[ (0.151395) withdrawlmedium for 2 another(0.134792) for another 13 days,] 13 replicate days, replicate[ 1 max(0.189566) 2 (0.167288) ] CEM 1 Ctr9 724.7 822.7 1045.5 P ( S | Z, I ) = 0.00 Rtf1 695.9 854.1 1081.9 Mean Corr = 0.30873 Paf1 321.8 478.4 481.8 Cdc73 2592.8 3257.3 4156.5 Leo1 581.6 943.3 1033.9 Wdr61 64.8 85.3 89.3 Pex2 180.7 224.4 254.5 Ddx42 946.0 963.2 1029.3 Morc2a 1199.6 1322.5 1612.7 Taf1a 222.9 329.5 345.2 Aggf1 1368.6 1620.7 1734.2 Taf1b 354.7 369.8 417.8 CEM 1 + Pak1ip1 2527.9 2708.9 3238.2 Top 10 Genes Actr6 480.3 744.3 759.8 Jade3 199.9 311.9 378.0 Cbfa2t2 582.6 617.7 649.7 Clpx 432.7 587.1 857.4

Null module GEO Series "GSE24061" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 88 -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=GSE24061 Status: Public on Sep 10 2010 Title: MAQC-II Project: Hamner data set Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 20676074 Summary & Design: Summary: The Hamner data set (endpoint A) was provided by The Hamner Institutes for Health Sciences (Research Triangle Park, NC, USA). The study objective was to apply microarray gene expression data from the lung of female B6C3F1 mice exposed to a 13-week treatment of chemicals to predict increased lung tumor incidence in the 2-year rodent cancer bioassays of the National Toxicology Program. If successful, the results may form the basis of a more efficient and economical approach for evaluating the carcinogenic activity of chemicals. Microarray analysis was performed using Affymetrix Mouse Genome 430 2.0 arrays on three to four mice per treatment group, and a total of 70 mice were analyzed and used as the MAQC-II's training set (GEO Series GSE6116). Additional data from another set of 88 mice were collected later and provided as the MAQC-II's external validation set (this Series). The training dataset had already been deposited in GEO by its provider and its accession number is GSE6116.

Overall design: 88 Samples

Background corr dist: KL-Divergence = 0.2466, L1-Distance = 0.0659, L2-Distance = 0.0092, Normal std = 0.3191

1.345 Kernel fit Pairwise Correlations Normal fit

Density 0.672

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

RT_0_13_116_ACO3_Lung_07008_Mouse430_2_RSTLRI000_2RT_0_13_117_ACO3_Lung_07008_Mouse430_2_RSTLRI000_2RT_0_13_119_ACO3_Lung_07008_Mouse430_2_RSTLRI000_2RT_0_13_120_ACO3_Lung_07008_Mouse430_2_RSTLRI000_2RT_0_13_171r_CCO6_Lung_07008_Mouse430_2_RSTLRI000_2RT_0_13_172_CCO6_Lung_07008_Mouse430_2_RSTLRI000_2RT_0_13_173_CCO6_Lung_07008_Mouse430_2_RSTLRI000_2RT_0_13_174_CCO6_Lung_07008_Mouse430_2_RSTLRI000_2RT_0_13_175r_CCO6_Lung_07008_Mouse430_2_RSTLRI000_2 (0.0152117)RT_0_13_225_CCO4_Mus_Lung_Mouse430_2_RT_HON07_MusLung (0.0188203)RT_0_13_227_CCO4_Mus_Lung_Mouse430_2_RT_HON07_MusLung (0.00782527)RT_0_13_232_CCO4_Mus_Lung_Mouse430_2_RT_HON07_MusLung (0.0205523)RT_0_13_235_CCO4_Mus_Lung_Mouse430_2_RT_HON07_MusLung (0.0151407)RT_0_13_236_ACO4_Lung_07008_Mouse430_2_RSTLRI000_2 (0.00711822)RT_0_13_237_ACO4_Lung_07008_Mouse430_2_RSTLRI000_2 (0.00773563)RT_0_13_238_ACO4_Lung_07008_Mouse430_2_RSTLRI000_2 (0.00486123)RT_0_13_239_ACO4_Lung_07008_Mouse430_2_RSTLRI000_2 (0.00486193)RT_0_13_240_ACO4_Lung_07008_Mouse430_2_RSTLRI000_2RT_0_13_258_FCO1_Mus_Lung_Mouse430_2_RT_HON07_MusLung (0.00797521)RT_0_13_260_FCO1_Mus_Lung_Mouse430_2_RT_HON07_MusLung (0.00511042)RT_0_13_263_FCO1_Mus_Lung_Mouse430_2_RT_HON07_MusLung (0.0142164)RT_0_13_266_FCO1_Mus_Lung_Mouse430_2_RT_HON07_MusLung (0.0100845) (0.0105246)RT_0_13_291_ACO5_Lung_07008_Mouse430_2_RSTLRI000_2 (0.0124099)RT_0_13_292_ACO5_Lung_07008_Mouse430_2_RSTLRI000_2 (0.00395417)RT_0_13_293_ACO5_Lung_07008_Mouse430_2_RSTLRI000_2 (0.00551344)RT_0_13_294_ACO5_Lung_07008_Mouse430_2_RSTLRI000_2 (0.0181105)RT_0_13_295_ACO5_Lung_07008_Mouse430_2_RSTLRI000_2RT_0_13_337_ACO1_Mus_Lung_Mouse430_2_RT_HON07_MusLung (0.0209666)RT_0_13_338_ACO1_Mus_Lung_Mouse430_2_RT_HON07_MusLung (0.0206325)RT_0_13_339_ACO1_Mus_Lung_Mouse430_2_RT_HON07_MusLung (0.00607249)RT_0_13_340_ACO1_Mus_Lung_Mouse430_2_RT_HON07_MusLung (0.0256564) (0.00939692)RT_0_13_51_CCO5_Lung_07008_Mouse430_2_RSTLRI000_2 (0.00515594)RT_0_13_52r_CCO5_Lung_07008_Mouse430_2_RSTLRI000_2 (0.00377295)RT_0_13_53r_CCO5_Lung_07008_Mouse430_2_RSTLRI000_2 (0.0148045)RT_0_13_54r_CCO5_Lung_07008_Mouse430_2_RSTLRI000_2 (0.0118155)RT_0_13_55r_CCO5_Lung_07008_Mouse430_2_RSTLRI000_2RT_100_13_227_ETOX-100_Lung_07008_Mouse430_2_RSTLRI000_2 (0.0176324)RT_100_13_228_ETOX-100_Lung_07008_Mouse430_2_RSTLRI000_2 (0.0140766)RT_100_13_229_ETOX-100_Lung_07008_Mouse430_2_RSTLRI000_2 (0.0117049)RT_100_13_230_ETOX-100_Lung_07008_Mouse430_2_RSTLRI000_2 (0.00888476)(0.00422514)RT_1000_13_248_TDPP_Mus_Lung_Mouse430_2_RT_HON07_MusLung (0.00690287)RT_1000_13_250_TDPP_Mus_Lung_Mouse430_2_RT_HON07_MusLung (0.00838475)RT_1000_13_252_TDPP_Mus_Lung_Mouse430_2_RT_HON07_MusLung (0.0163574)RT_1000_13_256_TDPP_Mus_Lung_Mouse430_2_RT_HON07_MusLung (0.00653855)RT_1200_13_96_PGBE-1200_Lung_07008_Mouse430_2_RSTLRI000_2RT_1200_13_97_PGBE-1200_Lung_07008_Mouse430_2_RSTLRI000_2 (0.00436938)RT_1200_13_98_PGBE-1200_Lung_07008_Mouse430_2_RSTLRI000_2 (0.00101193)RT_1200_13_99_PGBE-1200_Lung_07008_Mouse430_2_RSTLRI000_2 (0.0131039)RT_1250_13_267_TFEL_Mus_Lung_Mouse430_2_RT_HON07_MusLung (0.0224219)RT_1250_13_269_TFEL_Mus_Lung_Mouse430_2_RT_HON07_MusLung (0.0110575)RT_1250_13_272_TFEL_Mus_Lung_Mouse430_2_RT_HON07_MusLung (0.0252374)RT_1250_13_276_TFEL_Mus_Lung_Mouse430_2_RT_HON07_MusLung (0.00950445)RT_2_13_106_VANP-2_Lung_07008_Mouse430_2_RSTLRI000_2 (0.00699971)RT_2_13_107_VANP-2_Lung_07008_Mouse430_2_RSTLRI000_2 (0.016705)RT_2_13_108_VANP-2_Lung_07008_Mouse430_2_RSTLRI000_2 (0.00554688)RT_2_13_109_VANP-2_Lung_07008_Mouse430_2_RSTLRI000_2 (0.0131441)RT_20000_13_237_ABDQ_Mus_Lung_Mouse430_2_RT_HON07_MusLung (0.00588587)RT_20000_13_241_ABDQ_Mus_Lung_Mouse430_2_RT_HON07_MusLung (0.00953405)RT_20000_13_243_ABDQ_Mus_Lung_Mouse430_2_RT_HON07_MusLung (0.00575599)RT_20000_13_245_ABDQ_Mus_Lung_Mouse430_2_RT_HON07_MusLung (0.007226)RT_30_13_282_NPTH-30_Lung_07008_Mouse430_2_RSTLRI000_2 (0.00872816)(0.00277031)RT_30_13_283_NPTH-30_Lung_07008_Mouse430_2_RSTLRI000_2 (0.0129575)RT_30_13_284_NPTH-30_Lung_07008_Mouse430_2_RSTLRI000_2 (0.0242104)RT_30_13_285_NPTH-30_Lung_07008_Mouse430_2_RSTLRI000_2 (0.0269449)RT_3925_13_201_TCFM_Mus_Lung_Mouse430_2_RT_HON07_MusLungRT_3925_13_203_TCFM_Mus_Lung_Mouse430_2_RT_HON07_MusLung (0.024662)RT_3925_13_209_TCFM_Mus_Lung_Mouse430_2_RT_HON07_MusLung (0.0200833)RT_3925_13_210_TCFM_Mus_Lung_Mouse430_2_RT_HON07_MusLung (0.03329)RT_4000_13_216_MECL-4000_Lung_07008_Mouse430_2_RSTLRI000_2 (0.0226334)(0.00607419)RT_4000_13_217_MECL-4000_Lung_07008_Mouse430_2_RSTLRI000_2 (0.00560567)RT_4000_13_218_MECL-4000_Lung_07008_Mouse430_2_RSTLRI000_2 (0.00505356)RT_4000_13_220_MECL-4000_Lung_07008_Mouse430_2_RSTLRI000_2 (0.00582207)RT_50000_13_289_TFEA_Mus_Lung_Mouse430_2_RT_HON07_MusLungRT_50000_13_290_TFEA_Mus_Lung_Mouse430_2_RT_HON07_MusLung (0.0110587)RT_50000_13_292_TFEA_Mus_Lung_Mouse430_2_RT_HON07_MusLung (0.0111788)RT_50000_13_293_TFEA_Mus_Lung_Mouse430_2_RT_HON07_Mus CEM 1 Ctr9 101.3 316.9 524.2 P ( S | Z, I ) = 0.00 Rtf1 221.6 514.1 799.4 Mean Corr = 0.39110 Paf1 146.0 294.7 474.4 Cdc73 323.4 1061.3 1689.5 Leo1 34.4 240.4 462.4 Wdr61 22.7 61.1 112.9 Pex2 96.2 260.8 528.1 Ddx42 208.7 476.8 669.1 Morc2a 525.7 791.4 969.1 Taf1a 134.6 309.0 454.5 Aggf1 458.2 1286.8 1832.4 Taf1b 83.4 262.2 440.0 CEM 1 + Pak1ip1 1471.7 2001.8 3003.6 Top 10 Genes Actr6 139.5 484.3 956.9 Jade3 38.4 196.6 431.2 Cbfa2t2 530.6 727.6 1031.7 Clpx 138.9 670.8 1436.0

Null module GEO Series "GSE18308" 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=GSE18308 Status: Public on Jan 01 2010 Title: FoxOs cooperatively regulate diverse pathways governing neural stem cell homeostasis Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 19896444 Summary & Design: Summary: FoxOs cooperatively regulate diverse pathways governing neural stem cell homeostasis

Overall design: expression profile between six independant neural stem cell lines (three FoxO null and three wild type) were compared

Background corr dist: KL-Divergence = 0.0468, L1-Distance = 0.0219, L2-Distance = 0.0006, Normal std = 0.5893

0.685 Kernel fit Pairwise Correlations Normal fit

Density 0.342

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

NSC_FOXO_NULL-1NSC_FOXO_NULL-2NSC_FOXO_NULL-3 (0.0778237)NSC_FOXO_WT-1 (0.132417)NSC_FOXO_WT-2 (0.302169)NSC_FOXO_WT-3 (0.11492) (0.201403) (0.171267) [ min ] [ medium ] [ max ] CEM 1 Ctr9 1312.4 1509.8 1633.3 P ( S | Z, I ) = 0.00 Rtf1 564.5 808.9 885.3 Mean Corr = 0.31983 Paf1 300.5 439.7 471.1 Cdc73 711.3 1062.3 1282.9 Leo1 533.0 670.1 823.9 Wdr61 13.1 88.6 111.5 Pex2 193.2 266.9 322.0 Ddx42 339.8 548.3 629.8 Morc2a 975.7 1093.0 1314.1 Taf1a 119.3 201.2 278.0 Aggf1 1314.2 1717.1 2020.6 Taf1b 341.8 399.2 536.5 CEM 1 + Pak1ip1 951.7 1204.0 1413.7 Top 10 Genes Actr6 686.7 854.7 943.2 Jade3 169.8 187.0 240.8 Cbfa2t2 876.9 1088.7 1095.5 Clpx 384.2 534.1 643.4

Null module GEO Series "GSE4288" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 36 -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=GSE4288 Status: Public on Feb 05 2008 Title: Polysomal, free mRNP, and total cellular mRNA of J774.1 before and after LPS stimulation Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 18230670 Summary & Design: Summary: Bacterial lipopolysaccharide(LPS) dramatically activates macrophages. So far, dozen of papers indicated that many proinflammatory molecules are transcriptionaly regulated during response. Despite of this,translational regulation is not fully elucidated especially in a comprehensive fashion. In this series, we investigated expression profiles of translation active (polysome) inactive (free mRNP) mRNAs of a typical mouse macrophage cell line, J774.1. Moreover, we also measured total cellular RNA level as a reference.

Keywords: time-course

Overall design: Triplicates for each time points are included.

Background corr dist: KL-Divergence = 0.1306, L1-Distance = 0.0311, L2-Distance = 0.0019, Normal std = 0.3960

1.007 Kernel fit Pairwise Correlations Normal fit

Density 0.504

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

PolysomePolysome of J774-intact-rep1Polysome of J774-intact-rep2Polysome of J774-intact-rep3 Polysome(0.0231415) of J774-LPS Polysome(0.0293679) of J774-LPS Polysome(0.00261403) 1hr-rep1 of J774-LPSPolysome 1hr-rep2 (0.00740558) of J774-LPSPolysome 1hr-rep3 (0.0164483) of J774-LPSPolysome 2hr-rep1 (0.00901475) of J774-LPSPolysome 2hr-rep2 (0.0262728) of J774-LPSPolysome 2hr-rep3 (0.0353681) of J774-LPSFree 4hr-rep1 (0.0163812) of mRNP J774-LPSFree 4hr-rep2 (0.0417617) ofmRNP J774-intact-rep1Free 4hr-rep3 (0.0498897) ofmRNP J774-intact-rep2Free (0.0189396) ofmRNP J774-intact-rep3Free (0.0199096) ofmRNP J774-LPSFree (0.0232408) ofmRNP J774-LPSFree (0.0238777) 1hr-rep1 ofmRNP J774-LPSFree 1hr-rep2 (0.0322721) ofmRNP J774-LPSFree 1hr-rep3 (0.0359653) ofmRNP J774-LPSFree 2hr-rep1 (0.0682956) ofmRNP J774-LPSFree 2hr-rep2 (0.039019) ofmRNP J774-LPSFree 2hr-rep3 (0.0413903) ofmRNP J774-LPSTotal 4hr-rep1 (0.0514812) of cellular J774-LPSTotal 4hr-rep2 (0.0349693) cellularmRNATotal 4hr-rep3 (0.049136) cellularofmRNATotal J774-intact-rep1 (0.0397697) cellularofmRNATotal J774-intact-rep2 cellularofmRNATotal J774-intact-rep3 (0.0197891) cellularofmRNATotal J774-LPS (0.00711144) cellularofmRNATotal J774-LPS (0.0270681) 1hr-rep1 cellularofmRNATotal J774-LPS 1hr-rep2 (0.0126172) cellularofmRNATotal J774-LPS 1hr-rep3 (0.00621954) cellularofmRNATotal J774-LPS 2hr-rep1 (0.0147435) cellularofmRNATotal J774-LPS 2hr-rep2 (0.0117902) cellularofmRNA J774-LPS 2hr-rep3 (0.0301952) ofmRNA J774-LPS 4hr-rep1 (0.0299749) of J774-LPS 4hr-rep2 (0.0265319)[ min4hr-rep3 (0.0302733) ](0.0477539) [ medium ] [ max ] CEM 1 Ctr9 7.0 282.0 717.8 P ( S | Z, I ) = 0.00 Rtf1 124.1 633.6 900.2 Mean Corr = 0.34370 Paf1 180.6 584.0 1092.3 Cdc73 258.4 2013.9 3731.6 Leo1 22.6 928.3 1658.8 Wdr61 4.3 58.7 169.3 Pex2 2.0 98.4 187.2 Ddx42 224.9 706.7 1050.1 Morc2a 465.0 1146.3 1466.8 Taf1a 73.7 286.8 495.8 Aggf1 506.8 1618.5 2414.4 Taf1b 187.2 634.5 1079.6 CEM 1 + Pak1ip1 2647.1 4288.5 7685.9 Top 10 Genes Actr6 118.7 652.7 1325.0 Jade3 2.9 77.7 184.8 Cbfa2t2 10.7 483.2 729.8 Clpx 99.8 744.1 1375.3

Null module GEO Series "GSE36513" 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=GSE36513 Status: Public on Feb 18 2013 Title: Long noncoding RNA as regulatory switch of protein turnover Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 24521543 Summary & Design: Summary: Long intervening noncoding RNAs (lincRNAs) are prevalent genes with poorly understood functions. Here we discover a pathway of lincRNA-regulated proteolysis. The enhancer-like lincRNA HOTTIP extends the half-life of its binding protein WDR5, a subunit of the MLL H3K4 methylase complex, resulting in increased chromatin occupancy and gene activation. LincRNA-mediated stabilization requires direct RNA-protein interaction in a long RNA context, and blocks turnover at a step after target protein poly-ubiquitination. We elucidate the lincRNA binding interface on WDR5. A WDR5 mutant that selectively abrogates lincRNA binding becomes unstable, and is defective in gene activation, maintenance of histone H3 lysine 4 trimethylation, and embryonic stem cell self renewal. The ability to modulate protein turnover may allow lincRNAs to control the lifespan of molecular interactions at chromatin and elsewhere, broadening their scope in epigenetics and cell fate control.

Overall design: Gene expression analysis: To establish a differentiation signature for mouse V6.5 ES cells infected with anti mouse WDR5 shRNA, rescued with doxycycline inducible WDR5 WT or WDR5 F266A, total RNA was isolated in biologic duplicate from cells in different conditions and hybridized to Affymetrix Mouse 430 2.0 arrays.

Background corr dist: KL-Divergence = 0.0512, L1-Distance = 0.0247, L2-Distance = 0.0007, Normal std = 0.5684

0.721 Kernel fit Pairwise Correlations Normal fit

Density 0.360

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

WDR5_WT_dox_rep1WDR5_WT_dox_rep2WDR5_WT_NOdox_rep1 (0.329031)WDR5_WT_NOdox_rep2 (0.108365)WDR5_F266A_dox_rep1WDR5_F266A_dox_rep2 (0.0712337)WDR5_F266A_NOdox_rep1 (0.17403)WDR5_F266A_NOdox_rep2 (0.176164) (0.023564) (0.0850398) (0.0325719)[ min ] [ medium ] [ max ] CEM 1 Ctr9 486.8 669.9 863.4 P ( S | Z, I ) = 0.00 Rtf1 828.5 1010.0 1163.1 Mean Corr = 0.43509 Paf1 517.8 705.3 752.2 Cdc73 1948.5 2535.9 3003.8 Leo1 1066.9 1374.7 1463.7 Wdr61 197.2 238.1 274.6 Pex2 128.9 141.5 153.5 Ddx42 941.8 1075.4 1124.2 Morc2a 1468.1 1680.2 1798.0 Taf1a 306.3 387.9 416.7 Aggf1 2714.4 3340.1 3561.5 Taf1b 351.1 590.5 685.2 CEM 1 + Pak1ip1 4441.2 4972.8 5219.3 Top 10 Genes Actr6 1185.4 1315.8 1663.5 Jade3 813.0 1055.3 1158.3 Cbfa2t2 1483.1 2105.7 2314.1 Clpx 886.2 1175.1 1243.3

Null module GEO Series "GSE12748" 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=GSE12748 Status: Public on Sep 10 2009 Title: Weighted Gene Coexpression Network Analysis Identifies Biomarkers in Glycerol Kinase Deficient Mice Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 19546021 Summary & Design: Summary: Symptomatic glycerol kinase deficiency (GKD) is associated with episodic metabolic and central nervous system deterioration. We report here the first application of Weighted Gene Co-Expression Network Analysis (WGCNA) to investigate a knockout (KO) murine model of a human genetic disease. WGCNA identified networks and key hub transcripts from liver mRNA of glycerol kinase (Gyk) KO and wild type (WT) mice. Day of life 1 (dol1) samples from KO mice contained a network module enriched for organic acid metabolism before Gyk KO mice develop organic acidemia and die on dol3-4 and the module containing Gyk was enriched with apoptotic genes. Roles for the highly connected Acot, Psat and Plk3 transcripts were confirmed in cell cultures and subsequently validated by causality testing. We provide evidence that GK may have an apoptotic moonlighting role that is lost in GKD. This systems biology strategy has improved our understanding of GKD pathogenesis and suggests possible treatments.

Overall design: Male WT and KO mouse pups were sacrificed on day of life (dol) 1 and each liver was harvested. Total RNA from 4 KO and 3 WT livers was isolated individually. Affymetrix mus 430 2.0 GeneChips were used to analyze differences in liver gene expression between KO and WT mice. Dol1 and 3 Gyk KO mice represent different disease states. Dol 1 was chosen because mice are phenotypically asymptomatic with respect to Glycerol Kinase Deficiency (GKD) and allowed us to look at alterations that occur before the overt disease state. Dol 3 mice are phenotypically symptomatic with respect to GKD.

Background corr dist: KL-Divergence = 0.0602, L1-Distance = 0.0183, L2-Distance = 0.0005, Normal std = 0.5298

0.753 Kernel fit Pairwise Correlations Normal fit

Density 0.376

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

dol_1_liver_wildtype1dol_1_liver_wildtype2dol_1_liver_wildtype3 dol_1_liver_KnockOut1(0.366234) dol_1_liver_KnockOut2(0.0394013) dol_1_liver_KnockOut3(0.0113958)dol_1_liver_KnockOut4 (0.144016) (0.169881) (0.120019) (0.149052)[ min ] [ medium ] [ max ] CEM 1 Ctr9 592.3 690.1 868.7 P ( S | Z, I ) = 0.00 Rtf1 633.8 792.4 1061.0 Mean Corr = 0.30331 Paf1 254.3 318.5 504.6 Cdc73 909.8 1235.1 1514.6 Leo1 398.4 427.8 486.2 Wdr61 70.2 121.4 207.9 Pex2 334.1 418.1 473.4 Ddx42 455.5 699.7 885.0 Morc2a 675.6 820.6 1143.5 Taf1a 145.7 190.7 222.7 Aggf1 899.3 1228.9 1466.3 Taf1b 167.8 205.9 329.8 CEM 1 + Pak1ip1 1899.0 2051.3 2408.6 Top 10 Genes Actr6 472.7 550.0 774.5 Jade3 113.7 209.4 268.5 Cbfa2t2 511.9 532.9 695.6 Clpx 1910.4 3944.6 4764.1

Null module GEO Series "GSE10989" 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=GSE10989 Status: Public on Dec 22 2010 Title: Expression data of cystic renal epithelial tissue from mice deficient for fumarate hydratase. Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: Fumarate hydratase (FH) mutations cause hereditary leiomyomatosis and renal cell cancer (HLRCC). We have conditionally inactivated the murine ortholog (Fh1) in renal tubular epithelial cells in order to generate an in vivo model of HLRCC. Fh1 knockout mice recapitulates important aspects of HLRCC including the development of renal cysts that overexpress hypoxia inducible factor alpha (Hifa) and Hif-target genes.

We used microarrays to detail the global programme of gene expression underlying cyst development in Fh1 knockout mice and identified distinct classes of up-regulated genes during this process.

Keywords: gene expression, comparison (wild-type n=3 vs knockout n=3)

Overall design: Renal epithelial tissue was macro-dissected from Fh1 knockout mice and sex-matched litter mate control disease-free animals for RNA extraction and hybridization on Affymetrix microarrays.

Background corr dist: KL-Divergence = 0.0186, L1-Distance = 0.0758, L2-Distance = 0.0076, Normal std = 0.9701

0.411 Kernel fit Pairwise Correlations Normal fit

Density 0.206

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

wild-typewild-type mousewild-type kidneymouseknockout -kidneymouse 1 (0.0632484)knockout -kidneymouse 2 (0.163163)knockout -kidneymouse 3 (0.314356) -kidneymouse 1 (0.157803) -kidney 2 (0.184937) - 3 (0.116493)[ min ] [ medium ] [ max ] CEM 1 Ctr9 479.4 593.3 627.0 P ( S | Z, I ) = 0.00 Rtf1 579.0 743.7 850.6 Mean Corr = 0.37356 Paf1 404.2 458.0 480.8 Cdc73 860.8 1075.0 1123.1 Leo1 395.7 546.4 567.7 Wdr61 43.6 52.4 63.7 Pex2 152.3 176.6 189.9 Ddx42 395.7 484.7 544.4 Morc2a 557.3 647.1 700.7 Taf1a 210.6 282.4 330.3 Aggf1 924.9 1182.6 1269.4 Taf1b 279.6 312.0 338.2 CEM 1 + Pak1ip1 1582.9 1984.8 2080.7 Top 10 Genes Actr6 320.5 411.4 549.4 Jade3 127.0 180.9 222.4 Cbfa2t2 615.1 633.3 674.4 Clpx 1885.1 3315.8 4052.9

Null module 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 (0.0454169)liver-2BE-4hours-rep 2 (0.0313413)liver-2BE-4hours-rep 3 (0.0270662) 1liver-2BE-4hours-rep (0.0264958) 2spleen-vehicle-4hours-rep (0.0352487) 3spleen-vehicle-4hours-rep (0.0263596) 4spleen-vehicle-4hours-rep (0.032966)spleen-vehicle-4hours-rep 1 (0.0189353)spleen-2BE-4hours-rep 2 (0.0402019)spleen-2BE-4hours-rep 3 (0.0261205)spleen-2BE-4hours-rep 4 (0.015983)spleen-2BE-4hours-rep 1 (0.0134173)liver-vehicle-7days-rep 2 (0.0200068)liver-vehicle-7days-rep 3 (0.0210137)liver-vehicle-7days-rep 4 (0.0149619)liver-vehicle-7days-rep 1 (0.0276694)liver-2BE-7days-rep 2 (0.0314059)liver-2BE-7days-rep 3 (0.0297379)liver-2BE-7days-rep 4 (0.0240199) 1 (0.028257)liver-2BE-7days-rep 2 (0.0406254)liver-2BE-7days-rep 3 (0.0276786)bone 4marrow-vehicle-7days-rep (0.0301715)bone 5marrow-vehicle-7days-rep (0.0410306)bone marrow-vehicle-7days-repbone marrow-vehicle-7days-repbone 1 (0.0117089) marrow-vehicle-7days-repbone 2 (0.0148964) marrow-2BE-7days-repbone 3 (0.0116898) marrow-2BE-7days-repbone 4 (0.0153175) marrow-2BE-7days-repbone 5 (0.0101783) marrow-2BE-7days-rep 1bone (0.0158668) marrow-2BE-7days-rep 2spleen-vehicle-7days-rep (0.0283844) 3spleen-vehicle-7days-rep (0.0115029) 4spleen-vehicle-7days-rep (0.021562) 5spleen-vehicle-7days-rep (0.0134579) 1 (0.0315367)spleen-vehicle-7days-rep 2 (0.019026)spleen-2BE-7days-rep 3 (0.012042)spleen-2BE-7days-rep 4 (0.0173103)spleen-2BE-7days-rep 5 (0.033073) spleen-2BE-7days-rep1 (0.0117125) spleen-2BE-7days-rep2 (0.00836271) 3 (0.00839299) 4 (0.00952117) 5 (0.0183264)[ min ] [ medium ] [ max ] CEM 1 Ctr9 514.5 771.7 1030.6 P ( S | Z, I ) = 0.00 Rtf1 466.2 921.6 1128.7 Mean Corr = 0.40125 Paf1 412.3 501.3 707.1 Cdc73 499.7 884.4 1213.6 Leo1 270.8 404.8 494.6 Wdr61 50.3 195.6 272.8 Pex2 166.9 317.9 455.9 Ddx42 331.4 642.1 880.2 Morc2a 418.9 625.8 1082.2 Taf1a 126.0 207.0 391.0 Aggf1 1136.1 1566.1 1929.5 Taf1b 144.7 342.3 459.6 CEM 1 + Pak1ip1 1529.2 2123.2 2628.0 Top 10 Genes Actr6 419.9 595.4 987.9 Jade3 52.3 154.0 346.9 Cbfa2t2 381.8 518.0 650.9 Clpx 710.1 983.8 13155.6

Null module GEO Series "GSE39770" 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=GSE39770 Status: Public on Aug 01 2012 Title: Expression data from embryonic stem cells following siRNA transfection of UPS members [Differentiation_ES] Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 23103054 Summary & Design: Summary: While transcriptional regulation of stem cell self-renewal and differentiation has been extensively studied, only a small number of studies have addressed the roles for post-translational modifications in these processes. A key mechanism of post-translational modification is ubiquitination by the ubiquitin-proteasome system (UPS). Using UPS-targeted RNAi screens, we identify novel regulators of pluripotency and differentiation. We focus on two of these proteins, the deubiquitinating enzyme, Psmd14, and the E3 ligase, Fbxw7, and characterize their importance in ES cell pluripotency and cellular reprogramming.

Overall design: Embryonic stem cells were reverse transfected with siRNA, and differentiated for 48hrs in conditions with retinoic acid, 48 hrs post transfection cells were isloated for RNA extraction and hybridization on Affymetrix microarrays

Background corr dist: KL-Divergence = 0.0856, L1-Distance = 0.0226, L2-Distance = 0.0006, Normal std = 0.4634

0.861 Kernel fit Pairwise Correlations Normal fit

Density 0.430

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

siNonTargetsiNonTarget replicate1siSox17 replicate2siSox17 (0.196858)replicate1siFbxw7 (0.0772643)replicate2 (0.0727313)siFbxw7 replicate1 (0.0331519)siSocs3 replicate2 (0.162146)siSocs3 replicate1 (0.02646)siRnf31 replicate2 (0.121001)siRnf31 replicate1 (0.163158) replicate2 (0.0714946) (0.0757345)[ min ] [ medium ] [ max ] CEM 1 Ctr9 513.4 767.2 1038.0 P ( S | Z, I ) = 0.00 Rtf1 879.6 980.3 1157.9 Mean Corr = 0.23897 Paf1 503.1 719.0 812.7 Cdc73 2212.8 2570.2 3123.6 Leo1 1145.5 1379.4 1518.4 Wdr61 76.1 116.4 164.1 Pex2 77.4 87.8 96.3 Ddx42 867.5 1128.7 1298.1 Morc2a 1861.3 2007.3 2234.1 Taf1a 277.9 311.4 357.6 Aggf1 2608.2 3218.5 3965.3 Taf1b 526.1 590.9 717.0 CEM 1 + Pak1ip1 2839.2 3626.6 3952.4 Top 10 Genes Actr6 837.1 927.0 1049.2 Jade3 452.9 601.3 679.2 Cbfa2t2 797.9 974.4 1105.4 Clpx 926.9 1025.0 1163.7

Null module GEO Series "GSE30176" 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=GSE30176 Status: Public on Jul 19 2011 Title: Retinoic acid (RA) induction time-course to profile gene expression during mES cell differentiation. Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21764852 Summary & Design: Summary: Murine ES cell gene expression before RA induction are used to compare gene expression for time-points of 2, 4, 6hrs post-induction.

Overall design: KH2 ES Cell RA Differentiation Time-course

Background corr dist: KL-Divergence = 0.0719, L1-Distance = 0.0287, L2-Distance = 0.0010, Normal std = 0.5040

0.814 Kernel fit Pairwise Correlations Normal fit

Density 0.407

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-A (0.0890679)WT-B (0.0462345)WT-C (0.100489)2HR-A (0.0557659)2HR-B (0.110791)2HR-C (0.0839613)4HR-A (0.105272)4HR-B (0.0589562)4HR-C (0.0417603)6HR-A (0.105483)6HR-B (0.0857137)6HR-C (0.116505) [ min ] [ medium ] [ max ] CEM 1 Ctr9 244.1 306.0 343.1 P ( S | Z, I ) = 0.00 Rtf1 882.4 960.2 1039.7 Mean Corr = 0.36844 Paf1 594.5 782.8 950.9 Cdc73 2943.5 4132.5 4607.7 Leo1 814.1 1010.6 1132.7 Wdr61 127.3 141.8 184.8 Pex2 127.1 141.2 167.8 Ddx42 751.8 872.9 1005.8 Morc2a 1308.4 1715.5 1864.8 Taf1a 390.9 534.0 591.8 Aggf1 3603.8 4107.9 4365.4 Taf1b 842.8 1210.7 1312.1 CEM 1 + Pak1ip1 2721.5 3083.8 3508.1 Top 10 Genes Actr6 962.0 1065.4 1229.0 Jade3 350.0 428.8 516.7 Cbfa2t2 1787.2 2348.9 2831.3 Clpx 998.6 1133.4 1347.1

Null module GEO Series "GSE2527" 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=GSE2527 Status: Public on May 06 2005 Title: Gata-1 Knock Down - Wild Type Megakaryocyte Gene Expression Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 15860665 Summary & Design: Summary: Hematopoietic progenitor cells were isolated from 13.5 day mouse fetal livers by lineage depletion and expanded for three days. Fetal livers were isolated from both wild type and Gata-1 knock embryos. Gata-1 knock embryos contain a deletion of the Gata-1 promoter sequence that results in undetectable levels of Gata-1 protein specifically in the megakaryocyte lineage. Following progenitor outgrowth megakaryocytes were enriched in a differentiation media for three days and isolated on a discontinuous BSA gradient. The resulting megakaryocytes were >90% pure as determined by acetylcholinesterase staining. These cells were lysed in Trizol and the resulting RNA was used for hybridization.

Keywords = Gata-1

Keywords = Megakaryocytes

Keywords: other

Overall design:

Background corr dist: KL-Divergence = 0.0240, L1-Distance = 0.0329, L2-Distance = 0.0011, Normal std = 0.7666

0.546 Kernel fit Pairwise Correlations Normal fit

Density 0.273

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

Gata-1 KnockGata-1 DownKnockGata-1 A Down KnockGata-1(0.221222) B Down WildGata-1(0.160412) Type C WildGata-1(0.176587) A Type(0.124494) Wild B Type(0.204937) C (0.112348)[ min ] [ medium ] [ max ] CEM 1 Ctr9 472.7 784.4 905.4 P ( S | Z, I ) = 0.00 Rtf1 806.9 915.8 977.3 Mean Corr = 0.26099 Paf1 489.4 584.7 624.8 Cdc73 1577.6 1825.4 1994.7 Leo1 646.8 855.8 913.7 Wdr61 36.3 89.9 120.2 Pex2 201.1 266.5 424.1 Ddx42 386.5 552.5 604.8 Morc2a 870.6 1059.3 1387.1 Taf1a 114.2 254.4 273.8 Aggf1 1050.5 1243.7 1690.5 Taf1b 460.5 563.1 620.8 CEM 1 + Pak1ip1 3249.7 3575.6 3894.2 Top 10 Genes Actr6 738.3 816.0 1018.5 Jade3 146.2 233.5 258.4 Cbfa2t2 522.1 614.1 766.9 Clpx 453.5 588.7 644.3

Null module 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 (0.0622165)neuroninduced rep2 Tcells (0.0445789)neuroninduced FoxA1Treg rep3 (0.0351548)Treginduced FoxA1Treg rep1rep1Treg FoxA1Treg (0.067436)(0.0876337) rep2rep2Treg (0.0932795)(0.0770457) rep3rep3IFN-beta (0.0466706)(0.0524327)IFN-beta inducedIFN-beta induced FoxA1Treg induced FoxA1Treg rep1 FoxA1Treg (0.121933) rep2 (0.133168) rep3[ min (0.17845) ] [ medium ] [ max ] CEM 1 Ctr9 258.3 412.7 522.6 P ( S | Z, I ) = 0.00 Rtf1 1543.2 1695.1 1941.0 Mean Corr = 0.41235 Paf1 422.6 452.5 515.5 Cdc73 1576.2 2161.2 2351.6 Leo1 282.2 417.0 500.8 Wdr61 62.4 84.2 105.2 Pex2 89.7 224.1 272.6 Ddx42 534.3 846.2 873.8 Morc2a 535.0 634.6 717.3 Taf1a 128.1 173.2 199.9 Aggf1 1765.6 2083.6 2241.8 Taf1b 595.5 901.0 975.9 CEM 1 + Pak1ip1 2337.3 2917.1 3056.3 Top 10 Genes Actr6 503.2 572.3 672.7 Jade3 76.2 113.0 125.5 Cbfa2t2 415.7 487.7 642.7 Clpx 545.1 582.0 710.9

Null module GEO Series "GSE38031" 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=GSE38031 Status: Public on Jul 25 2013 Title: DNA damage-induced differentiation of NSC Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 24052948 Summary & Design: Summary: Murine ES-derived neural stem cells (NSC) were not irradiated (ctrl) or irradiated with 10Gy and cultured for 7 days (irr).

The goal was to study the gene expression changes in NSC at d7 after irradiation.

Overall design: Total RNA was extracted from 4 ctrl and 4 irr samples (biological quadruplicates).

Background corr dist: KL-Divergence = 0.0114, L1-Distance = 0.0339, L2-Distance = 0.0011, Normal std = 0.9128

0.456 Kernel fit Pairwise Correlations Normal fit

Density 0.228

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_rep1ctrl_rep2 (0.2584)ctrl_rep3 (0.145151)ctrl_rep4 (0.079102)irr_rep1 (0.0719856)irr_rep2 (0.0730377)irr_rep3 (0.0579881)irr_rep4 (0.116791) (0.197546) [ min ] [ medium ] [ max ] CEM 1 Ctr9 395.7 614.6 746.7 P ( S | Z, I ) = 0.00 Rtf1 977.0 1416.5 1571.1 Mean Corr = 0.18475 Paf1 526.8 577.3 605.5 Cdc73 1265.3 1694.5 1783.8 Leo1 839.9 941.0 1040.5 Wdr61 40.7 52.3 55.2 Pex2 105.8 109.2 120.9 Ddx42 679.1 768.9 811.3 Morc2a 1145.0 1263.8 1318.6 Taf1a 214.2 238.4 266.4 Aggf1 2043.4 2154.1 2230.5 Taf1b 342.2 394.6 428.2 CEM 1 + Pak1ip1 2758.5 3147.1 3405.6 Top 10 Genes Actr6 697.1 755.7 912.0 Jade3 188.8 234.6 290.7 Cbfa2t2 618.8 685.0 730.8 Clpx 657.0 753.8 884.7

Null module GEO Series "GSE55809" 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=GSE55809 Status: Public on Mar 12 2014 Title: Cell autonomous and non-autonomous interactions of a western-style diet and the vitamin D receptor in intestinal homeostasis and tumorigenesis Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: These data suggest that co-culture with macrophages increases expression of NDRG-1 in epithelial cell lines. The finding is confirmed in 2 human epithelial cell lines, and in tissue derived from mice genetically and dietetically altered to increase macrophage infiltration of the small and large intestinal epithelium. NDRG1 is identified as a potential mediator of macrophage effects on tumorigenesis in the large and small intestine.

Array data is part of a larger study involving the effects of Vitamin D, in concert with macrophages, on intestinal homeostasis and tumorigenesis.

Overall design: Cells from mouse epithelial cell line CT26 were cultured either alone, or with RAW macrophages in a system which allowed no physical contact but exchange of soluble factors between the cell types. The experiment was peformed twice.

Background corr dist: KL-Divergence = 0.0280, L1-Distance = 0.0347, L2-Distance = 0.0014, Normal std = 0.7125

0.596 Kernel fit Pairwise Correlations Normal fit

Density 0.298

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

CT26_cells_alone_rep1CT26_macrophage_coculture_rep1RAW_macrophage_alone_rep1RAW_macrophage_CT26_coculture_rep1 (0.0831259)CT26_cells_alone_rep2CT26_macrophage_coculture_rep2 (0.0993322)RAW_macrophage_alone_rep2 (0.175614)RAW_macrophage_CT26_coculture_rep2 (0.101659) (0.164001) (0.167515) (0.08395)[ min ](0.124803) [ medium ] [ max ] CEM 1 Ctr9 508.5 682.1 838.6 P ( S | Z, I ) = 0.00 Rtf1 627.5 912.8 1327.9 Mean Corr = 0.20638 Paf1 373.4 544.4 660.9 Cdc73 1699.5 2336.4 2464.3 Leo1 522.7 843.8 885.8 Wdr61 66.5 110.8 156.2 Pex2 142.7 194.1 233.6 Ddx42 486.4 555.5 657.3 Morc2a 989.3 1098.8 1295.4 Taf1a 177.9 374.7 451.6 Aggf1 1441.1 2202.6 2841.5 Taf1b 338.5 494.5 822.7 CEM 1 + Pak1ip1 2759.8 3992.3 5147.7 Top 10 Genes Actr6 597.8 845.0 1197.5 Jade3 195.0 220.2 244.0 Cbfa2t2 459.2 804.5 938.2 Clpx 708.9 1099.4 1546.7

Null module GEO Series "GSE54207" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 9 -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=GSE54207 Status: Public on Jan 18 2014 Title: Expression data from mouse limb tendon cells during development. Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: We have undertaken a screen of mouse limb tendon cells in order to identify molecular pathways involved in tendon development. Mouse limb tendon cells were isolated based on Scleraxis (Scx) expression at different stages of development: E11.5, E12.5 and E14.5

Microarray comparisons were carried out between tendon progenitor and differentiated stages.

Overall design: Forelimbs from E11.5, E12.5 and E14.5 Scx-GFP embryos were collected and dissociated with trypsin to obtain cell suspensions. Scx-positive tendon cells were isolated by FACS. RNA was extracted and Fragmented biotin-labelled cRNA samples were hybridized on Affymetrix Gene Chip Mouse Genome 430 2.0 arrays.

Background corr dist: KL-Divergence = 0.0661, L1-Distance = 0.0279, L2-Distance = 0.0010, Normal std = 0.5212

0.781 Kernel fit Pairwise Correlations Normal fit

Density 0.391

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

E11.5 AE12.5 (0.142989) AE14.5 (0.0734906) AE11.5 (0.173991) BE12.5 (0.242896) BE14.5 (0.0157194) BE11.5 (0.100972) CE12.5 (0.0556915) CE14.5 (0.0268564) C (0.167394) [ min ] [ medium ] [ max ] CEM 1 Ctr9 304.7 490.2 580.1 P ( S | Z, I ) = 0.00 Rtf1 1197.7 1653.5 2065.0 Mean Corr = 0.23444 Paf1 488.7 590.6 757.7 Cdc73 1278.9 1781.3 2115.3 Leo1 593.5 886.1 1125.8 Wdr61 100.3 164.8 281.8 Pex2 85.9 132.8 233.8 Ddx42 792.3 1012.3 1228.2 Morc2a 1689.1 2007.8 2358.6 Taf1a 294.6 417.7 508.4 Aggf1 1430.1 2178.4 2715.1 Taf1b 292.9 364.3 472.1 CEM 1 + Pak1ip1 974.7 1344.4 1779.0 Top 10 Genes Actr6 780.7 1037.9 1236.2 Jade3 160.4 347.5 519.3 Cbfa2t2 1360.9 1589.0 2024.6 Clpx 805.1 1129.5 1629.3

Null module GEO Series "GSE8488" 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=GSE8488 Status: Public on Jan 31 2008 Title: Inhibitor Trials Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 20111593 Summary & Design: Summary: Objectives: To identify similarities and differences in gene expression data in the MEK/ERK and PI3K pathways and to determine how histone modification affects these same pathways.

Goal: To identify and functionally characterize novel targets of these signaling pathways in the context of chondrocyte differentiation.

Keywords: Teatment, signaling, one-colour array, signaling pathway comparison

Overall design: A total of 15 genechips were analyzed between 4 treatments and the vehicle (DMSO) control. Three biological replicates per treatment were executed.

Background corr dist: KL-Divergence = 0.0412, L1-Distance = 0.0165, L2-Distance = 0.0004, Normal std = 0.5968

0.668 Kernel fit Pairwise Correlations Normal fit

Density 0.334

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

DMSO_1DMSO_2 (0.0654008)DMSO_3 (0.0518083)LY_1 (0.0308877) (0.0382408)LY_2 (0.0137607)LY_3 (0.0589104)UO126_1UO126_2 (0.0404167)UO126_3 (0.0629972)TSA_1 (0.0114362) (0.258342)TSA_2 (0.167879)TSA_3 (0.141788)SB90_1SB90_2 (0.0252973)SB90_3 (0.012319) (0.0205155) [ min ] [ medium ] [ max ] CEM 1 Ctr9 484.9 567.2 1227.3 P ( S | Z, I ) = 0.00 Rtf1 638.8 775.5 1056.9 Mean Corr = 0.06038 Paf1 423.2 475.7 893.3 Cdc73 1137.9 1396.3 1666.9 Leo1 623.6 685.9 997.4 Wdr61 49.8 56.9 67.8 Pex2 299.5 348.5 420.5 Ddx42 470.4 554.7 638.8 Morc2a 822.5 982.7 1129.5 Taf1a 152.0 198.8 224.7 Aggf1 753.6 921.8 1139.7 Taf1b 471.6 551.8 638.7 CEM 1 + Pak1ip1 1832.2 2118.5 3515.3 Top 10 Genes Actr6 434.0 556.2 665.1 Jade3 134.6 157.2 222.1 Cbfa2t2 763.4 924.9 1326.2 Clpx 687.0 819.0 1200.3

Null module GEO Series "GSE39082" 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=GSE39082 Status: Public on Jul 04 2012 Title: Expression data from cultured c-Kit+Sca-1+Lin- (KSL)cells Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: The Notch signaling pathway plays a critical role in regulating the proliferation and differentiation of stem and progenitor cells including hematopoietic stem and progenitor cells (HSPCs). Notch receptors and ligands are expressed in BM stromal and hematopoietic cells. A large body of evidence has demonstrated that activating Notch signaling enhances HSCs self-renewal and facilitates its expansion ex vivo. We report that an endothelium-targeted soluble Notch ligand, the DSL domain of mouse Delta-like 1 fused with a RGD motif (mD1R), efficiently promotes the expansion ex vivo of mouse bone marrow HSPCs in a Notch signaling and endocytosis dependent manner. HSPCs expanded in the presence of mD1R kept long-term HSPC repopulation capacity.

We used microarrays to compare the gene expression profiles of HSPCs expanded in the presence of PBS and mD1R.

Overall design: KSL cells were plated on Human umbilical vein endothelial cells (HUVECs) and cultured in a serum-free medium supplemented with a cocktail containing 5 types of mouse cytokines (m5GF) in the presence of PBS or mD1R for 7 days. Then KSL cells were sorted from these cultured hematopoietic cells for RNA extraction and hybridization on Affymetrix microarrays. The experiments were repeated 3 times.

Background corr dist: KL-Divergence = 0.0342, L1-Distance = 0.0284, L2-Distance = 0.0010, Normal std = 0.6605

0.620 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

PBS-expandedPBS-expanded PBS-expandedKSL cells, mD1R-expandedKSL biological cells, mD1R-expandedKSL biological cells, rep1mD1R-expanded KSL biological(0.26076) rep2cells, KSL (0.0448861) biological rep3cells, KSL (0.0932024) biological cells, rep1 biological(0.192516)[ rep2 min (0.274796) rep3 ] (0.133839) [ medium ] [ max ] CEM 1 Ctr9 213.2 352.0 538.9 P ( S | Z, I ) = 0.00 Rtf1 714.6 869.4 875.7 Mean Corr = 0.40193 Paf1 327.9 574.6 669.0 Cdc73 1056.7 1486.4 1584.3 Leo1 265.7 410.4 537.8 Wdr61 45.2 77.6 119.7 Pex2 72.2 128.3 142.5 Ddx42 594.8 724.4 834.0 Morc2a 554.2 645.0 767.0 Taf1a 102.5 184.7 207.2 Aggf1 1648.6 2204.5 2483.4 Taf1b 292.6 528.6 631.7 CEM 1 + Pak1ip1 2369.3 2738.9 2967.9 Top 10 Genes Actr6 692.5 899.8 1138.0 Jade3 106.9 150.7 228.2 Cbfa2t2 516.9 704.0 816.0 Clpx 702.4 788.3 939.8

Null module GEO Series "GSE15767" 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=GSE15767 Status: Public on Jun 05 2009 Title: Heterogeneity of LN resident macrophage Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 19503106 Summary & Design: Summary: LN resident macrophages lining the lymphatic sinuses play critical roles in antigen capture and presentation as well as degradation.

We used microarray to examine global gene expression profiles to compare SCS and med macrophages to determine the underlying molecular basis of their differential handling of antigens.

Overall design: Primary SCS and med macrophages were isolated and purified from LNs by flourescence-activated cell sorting and RNA extracted, amplified and hybridized for Affymetrix analysis.

Background corr dist: KL-Divergence = 0.0309, L1-Distance = 0.0215, L2-Distance = 0.0005, Normal std = 0.6738

0.602 Kernel fit Pairwise Correlations Normal fit

Density 0.301

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

med macs-LN-1med macs-LN-2med (0.2187) macs-LN-3SCS (0.150144) macs-LN-1SCS (0.16743) macs-LN-2SCS (0.231985) macs-LN-3 (0.131035) (0.100706) [ min ] [ medium ] [ max ] CEM 1 Ctr9 128.3 181.0 191.0 P ( S | Z, I ) = 0.00 Rtf1 975.5 1228.6 1342.6 Mean Corr = 0.37832 Paf1 2855.2 3318.2 3832.6 Cdc73 921.2 1155.5 1285.2 Leo1 325.5 857.7 916.5 Wdr61 25.2 45.1 84.0 Pex2 65.0 89.9 161.6 Ddx42 3449.8 4049.8 4443.1 Morc2a 1153.3 1376.5 1596.0 Taf1a 202.4 269.0 421.8 Aggf1 2883.0 2940.5 3078.9 Taf1b 438.3 598.5 700.2 CEM 1 + Pak1ip1 1908.3 2214.1 2392.1 Top 10 Genes Actr6 168.3 255.6 299.3 Jade3 186.1 276.5 304.4 Cbfa2t2 518.3 701.3 747.4 Clpx 241.3 330.9 424.7

Null module GEO Series "GSE31792" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 18 -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=GSE31792 Status: Public on Jul 01 2012 Title: Distinct and Overlapping Gene Regulatory Networks in BMP- and HDAC-Controlled Cell Fate Determination in the Embryonic Forebrain Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 22748179 Summary & Design: Summary: Both bone morphogenetic proteins (BMPs) and histone deacetylases (HDACs) have previously been established to play a role in the development of the three major cell types of the central nervous system: neurons, astrocytes, and oligodendrocytes. We have previously established a connection between these two protein families, showing that HDACs suppress BMP-promoted astrogliogenesis in the embryonic striatum. Since HDACs act in the nucleus to effect changes in transcription, an unbiased analysis of their transcriptional targets could shed light on their downstream effects on BMP-signaling. Using neurospheres from the embryonic striatum as an in vitro system to analyze this phenomenon, we have performed microarray expression profiling on BMP2- and trichostatin A (TSA)-treated cultures, followed by validation of the findings with quantitative RT-PCR and protein analysis.

Overall design: Neurospheres from the embryonic striatum were used to analyze cellular differentiation into neurons and astrocytes in vitro. To analyze the role of BMP2 and the HDAC-inhibitor TSA in this system, neurospheres were treated with TSA or BMP2 for 24 h, and mRNA was extracted after 6 and 24 h of the respective treatment.

Background corr dist: KL-Divergence = 0.1556, L1-Distance = 0.0355, L2-Distance = 0.0026, Normal std = 0.3698

1.079 Kernel fit Pairwise Correlations Normal fit

Density 0.539

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

Control,Control, 6h, rep1Control, 6h, (0.0627687) rep2Control, 24h, (0.0111571) rep1Control, 24h, (0.0431836) rep2Control, 24h, (0.0382868) rep3Control, 24h, (0.0602745) rep4Control, 24h, (0.00892005) rep5BMP2 24h, (0.0238372) rep6treatment,BMP2 (0.0332574) treatment,BMP2 6h, rep1treatment,BMP2 6h, (0.015494) rep2treatment,TSA 24h, (0.0181623) treatment, rep1TSA 24h, (0.0366753)treatment, rep2TSA 6h, rep1(0.0471144)treatment,TSA 6h, (0.232096) rep2treatment,TSA 24h, (0.184781) treatment, rep1TSA 24h, (0.0760351) treatment, rep2 24h, (0.0519507) rep3 24h, (0.0367496) rep4 (0.0192568)[ min ] [ medium ] [ max ] CEM 1 Ctr9 302.7 632.7 1402.2 P ( S | Z, I ) = 0.00 Rtf1 1040.4 1469.7 2089.9 Mean Corr = 0.33178 Paf1 405.1 555.5 1469.9 Cdc73 1265.5 1556.0 1817.8 Leo1 513.8 657.2 900.4 Wdr61 60.5 86.7 123.9 Pex2 98.4 161.0 213.1 Ddx42 475.5 643.6 964.0 Morc2a 750.5 1127.6 1496.5 Taf1a 95.3 153.3 270.4 Aggf1 2084.4 2815.5 3303.2 Taf1b 308.9 388.8 609.6 CEM 1 + Pak1ip1 1091.4 2179.9 3008.4 Top 10 Genes Actr6 856.2 1176.3 1809.4 Jade3 80.1 97.3 142.9 Cbfa2t2 747.3 879.9 1621.8 Clpx 639.2 992.2 1523.1

Null module GEO Series "GSE21041" 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=GSE21041 Status: Public on Jul 15 2010 Title: Transcriptome analysis of miR-144/451-null bone marrow erythroid cells Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 20679398 Summary & Design: Summary: microRNA miR-144/451 is highly expressed during erythropoiesis. We deleted the miR-144/451 gene locus in mice and compared the transcriptomes of miR-144/451-null bone marrow erythroid precursors to stage-matched wild-type control cells.

Overall design: Ter119+/CD71+/FSC-high bone marrow erythroblasts were sorted directly into Trizol LS reagent. Total RNAs extracted from three miR-144/451 knock-out and three wide type mice were analyzed using Affymetrix Mouse Genome 430 2.0 Arrays.

Background corr dist: KL-Divergence = 0.0360, L1-Distance = 0.0159, L2-Distance = 0.0003, Normal std = 0.6337

0.634 Kernel fit Pairwise Correlations Normal fit

Density 0.317

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_497WT_504 (0.149269)WT_550 (0.116286)KO_493 (0.0965909)KO_548 (0.275029)KO_551 (0.256263) (0.106563) [ min ] [ medium ] [ max ] CEM 1 Ctr9 119.9 144.3 148.0 P ( S | Z, I ) = 0.00 Rtf1 761.6 1051.1 1341.8 Mean Corr = 0.31270 Paf1 1084.5 1466.1 1670.1 Cdc73 1197.4 1367.9 1428.1 Leo1 291.2 361.0 424.6 Wdr61 97.0 118.8 145.6 Pex2 101.1 108.1 128.5 Ddx42 2624.4 2922.7 3110.3 Morc2a 475.3 593.5 754.8 Taf1a 199.9 218.3 257.4 Aggf1 2414.9 2521.2 2713.1 Taf1b 222.2 354.0 390.7 CEM 1 + Pak1ip1 2361.8 2683.5 2862.0 Top 10 Genes Actr6 269.3 396.2 514.8 Jade3 651.6 918.3 993.0 Cbfa2t2 486.3 561.5 724.0 Clpx 821.9 939.5 1134.4

Null module