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: 6 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. Tomm70a Tomm20l Tomm40 Tomm22 Tomm20 Tomm7 Num ofGenesinQueryGeneset:6.CEMs:1. Overview ofCo-ExpressionModules(CEMs) with DatasetWeighting

Tomm20 Tomm22 Tomm40 Tomm70a Tomm7 Tomm20l Singletons CEM 1(287datasets) 0.0 Scale ofaveragePearsoncorrelations 0.2 0.4 0.6 0.8 1.0 Symbol Num ofCEMGenes:5.Predicted693.SelectedDatasets:287.Strength:1.5 CEM 1,Geneset"[G]mitochondrialoutermembranetranslocasecomplex",Page1 Ebna1bp2 Tomm70a Timm17a Mrps18b Tomm40 Tomm22 Tomm20 Psmd12 Timm10 Timm13 Ranbp1 Ccdc58 Tomm7 Exosc4 Mrps22 Mrps10 Mrps23 Stoml2 Rsl1d1 Psmb3 Psmg1 Eef1e1 Mrpl46 Mrpl18 Mrpl11 Mrpl20 Mrpl12 Polr2h C1qbp Aimp2 Nop16 Nop10 Hspe1 Pa2g4 Naa10 Gtf2f2 Polr2f Banf1 Yars2 Nme1 Bola2 Emg1 Lsm4 Lsm2 Nhp2 Kti12 Pno1 Phb2 Imp4 Clpp 0.0 1.0

GSE30160 [6] GSE8044 [6]

GSE17886 [16] Only showingfirst200datasets-Seetxtoutputforfulldetails. GSE26096 [10] GSE27092 [6] GSE16874 [12] GSE23833 [12] GSE19885 [9] GSE13408 [14] GSE19079 [6] GSE44175 [18] GSE20954 [14] GSE6482 [9] GSE7275 [8] GSE12518 [6] GSE8295 [16] GSE7069 [8] GSE6998 [32] GSE38257 [14] GSE27720 [6] GSE13302 [30] GSE48397 [10] GSE42299 [8] GSE26616 [6] GSE6689 [12] GSE27114 [6] GSE46090 [12] GSE38031 [8] GSE31013 [12] GSE46606 [30] GSE31313 [22] GSE16675 [72] GSE48790 [8] GSE18396 [6] GSE17709 [18] GSE20696 [8] GSE55356 [6] GSE17553 [16] GSE28408 [6] GSE20177 [14] GSE26568 [6] GSE45619 [6] GSE7897 [60] GSE28389 [20] GSE31598 [12] GSE27429 [8] GSE53077 [8] GSE16002 [9] GSE10587 [6] GSE18042 [18] GSE33199 [64] GSE40230 [15] GSE10589 [6] GSE29485 [12] GSE54653 [6] GSE20391 [11] GSE35785 [10] GSE9760 [12] GSE7683 [12] GSE24813 [10] GSE46797 [6] GSE14004 [9] GSE10273 [9] GSE21278 [48] GSE9913 [9] GSE15433 [9] GSE27378 [8] GSE1435 [27] GSE39897 [36] GSE14012 [24] GSE6837 [8] GSE21063 [24] GSE6675 [8] GSE15267 [8] GSE11220 [44] GSE20513 [12] GSE22005 [23] GSE17462 [8] GSE42135 [42] GSE56755 [13] GSE13547 [12] GSE17373 [24] GSE56345 [9] GSE5011 [10] GSE15808 [29] GSE19684 [14] GSE32937 [8] GSE35593 [6] GSE32277 [33] GSE16454 [24] GSE18281 [33] GSE5976 [12] GSE36814 [20] GSE6623 [12] GSE8025 [21] GSE54207 [9] GSE7694 [12] GSE7050 [18] GSE42883 [12] GSE27816 [14] GSE58368 [15] GSE40087 [15] GSE21996 [14] GSE33471 [12] GSE21944 [6] GSE13611 [8] GSE10246 [182] GSE10627 [51] GSE12499 [10] GSE31940 [8] GSE46854 [20] GSE34126 [19] GSE11222 [42] GSE11018 [6] GSE15161 [26] GSE51080 [18] GSE15330 [27] GSE6674 [15] GSE13044 [59] GSE18135 [18] GSE17513 [12] GSE21902 [31] GSE11186 [33] GSE33121 [10] GSE25295 [25] GSE39442 [11] GSE39984 [18] GSE21687 [192] GSE27379 [6] GSE21836 [8] GSE29632 [42] GSE4535 [6] GSE31028 [6] GSE23101 [20] GSE32986 [18] GSE7759 [112] GSE7310 [10] GSE15268 [16] GSE15155 [12] GSE32034 [14] GSE46970 [15] GSE45618 [6] GSE9247 [15] GSE7784 [12] GSE27329 [24] GSE9199 [50] GSE42021 [27] GSE41005 [8] GSE14406 [54] GSE53951 [10] GSE46185 [6] GSE4712 [21] GSE39458 [6] GSE42930 [10] CEM+ CEM GSE19732 [20] GSE25088 [24] GSE9355 [51] GSE12498 [12] GSE38304 [8] GSE20398 [30] 0.0 GSE33942 [12] GSE56542 [8]

GSE18064 [12] Scale ofaveragePearsoncorrelations GSE32386 [13] GSE25423 [10] GSE31406 [12] GSE51432 [15] GSE8564 [20] GSE4288 [36] 0.2 GSE6526 [16] GSE25908 [111] GSE13692 [8] GSE5035 [12] GSE5332 [12] GSE13707 [20] GSE39592 [8] GSE33726 [48] GSE50399 [18] 0.4 GSE24061 [88] GSE6383 [6] GSE16925 [15] GSE14753 [6] GSE11898 [9] GSE22180 [60] GSE12982 [53] GSE26745 [24] GSE8660 [6] 0.6 GSE20987 [12] GSE15121 [6] GSE33761 [9] GSE32223 [12] GSE6957 [12] GSE7699 [6] GSE34902 [6] GSE8836 [56] GSE17825 [18] 0.8 GSE34006 [6] GSE48204 [6] GSE24625 [12] GSE27563 [93] Score 192.85 193.42 194.51 194.59 196.47 196.84 197.44 198.56 198.75 198.89 199.38 200.95 201.62 202.10 202.12 202.62 203.55 204.40 206.31 206.51 207.64 208.15 208.38 211.38 214.52 216.55 217.08 219.27 219.51 220.22 220.80 221.57 224.06 228.19 228.49 231.41 231.99 236.20 237.28 253.27 256.48 264.53 280.26 298.68 312.60 1.0 Notes Symbol Num ofCEMGenes:5.Predicted693.SelectedDatasets:287.Strength:1.5 CEM 1,Geneset"[G]mitochondrialoutermembranetranslocasecomplex",Page2 Rps19bp1 Mybbp1a Timm23 Chchd1 Mrps35 Sssca1 Dctpp1 Nudt21 Psmb5 Rps27l Psma1 Psma7 Psmc4 Psma6 Psma4 Mrpl50 Mrpl36 Mrpl42 Mrpl40 Magoh Grpel1 Grwd1 Polr1d Nop56 Nsun2 Wdr74 Wdr18 Ddx56 Ddx49 Dpy30 Rpl7l1 Eif1ad Ddx39 Cdc34 Mrps7 Snrpg Prmt1 Gspt1 Polr2j Pfdn4 Sf3b5 Uchl5 Emc6 Txnl1 Glrx3 Strap Cct5 Ifrd2 Nip7 Adsl 0.0 1.0

GSE30160 [6] GSE8044 [6]

GSE18064 [12] Scale ofaveragePearsoncorrelations GSE32386 [13] GSE25423 [10] GSE31406 [12] GSE51432 [15] GSE8564 [20] GSE4288 [36] 0.2 GSE6526 [16] GSE25908 [111] GSE13692 [8] GSE5035 [12] GSE5332 [12] GSE13707 [20] GSE39592 [8] GSE33726 [48] GSE50399 [18] 0.4 GSE24061 [88] GSE6383 [6] GSE16925 [15] GSE14753 [6] GSE11898 [9] GSE22180 [60] GSE12982 [53] GSE26745 [24] GSE8660 [6] 0.6 GSE20987 [12] GSE15121 [6] GSE33761 [9] GSE32223 [12] GSE6957 [12] GSE7699 [6] GSE34902 [6] GSE8836 [56] GSE17825 [18] 0.8 GSE34006 [6] GSE48204 [6] GSE24625 [12] GSE27563 [93] Score 162.04 162.24 163.18 163.49 163.70 164.35 167.18 167.43 167.83 168.45 168.53 168.62 169.13 169.23 172.26 172.74 173.62 174.29 174.47 175.17 175.48 176.42 177.51 177.64 178.22 178.47 179.33 180.93 181.30 181.60 181.73 182.69 182.95 182.96 184.35 184.52 184.62 184.77 185.84 186.02 186.70 186.73 186.74 186.99 187.95 189.49 189.59 190.11 190.52 192.42 1.0 Notes Symbol Num ofCEMGenes:5.Predicted693.SelectedDatasets:287.Strength:1.5 CEM 1,Geneset"[G]mitochondrialoutermembranetranslocasecomplex",Page3 Tmem11 Cacybp Exosc3 Mrps16 Mrps17 Mrps28 Snrpd3 Rbm8a Psmb4 Psmb7 Psma2 Mrpl22 Mrpl28 Mrpl13 Mrpl45 Bri3bp Atp5f1 Nubp1 Polr2c Cops5 Rpp30 Apex1 Eif2b3 Actl6a Ddx18 Znhit3 Gmps Rrp15 Eif3m Phf5a Nol11 Cct6a Smn1 Mrpl2 Snrpf Nop9 Bop1 Stip1 Eif3d Rae1 Rcc1 Pes1 Ftsj3 Mtx1 Slirp Eif3l Tbl3 Srm Parl Nifk 0.0 1.0

GSE30160 [6] GSE8044 [6]

GSE18064 [12] Scale ofaveragePearsoncorrelations GSE32386 [13] GSE25423 [10] GSE31406 [12] GSE51432 [15] GSE8564 [20] GSE4288 [36] 0.2 GSE6526 [16] GSE25908 [111] GSE13692 [8] GSE5035 [12] GSE5332 [12] GSE13707 [20] GSE39592 [8] GSE33726 [48] GSE50399 [18] 0.4 GSE24061 [88] GSE6383 [6] GSE16925 [15] GSE14753 [6] GSE11898 [9] GSE22180 [60] GSE12982 [53] GSE26745 [24] GSE8660 [6] 0.6 GSE20987 [12] GSE15121 [6] GSE33761 [9] GSE32223 [12] GSE6957 [12] GSE7699 [6] GSE34902 [6] GSE8836 [56] GSE17825 [18] 0.8 GSE34006 [6] GSE48204 [6] GSE24625 [12] GSE27563 [93] Score 140.16 140.40 140.72 140.99 141.04 141.76 142.44 142.61 143.08 143.46 143.63 144.15 144.79 145.00 145.37 145.46 145.64 145.71 145.74 146.45 146.96 147.97 149.24 149.42 150.23 150.24 150.52 152.10 152.91 152.96 153.77 153.82 153.83 153.83 154.39 154.64 155.69 156.00 156.08 156.10 156.73 157.14 157.26 157.85 158.40 158.49 158.65 158.67 159.67 160.79 1.0 Notes 9430016H08Rik Gadd45gip1 Symbol Num ofCEMGenes:5.Predicted693.SelectedDatasets:287.Strength:1.5 CEM 1,Geneset"[G]mitochondrialoutermembranetranslocasecomplex",Page4 Zmynd19 Aurkaip1 Wbscr22 Samm50 Tamm41 Chchd4 Exosc5 Mrps34 Mrps27 Mrps30 Mrps26 Arpp19 Metap2 Malsu1 Ruvbl2 Ruvbl1 Cmss1 Psmg3 Psmb6 Psmb2 Psmc5 Mrpl34 Mrpl55 Mrpl54 Mrpl47 Mrpl37 Mrpl32 Polr1e Wdr55 Aimp1 Eif2b5 Ddx27 Usp14 Eif4a1 Noc4l Noc2l Ptcd3 Lsm6 Crls1 Pus1 Txn2 Drg1 Cct2 Lyar Bysl Ipo5 Ltv1 Ncl 0.0 1.0

GSE30160 [6] GSE8044 [6]

GSE18064 [12] Scale ofaveragePearsoncorrelations GSE32386 [13] GSE25423 [10] GSE31406 [12] GSE51432 [15] GSE8564 [20] GSE4288 [36] 0.2 GSE6526 [16] GSE25908 [111] GSE13692 [8] GSE5035 [12] GSE5332 [12] GSE13707 [20] GSE39592 [8] GSE33726 [48] GSE50399 [18] 0.4 GSE24061 [88] GSE6383 [6] GSE16925 [15] GSE14753 [6] GSE11898 [9] GSE22180 [60] GSE12982 [53] GSE26745 [24] GSE8660 [6] 0.6 GSE20987 [12] GSE15121 [6] GSE33761 [9] GSE32223 [12] GSE6957 [12] GSE7699 [6] GSE34902 [6] GSE8836 [56] GSE17825 [18] 0.8 GSE34006 [6] GSE48204 [6] GSE24625 [12] GSE27563 [93] Score 123.36 123.41 123.86 123.92 124.12 124.33 124.33 124.40 124.44 124.91 124.92 125.34 125.63 125.67 125.87 126.81 127.49 127.67 127.84 128.61 128.78 129.17 130.77 131.69 131.72 131.75 131.81 132.10 132.74 133.64 134.16 134.32 134.71 134.98 135.46 135.51 136.26 136.60 136.82 136.89 137.15 137.51 137.58 137.61 137.72 137.91 138.01 138.43 138.80 138.84 1.0 Notes 1810009A15Rik Symbol Num ofCEMGenes:5.Predicted693.SelectedDatasets:287.Strength:1.5 CEM 1,Geneset"[G]mitochondrialoutermembranetranslocasecomplex",Page5 BC003965 Snrnp40 Slc25a5 Ndufaf6 Nudcd2 Exosc2 Ndufb6 Aarsd1 Atp5g1 Ndufv2 Atad3a Pgam5 Cenpw Mrpl16 Mrpl39 Mrpl44 Rangrf Cirh1a Polr1c Nop58 Hspa4 Abce1 Pdap1 Pbdc1 Snrpc Rrp12 Prmt5 Hmbs l7Rn6 Pold2 Cisd1 Lsm3 Dohh Hint1 Nob1 Nop2 Eif3b Dkc1 Ppil1 Tfam Ece2 Tcp1 Hdgf Dars Yrdc Utp6 Rfc4 Eif3i Gart 0.0 1.0

GSE30160 [6] GSE8044 [6]

GSE18064 [12] Scale ofaveragePearsoncorrelations GSE32386 [13] GSE25423 [10] GSE31406 [12] GSE51432 [15] GSE8564 [20] GSE4288 [36] 0.2 GSE6526 [16] GSE25908 [111] GSE13692 [8] GSE5035 [12] GSE5332 [12] GSE13707 [20] GSE39592 [8] GSE33726 [48] GSE50399 [18] 0.4 GSE24061 [88] GSE6383 [6] GSE16925 [15] GSE14753 [6] GSE11898 [9] GSE22180 [60] GSE12982 [53] GSE26745 [24] GSE8660 [6] 0.6 GSE20987 [12] GSE15121 [6] GSE33761 [9] GSE32223 [12] GSE6957 [12] GSE7699 [6] GSE34902 [6] GSE8836 [56] GSE17825 [18] 0.8 GSE34006 [6] GSE48204 [6] GSE24625 [12] GSE27563 [93] Score 108.24 108.28 108.41 108.49 108.60 109.30 109.55 110.10 110.18 110.33 110.34 110.53 110.96 111.05 112.44 113.04 113.41 113.61 113.77 114.08 114.27 114.31 114.49 114.49 115.22 115.84 115.86 116.17 117.83 118.19 118.38 118.54 118.68 118.91 119.06 119.66 119.87 119.90 120.15 120.34 120.36 120.51 121.27 121.37 121.64 121.86 121.90 122.24 122.24 122.38 1.0 Notes Symbol Num ofCEMGenes:5.Predicted693.SelectedDatasets:287.Strength:1.5 CEM 1,Geneset"[G]mitochondrialoutermembranetranslocasecomplex",Page6 Xrcc6bp1 Tmem97 Mrps18a Rabggtb Trmt10c Dnajc11 N6amt2 Mrps33 Mrps12 Gtpbp4 Prkrip1 H2-Ke2 Ppm1g Psmd6 Psmc1 Adrm1 Gtf2h5 Prpf31 Nubp2 Rpp40 Nup43 Wdr36 Eif2b1 Cox5a Eif2s2 Naa38 Mrp63 Snrpb Dus1l Nif3l1 U2af1 Mrpl4 Siva1 Sdhd Ccnh Ppan Pop7 Rpa3 Coa7 Tufm Hax1 Lap3 Mtx2 Rrp9 Taf9 Aprt Atic Itpa Uxt Mif 0.0 1.0

GSE30160 [6] GSE8044 [6]

GSE18064 [12] Scale ofaveragePearsoncorrelations GSE32386 [13] GSE25423 [10] GSE31406 [12] GSE51432 [15] GSE8564 [20] GSE4288 [36] 0.2 GSE6526 [16] GSE25908 [111] GSE13692 [8] GSE5035 [12] GSE5332 [12] GSE13707 [20] GSE39592 [8] GSE33726 [48] GSE50399 [18] 0.4 GSE24061 [88] GSE6383 [6] GSE16925 [15] GSE14753 [6] GSE11898 [9] GSE22180 [60] GSE12982 [53] GSE26745 [24] GSE8660 [6] 0.6 GSE20987 [12] GSE15121 [6] GSE33761 [9] GSE32223 [12] GSE6957 [12] GSE7699 [6] GSE34902 [6] GSE8836 [56] GSE17825 [18] 0.8 GSE34006 [6] GSE48204 [6] GSE24625 [12] GSE27563 [93] Score 91.41 91.99 92.03 92.94 93.82 93.84 94.08 95.13 95.27 95.36 95.52 95.86 96.39 96.71 96.82 97.50 97.69 97.79 97.85 98.06 98.27 98.85 99.10 99.40 99.73 99.86 100.49 101.12 101.28 101.36 101.39 102.63 102.66 103.41 103.42 104.01 104.05 104.27 104.42 104.46 104.46 105.06 105.35 105.45 105.65 106.07 106.66 107.23 107.26 107.81 1.0 Notes 9130401M01Rik 0610009D07Rik Symbol Num ofCEMGenes:5.Predicted693.SelectedDatasets:287.Strength:1.5 CEM 1,Geneset"[G]mitochondrialoutermembranetranslocasecomplex",Page7 Rnaseh2a Ccdc124 Hnrnpab Psmd14 Timm8b Ndufaf2 Gemin5 Nudcd1 Uqcr11 Nudt19 Pmpcb Smyd5 Dcaf13 Psmg4 Psmc2 Mrpl43 Lrpprc Gtf2e2 Polr2d Nedd8 Ncbp1 Cpsf3l Slmo2 Ahsa1 Naa15 Thoc6 Dimt1 Abcf2 Riok2 Taf10 Mbd3 Bzw2 Bzw1 Coq7 Eif3g Ppa1 Qtrt1 Fen1 Lsg1 Gars Drg2 Rars Ctu2 Ppat Hat1 Rcl1 Fxn Cs 0.0 1.0

GSE30160 [6] GSE8044 [6]

GSE18064 [12] Scale ofaveragePearsoncorrelations GSE32386 [13] GSE25423 [10] GSE31406 [12] GSE51432 [15] GSE8564 [20] GSE4288 [36] 0.2 GSE6526 [16] GSE25908 [111] GSE13692 [8] GSE5035 [12] GSE5332 [12] GSE13707 [20] GSE39592 [8] GSE33726 [48] GSE50399 [18] 0.4 GSE24061 [88] GSE6383 [6] GSE16925 [15] GSE14753 [6] GSE11898 [9] GSE22180 [60] GSE12982 [53] GSE26745 [24] GSE8660 [6] 0.6 GSE20987 [12] GSE15121 [6] GSE33761 [9] GSE32223 [12] GSE6957 [12] GSE7699 [6] GSE34902 [6] GSE8836 [56] GSE17825 [18] 0.8 GSE34006 [6] GSE48204 [6] GSE24625 [12] GSE27563 [93] Score 73.99 74.11 75.38 75.52 75.72 76.32 76.33 76.61 76.87 76.99 77.39 77.48 77.53 77.82 78.07 78.60 79.58 79.85 80.07 80.53 81.08 81.26 81.63 81.82 82.07 82.28 83.25 83.29 83.32 83.71 84.00 85.78 87.02 87.61 88.33 88.71 89.49 89.53 89.58 89.67 89.94 89.97 90.16 90.34 90.47 90.96 91.00 91.03 91.15 91.22 1.0 Notes Symbol Num ofCEMGenes:5.Predicted693.SelectedDatasets:287.Strength:1.5 CEM 1,Geneset"[G]mitochondrialoutermembranetranslocasecomplex",Page8 Anapc15 Snrnp25 Rsl24d1 Hspbp1 Nup133 Exosc7 Zc3hc1 Dhrs7b Dnttip2 Uqcrc1 Ndufc1 Atp5a1 Pmpca Hnrnpf Mrpl10 Polr1b Nup35 Wdr43 Trip13 Asna1 Usp39 Naa25 Thoc3 Mettl5 Mettl1 Snrpe Atp5b Pfdn2 Tbrg4 Pfdn1 Galk1 Bccip Cse1l Coq3 Nudc Dhps Pycrl Ddx1 Uba2 Cyc1 Imp3 Rrs1 Gnl3 Cct4 Cct7 Dis3 Lias Isy1 Ppif Iars 0.0 1.0

GSE30160 [6] GSE8044 [6]

GSE18064 [12] Scale ofaveragePearsoncorrelations GSE32386 [13] GSE25423 [10] GSE31406 [12] GSE51432 [15] GSE8564 [20] GSE4288 [36] 0.2 GSE6526 [16] GSE25908 [111] GSE13692 [8] GSE5035 [12] GSE5332 [12] GSE13707 [20] GSE39592 [8] GSE33726 [48] GSE50399 [18] 0.4 GSE24061 [88] GSE6383 [6] GSE16925 [15] GSE14753 [6] GSE11898 [9] GSE22180 [60] GSE12982 [53] GSE26745 [24] GSE8660 [6] 0.6 GSE20987 [12] GSE15121 [6] GSE33761 [9] GSE32223 [12] GSE6957 [12] GSE7699 [6] GSE34902 [6] GSE8836 [56] GSE17825 [18] 0.8 GSE34006 [6] GSE48204 [6] GSE24625 [12] GSE27563 [93] Score 65.07 65.16 65.33 65.34 65.42 65.55 66.05 66.29 66.42 66.48 66.68 67.11 67.48 67.74 68.04 68.41 68.43 68.52 68.70 68.94 69.00 69.07 69.32 69.49 69.54 69.98 70.09 70.14 70.15 70.21 70.64 70.79 70.83 70.95 71.13 71.17 71.35 71.39 71.91 72.25 72.59 72.65 72.76 72.83 72.96 73.10 73.14 73.23 73.31 73.38 1.0 Notes 1110004E09Rik Symbol Num ofCEMGenes:5.Predicted693.SelectedDatasets:287.Strength:1.5 CEM 1,Geneset"[G]mitochondrialoutermembranetranslocasecomplex",Page9 Trnau1ap Dnajc24 Magohb Timm44 Uqcrfs1 Pabpc4 Mcmbp Ndufb5 Snrpa1 Trmt11 Rbm19 Dnaaf2 Psmd2 Pgam1 Mthfd1 Gtf2h2 Srfbp1 Med21 Mak16 Atp5j2 Cops3 Cops6 Shmt2 Cdc37 Ube2k Cks1b Haus1 Naa20 Mrps2 Alyref Mcm7 Mcm5 Nudt1 Gins4 Pomp Trap1 Sf3a3 Mrpl3 Elac2 Gtf3a Guk1 Psph Noa1 Eif3c Tipin Hars Nars Rfc3 Aatf 0.0 1.0

GSE30160 [6] GSE8044 [6]

GSE18064 [12] Scale ofaveragePearsoncorrelations GSE32386 [13] GSE25423 [10] GSE31406 [12] GSE51432 [15] GSE8564 [20] GSE4288 [36] 0.2 GSE6526 [16] GSE25908 [111] GSE13692 [8] GSE5035 [12] GSE5332 [12] GSE13707 [20] GSE39592 [8] GSE33726 [48] GSE50399 [18] 0.4 GSE24061 [88] GSE6383 [6] GSE16925 [15] GSE14753 [6] GSE11898 [9] GSE22180 [60] GSE12982 [53] GSE26745 [24] GSE8660 [6] 0.6 GSE20987 [12] GSE15121 [6] GSE33761 [9] GSE32223 [12] GSE6957 [12] GSE7699 [6] GSE34902 [6] GSE8836 [56] GSE17825 [18] 0.8 GSE34006 [6] GSE48204 [6] GSE24625 [12] GSE27563 [93] Score 48.57 48.65 49.04 49.29 49.86 50.16 50.19 50.45 51.20 51.21 51.22 51.33 51.96 52.09 52.26 53.10 54.44 54.48 54.60 55.33 55.48 55.76 56.35 56.36 56.40 56.50 57.04 57.40 57.80 58.40 58.63 58.63 58.94 59.14 59.53 59.78 60.20 61.24 61.33 61.37 61.59 61.64 61.77 61.99 62.14 63.92 64.02 64.77 64.92 64.94 1.0 Notes Symbol Num ofCEMGenes:5.Predicted693.SelectedDatasets:287.Strength:1.5 CEM 1,Geneset"[G]mitochondrialoutermembranetranslocasecomplex",Page10 Hsp90aa1 Eif4ebp1 Mrps18c Nr2c2ap Prpf38a Mrps36 Otud6b Cnot11 Rnmtl1 Ptpmt1 Tarbp2 Psmd5 Tcerg1 Psmd3 Psmd4 Mrpl49 G3bp1 Apitd1 Kpnb1 Polr1a Cops4 Hddc2 Nup93 Nop14 Cd320 Ppp5c Thoc5 Jagn1 Gmnn Tex30 Gins2 Gins1 Polr2i Cnih4 Nme6 Rpl27 Pwp1 Mnd1 Wdr4 Aven Rad1 Pdhx Eif3k Pcna Immt Mecr Rtcb Abt1 Nxt1 Mri1 0.0 1.0

GSE30160 [6] GSE8044 [6]

GSE18064 [12] Scale ofaveragePearsoncorrelations GSE32386 [13] GSE25423 [10] GSE31406 [12] GSE51432 [15] GSE8564 [20] GSE4288 [36] 0.2 GSE6526 [16] GSE25908 [111] GSE13692 [8] GSE5035 [12] GSE5332 [12] GSE13707 [20] GSE39592 [8] GSE33726 [48] GSE50399 [18] 0.4 GSE24061 [88] GSE6383 [6] GSE16925 [15] GSE14753 [6] GSE11898 [9] GSE22180 [60] GSE12982 [53] GSE26745 [24] GSE8660 [6] 0.6 GSE20987 [12] GSE15121 [6] GSE33761 [9] GSE32223 [12] GSE6957 [12] GSE7699 [6] GSE34902 [6] GSE8836 [56] GSE17825 [18] 0.8 GSE34006 [6] GSE48204 [6] GSE24625 [12] GSE27563 [93] Score 38.19 38.65 38.71 38.73 38.91 39.38 39.41 39.43 39.98 40.16 40.50 40.87 41.05 41.36 41.44 41.44 41.48 41.59 41.81 41.91 41.98 42.14 42.15 42.97 43.06 43.14 43.37 43.62 43.81 43.87 44.14 44.49 44.79 45.31 45.41 45.57 45.90 45.91 45.93 45.94 46.48 46.65 46.65 46.92 47.00 47.03 47.06 47.14 47.46 47.77 1.0 Notes Symbol Num ofCEMGenes:5.Predicted693.SelectedDatasets:287.Strength:1.5 CEM 1,Geneset"[G]mitochondrialoutermembranetranslocasecomplex",Page11 Thumpd3 Fam195a Wbscr16 Dnajc15 Pak1ip1 Fastkd5 Fam96a Prpf40a Enoph1 Csnk2b Rbmxl1 Cops7a Tubb4b Mthfd1l Sac3d1 Dazap1 Ndufb7 Ppp1r8 Ndufa7 Ndufs8 Psmc3 Mrpl27 Mrpl52 Med30 Nufip1 Wdr46 Nup62 Pdcd2 Ddx20 Ddx46 Msto1 Mcm2 Trub1 Trmt1 Ptcd2 Nol12 Szrd1 Emc4 Mrpl9 Mdh2 Gpn1 Nmt2 Acn9 Naca Ppa2 Vars Rfc5 Nle1 Tsr1 Bax 0.0 1.0

GSE30160 [6] GSE8044 [6]

GSE18064 [12] Scale ofaveragePearsoncorrelations GSE32386 [13] GSE25423 [10] GSE31406 [12] GSE51432 [15] GSE8564 [20] GSE4288 [36] 0.2 GSE6526 [16] GSE25908 [111] GSE13692 [8] GSE5035 [12] GSE5332 [12] GSE13707 [20] GSE39592 [8] GSE33726 [48] GSE50399 [18] 0.4 GSE24061 [88] GSE6383 [6] GSE16925 [15] GSE14753 [6] GSE11898 [9] GSE22180 [60] GSE12982 [53] GSE26745 [24] GSE8660 [6] 0.6 GSE20987 [12] GSE15121 [6] GSE33761 [9] GSE32223 [12] GSE6957 [12] GSE7699 [6] GSE34902 [6] GSE8836 [56] GSE17825 [18] 0.8 GSE34006 [6] GSE48204 [6] GSE24625 [12] GSE27563 [93] Score 29.86 29.94 30.05 30.45 31.35 31.46 31.46 31.51 31.64 31.93 32.00 32.11 32.24 32.26 32.94 33.08 33.46 33.51 33.86 34.20 34.24 34.25 34.34 34.35 34.35 34.39 34.64 34.72 34.84 34.87 35.22 35.47 35.68 35.80 35.84 35.93 35.93 36.00 36.08 36.19 36.39 36.96 36.97 36.98 37.13 37.28 37.29 37.67 37.83 37.95 1.0 Notes 2700094K13Rik 3110082I17Rik Symbol Num ofCEMGenes:5.Predicted693.SelectedDatasets:287.Strength:1.5 CEM 1,Geneset"[G]mitochondrialoutermembranetranslocasecomplex",Page12 Fam203a Ccdc101 Sigmar1 Nup107 Cox7a2 Arl6ip4 Ndufa9 Atp5g2 Ndufs7 Suclg1 Psmd8 Psmd9 Cbwd1 Mrpl23 Ptrhd1 Heatr3 Polr2g Atpaf2 Kpna2 Dtymk Afg3l2 Nup85 Ppp4c Mrps9 Tcea1 Mcm6 Ssrp1 Cetn3 Smu1 Nat10 Paics Lsm1 Ttc27 Gpn2 Ngdn Cstf2 Trnt1 Rpa2 Ecsit Aaas Mars Rrn3 Dctd Snf8 Ubl4 Tars Ssb Nln 0.0 1.0

GSE30160 [6] GSE8044 [6]

GSE18064 [12] Scale ofaveragePearsoncorrelations GSE32386 [13] GSE25423 [10] GSE31406 [12] GSE51432 [15] GSE8564 [20] GSE4288 [36] 0.2 GSE6526 [16] GSE25908 [111] GSE13692 [8] GSE5035 [12] GSE5332 [12] GSE13707 [20] GSE39592 [8] GSE33726 [48] GSE50399 [18] 0.4 GSE24061 [88] GSE6383 [6] GSE16925 [15] GSE14753 [6] GSE11898 [9] GSE22180 [60] GSE12982 [53] GSE26745 [24] GSE8660 [6] 0.6 GSE20987 [12] GSE15121 [6] GSE33761 [9] GSE32223 [12] GSE6957 [12] GSE7699 [6] GSE34902 [6] GSE8836 [56] GSE17825 [18] 0.8 GSE34006 [6] GSE48204 [6] GSE24625 [12] GSE27563 [93] Score 21.16 21.61 21.80 21.83 21.89 22.15 22.28 22.31 22.90 23.24 23.25 23.36 23.37 23.38 23.44 23.50 23.61 23.77 24.28 24.49 24.62 24.98 25.09 25.59 25.89 25.89 26.30 26.40 26.43 26.62 26.91 27.02 27.33 27.42 27.84 28.03 28.23 28.54 28.68 29.04 29.25 29.26 29.34 29.50 29.51 29.51 29.55 29.56 29.63 29.75 1.0 Notes Mphosph10 Symbol Num ofCEMGenes:5.Predicted693.SelectedDatasets:287.Strength:1.5 CEM 1,Geneset"[G]mitochondrialoutermembranetranslocasecomplex",Page13 Mphosph6 BC027231 Hsp90ab1 Tmem199 Nsmce4a Commd1 Psmc3ip Tmem70 Ndufaf4 Gemin2 Nup155 Pdcd11 Mrps24 Ndufs1 Ndufv1 Rnf126 Psme3 Med11 Dnph1 Rqcd1 Hspa9 Cdc26 Ddx51 Vdac2 Lage3 Atp5d Cfdp1 Nudt2 Parp1 Srp19 Xrcc6 Park7 Pycr2 Asf1a Rpl14 Tfdp1 Tcof1 Myg1 Sod2 Pop1 Pus7 Cycs Tefm Taf5l Orc6 Rrp8 Pgd Ak2 Ilf2 0.0 1.0

GSE30160 [6] GSE8044 [6]

GSE18064 [12] Scale ofaveragePearsoncorrelations GSE32386 [13] GSE25423 [10] GSE31406 [12] GSE51432 [15] GSE8564 [20] GSE4288 [36] 0.2 GSE6526 [16] GSE25908 [111] GSE13692 [8] GSE5035 [12] GSE5332 [12] GSE13707 [20] GSE39592 [8] GSE33726 [48] GSE50399 [18] 0.4 GSE24061 [88] GSE6383 [6] GSE16925 [15] GSE14753 [6] GSE11898 [9] GSE22180 [60] GSE12982 [53] GSE26745 [24] GSE8660 [6] 0.6 GSE20987 [12] GSE15121 [6] GSE33761 [9] GSE32223 [12] GSE6957 [12] GSE7699 [6] GSE34902 [6] GSE8836 [56] GSE17825 [18] 0.8 GSE34006 [6] GSE48204 [6] GSE24625 [12] GSE27563 [93] Score 8.97 9.08 9.15 9.24 9.63 9.73 10.02 10.09 10.12 10.70 11.05 11.26 12.05 12.48 12.71 12.91 13.11 13.14 13.85 13.88 13.95 14.01 14.12 14.52 14.64 15.08 15.50 15.56 15.66 15.67 15.87 15.91 16.15 16.41 16.72 17.24 17.50 17.52 17.74 17.97 18.52 19.08 19.34 19.38 19.90 20.01 20.58 20.68 20.69 21.14 1.0 Notes 1110008F13Rik 1110001J03Rik Symbol Num ofCEMGenes:5.Predicted693.SelectedDatasets:287.Strength:1.5 CEM 1,Geneset"[G]mitochondrialoutermembranetranslocasecomplex",Page14 Thumpd1 Commd2 Ccdc115 Mmachc Timm22 Cdc123 Uqcrc2 Heatr1 Cenph Polr3c Stra13 Nup54 Rad51 Uqcc2 Cox18 Usp10 Vps29 Fkbp3 Uqcrb Rrp36 Dars2 Prps1 Trmt6 Utp15 Adat2 Noc3l Tars2 Taf12 Glrx5 Apoo Plrg1 Srsf9 Dap3 Nelfe Shq1 Exo1 Cdt1 Clpb Ssr2 Elp5 Ppie Krr1 Faf1 Me2 Dlat Pdf 0.0 1.0

GSE30160 [6] GSE8044 [6]

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 (0.225053)knockin replicate 2 (0.2095)knockin replicate 3 (0.105063)knock replicate 1 (0.192525) in replicate 2 (0.110436) 3 (0.157424)[ min ] [ medium ] [ max ] CEM 1 Tomm20 6774.7 10460.2 11430.8 P ( S | Z, I ) = 1.00 Tomm22 5597.9 6886.3 7066.8 Mean Corr = 0.98938Tomm40 897.5 2311.1 2643.1 Tomm70a 1423.3 3076.4 3623.5 Tomm7 4709.4 5532.7 5751.8 Nhp2 2371.6 6199.9 8391.5 C1qbp 3445.2 7003.9 8124.8 Mrpl12 2474.1 5156.4 5912.2 Phb2 3652.4 5993.9 6610.0 Hspe1 2310.0 3465.6 4873.8 CEM 1 + Yars2 285.0 591.4 798.0 Top 10 Genes Rsl1d1 1495.7 2937.3 3864.5 Ccdc58 825.0 1447.6 1698.1 Timm13 4617.3 6911.4 8059.9 Pno1 1368.8 2109.0 3160.4

Null module Tomm20l GEO Series "GSE8044" 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=GSE8044 Status: Public on Jun 08 2007 Title: Brown versus white tissue adipose selective genes Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 17618855 Summary & Design: Summary: The aim of this study was to identify genes expressed selectively in brown adipose tissue as compared to white adipose tissue from the same animals. This analysis provides a gene set that is brown and white adipose selective.

Keywords: tissue comparison from mice

Overall design: Interscapular brown adipose tissue and epididymal white adipose tissue was carefully dissected from 3 male C57Bl/6 mice. These samples were profiled independently using Affymetrix mouse 430_2 gene arrays, representing 3 biological replicates for each brown and white adipose tissues.

Background corr dist: KL-Divergence = 0.0069, L1-Distance = 0.0138, L2-Distance = 0.0002, Normal std = 0.9444

0.428 Kernel fit Pairwise Correlations Normal fit

Density 0.214

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

White adiposeWhite adipose adultWhite rep1 adipose adultBrown (0.12977) rep2 adiposeadultBrown (0.231654) rep3 adiposeBrown adult (0.136825) rep1 adipose adult (0.120365) rep2 adult (0.170025) rep3 (0.211361)[ min ] [ medium ] [ max ] CEM 1 Tomm20 2001.8 3250.8 3644.2 P ( S | Z, I ) = 1.00 Tomm22 1376.5 3265.1 3765.8 Mean Corr = 0.95932Tomm40 474.5 1420.7 1558.3 Tomm70a 615.3 1327.5 1607.2 Tomm7 735.7 1635.3 1658.2 Nhp2 355.0 829.7 896.9 C1qbp 1140.9 2642.5 2961.6 Mrpl12 758.1 3854.3 4398.0 Phb2 3328.2 7093.6 7746.8 Hspe1 585.2 2504.8 2604.7 CEM 1 + Yars2 183.1 804.9 1038.3 Top 10 Genes Rsl1d1 514.7 717.9 845.6 Ccdc58 240.7 769.6 851.7 Timm13 2624.0 6282.6 6534.3 Pno1 1280.5 1944.1 1962.7

Null module Tomm20l 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 (0.110009) two-cell embryos,BCB Sample3 (0.108624) two-cell embryos,BCB Sample4 (0.0183896) two-cell embryos,BCB Sample1 (0.0259628) two-cell embryos,Î±-amantin-treated Sample2 (0.0581393) embryos,Î±-amantin-treated Sample3 (0.0797785)Î±-amantin-treated Sample4 (0.0763028) BBBÎ±-amantin-treated two-cell (0.0258307) BBBÎ±-amantin-treated two-cell embryos, BBBÎ±-amantin-treated two-cell embryos, BBB Sample1Î±-amantin-treated two-cell embryos, BCB Sample2 (0.0485822)Î±-amantin-treated two-cell embryos, BCB Sample3 (0.0717253) two-cell embryos, BCB Sample4 (0.0576285) two-cell embryos, BCB Sample1 (0.0766878) two-cell embryos, Sample2 (0.067829)[ embryos,min Sample3 (0.0389309) ] Sample4 (0.0535309) (0.0820489)[ medium ] [ max ] CEM 1 Tomm20 125.5 4264.7 5361.7 P ( S | Z, I ) = 1.00 Tomm22 183.9 1509.8 2293.1 Mean Corr = 0.93440Tomm40 202.5 601.4 822.7 Tomm70a 74.0 236.8 507.8 Tomm7 148.3 565.6 1056.7 Nhp2 150.7 1066.5 1475.5 C1qbp 324.3 5162.2 6428.1 Mrpl12 132.9 1567.1 2102.0 Phb2 1687.4 2275.1 2828.5 Hspe1 352.5 416.3 491.8 CEM 1 + Yars2 10.8 88.1 208.0 Top 10 Genes Rsl1d1 3541.9 5622.0 7030.0 Ccdc58 97.2 232.4 343.8 Timm13 131.9 303.7 435.8 Pno1 288.6 4121.1 4643.1

Null module Tomm20l GEO Series "GSE26096" 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=GSE26096 Status: Public on Jan 03 2011 Title: Widespread targeted chromatin remodeling during the initial phase of somatic cell reprogramming [expression] Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21211784 Summary & Design: Summary: Despite rapid progress in characterizing transcription factor-driven reprogramming of somatic cells to an induced pluripotent stem (iPS) cell state, many mechanistic questions still remain. To gain insight into the earliest events in the reprogramming process, we systematically analyzed the transcriptional and epigenetic changes that occur during early factor induction after discrete numbers of divisions. We observed rapid, genome-wide changes in the euchromatic histone modification, H3K4me2, at more than a thousand loci including large subsets of pluripotency or developmentally related gene promoters and enhancers. In contrast, patterns of the repressive H3K27me3 modification remained largely unchanged except for focused depletion specifically at positions where H3K4 methylation is gained. These chromatin regulatory events precede transcriptional changes within the corresponding loci. Our data provide evidence for an early, organized, and population-wide epigenetic response to ectopic reprogramming factors that clarify the temporal order through which somatic identity is reset during reprogramming.

Overall design: Gene expression was measured by Affymetric microarrays during the initial phase of the reprogramming of mouse embryonic fibroblasts.

Background corr dist: KL-Divergence = 0.0618, L1-Distance = 0.0293, L2-Distance = 0.0012, Normal std = 0.5376

0.765 Kernel fit Pairwise Correlations Normal fit

Density 0.383

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

Serum-starvedSerum-starved 96control, hr doxycycline 96control, biological hr doxycyclineMEFdox0Div_rep1 biological induction, rep1MEFdox0Div_rep2 (0.123312) induction, rep2 biologicalMEFdox1Div_rep1 (0.0828679) (0.0452857) biologicalMEFdox1Div_rep2 rep1 (0.0144156) (0.179951)MEFdox2Div_rep1 rep2 (0.100077) (0.396487)MEFdox2Div_rep2 (0.00854616) (0.00690263) (0.0421541)[ min ] [ medium ] [ max ] CEM 1 Tomm20 5719.0 8946.2 15498.2 P ( S | Z, I ) = 1.00 Tomm22 2795.9 3497.7 5439.5 Mean Corr = 0.93020Tomm40 612.6 1038.7 2068.3 Tomm70a 680.0 1247.6 2190.0 Tomm7 2496.5 3243.0 4592.5 Nhp2 868.4 2436.3 6079.4 C1qbp 2753.7 6124.0 10682.5 Mrpl12 1642.8 2438.0 4994.4 Phb2 2629.3 4796.7 7800.8 Hspe1 2836.6 4350.7 7098.5 CEM 1 + Yars2 178.8 362.4 674.0 Top 10 Genes Rsl1d1 1920.1 3431.5 5217.9 Ccdc58 1115.3 1316.4 1805.7 Timm13 4127.7 5419.5 8357.0 Pno1 1697.7 2637.7 5750.8

Null module Tomm20l GEO Series "GSE27092" 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=GSE27092 Status: Public on Mar 13 2011 Title: Expression data from P14 TCR cytotoxic T cells overexpressing HDAC7 phosphorylation deficient mutant Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21399638 Summary & Design: Summary: The present study reports an unbiased analysis of the cytotoxic T cell serine-threonine phosphoproteome using high resolution mass spectrometry. Approximately 2,000 phosphorylations were identified in CTLs of which approximately 450 were controlled by TCR signaling. A significantly overrepresented group of molecules identified in the phosphoproteomic screen were transcription activators, co-repressors and chromatin regulators. A focus on the chromatin regulators revealed that CTLs have high expression of the histone deacetylase HDAC7 but continually phosphorylate and export this transcriptional repressor from the nucleus. HDAC7 dephosphorylation results in its nuclear accumulation and suppressed expression of genes encoding key cytokines, cytokine receptors and adhesion molecules that determine CTL function. The screening of the CTL phosphoproteome thus reveals intrinsic pathways of serine-threonine phosphorylation that target chromatin regulators in CTLs and determine the CTL functional program. We used Affymetrix microarray analysis to explore the molecular basis for the role of HDAC7 in CTLs and the impact of GFP-HDAC7 phosphorylation deficient mutant expression on the CTL transcriptional profile.

Overall design: In vitro generated P14 TCR cytotoxic T cells were retrovirally infected with a construct encoding GFP-HDAC7 phosphorylation deficient mutant, sorted in base of GFP expression (GFP positive and GFP negative) and processed for microarray analysis in three biological replicas.

Background corr dist: KL-Divergence = 0.0166, L1-Distance = 0.0217, L2-Distance = 0.0007, Normal std = 0.7816

0.510 Kernel fit Pairwise Correlations Normal fit

Density 0.255

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

GFP negativeGFP negative 1GFP (biological negative 2GFP (biological replicapositive 3GFP (biological 1)replicapositive 1 (0.161931) GFP(biological 2)replicapositive 2 (0.162047) (biological replica3) 3 (0.169507) (biological 1)replica (0.162412) 2)replica (0.124604)[ min 3) (0.219499) ] [ medium ] [ max ] CEM 1 Tomm20 13314.8 19205.6 20918.0 P ( S | Z, I ) = 1.00 Tomm22 6560.6 8330.1 8529.9 Mean Corr = 0.92401Tomm40 1020.4 2179.0 2531.5 Tomm70a 1904.2 3844.0 4536.0 Tomm7 6079.3 6981.2 7116.0 Nhp2 6532.0 13597.8 13931.6 C1qbp 5822.3 12874.0 13712.0 Mrpl12 4911.2 8619.5 9450.4 Phb2 5667.8 9380.5 10267.0 Hspe1 3440.0 6857.4 7299.8 CEM 1 + Yars2 625.9 1062.6 1287.6 Top 10 Genes Rsl1d1 2880.4 5152.1 5701.6 Ccdc58 1409.0 2681.8 2962.9 Timm13 6431.4 10741.1 11328.6 Pno1 1954.1 4565.4 4756.7

Null module Tomm20l GEO Series "GSE16874" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 12 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

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

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

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

0.423 Kernel fit Pairwise Correlations Normal fit

Density 0.212

0.000 CEM 1

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

Pre-normalization Quantiles

BCells_WildType_day0_REP1BCells_WildType_day0_REP2BCells_WildType_day0_REP3BCells_Transgenic_day0_REP1 BCells_Transgenic_day0_REP2(0.0745261) BCells_Transgenic_day0_REP3(0.103519) BCells_WildType_day2_REP1(0.071103)BCells_WildType_day2_REP2 (0.0872712)BCells_WildType_day2_REP3 (0.053231)BCells_Transgenic_day2_REP1 (0.0989676) BCells_Transgenic_day2_REP2(0.0766632) BCells_Transgenic_day2_REP3(0.0884649) (0.103617) (0.0473628) (0.0426523)[ (0.152621)min ] [ medium ] [ max ] CEM 1 Tomm20 4625.6 9722.3 11717.5 P ( S | Z, I ) = 1.00 Tomm22 1421.0 2971.7 3481.1 Mean Corr = 0.92162Tomm40 535.8 2492.1 3225.6 Tomm70a 624.2 1534.1 1919.3 Tomm7 1494.3 2551.3 3705.2 Nhp2 1109.3 6414.3 8428.1 C1qbp 2098.9 11772.6 14129.1 Mrpl12 1107.2 4411.6 5738.2 Phb2 2907.2 7985.4 10560.4 Hspe1 1033.1 4554.7 6145.6 CEM 1 + Yars2 277.3 542.4 835.4 Top 10 Genes Rsl1d1 1292.0 5821.1 7207.8 Ccdc58 320.7 1752.7 1979.6 Timm13 1891.7 4827.6 5583.8 Pno1 926.4 6622.4 7842.1

Null module Tomm20l GEO Series "GSE23833" 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=GSE23833 Status: Public on Sep 01 2010 Title: The Forkhead factor FoxQ1 influences epithelial differentiation Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 20717954 Summary & Design: Summary: The Forkhead family of transcription factors comprises numerous members and is implicated in various cellular functions, including cell growth, apoptosis, migration and differentiation.In this study we identified the Forkhead factor FoxQ1 as increased in expression during TGF-beta1 induced changes in epithelial differentiation, suggesting functional roles of FoxQ1 for epithelial plasticity.The repression of FoxQ1 in mammary epithelial cells led to a change in cell morphology characterized by an increase in cell size, pronounced cell-cell contacts and an increased expression of several junction proteins (e.g. E-cadherin). In addition, FoxQ1 knock-down cells revealed rearrangements in the actin-cytoskeleton and slowed down cell cycle G1-phase progression.Furthermore, repression of FoxQ1 enhanced the migratory capacity of coherent mammary epithelial cells.Gene expression profiling of NM18 cells indicated that FoxQ1 is a relevant downstream mediator of TGF-beta1 induced gene expression changes. This included the differential expression of transcription factors involved in epithelial plasticity, e.g. Ets-1, Zeb1 and Zeb2.In summary, this study has elucidated the functional impact of FoxQ1 on epithelial differentiation

Overall design:

Background corr dist: KL-Divergence = 0.0453, L1-Distance = 0.0772, L2-Distance = 0.0080, Normal std = 0.6930

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

2h_co._enriched12h_co._enriched22h_co._enriched3 (0.0781236)2h_co._total1 (0.0692719)2h_co._total2 (0.046023) (0.0502169)2h_co._total3 (0.120956)2h_TGFbeta_enriched1 (0.221421)2h_TGFbeta_enriched22h_TGFbeta_enriched32h_TGFbeta_total1 (0.084008)2h_TGFbeta_total2 (0.0833581)2h_TGFbeta_total3 (0.0662432) (0.0478421) (0.0757659) (0.0567705)[ min ] [ medium ] [ max ] CEM 1 Tomm20 1616.5 5298.0 8191.4 P ( S | Z, I ) = 1.00 Tomm22 850.1 2616.6 3190.5 Mean Corr = 0.91755Tomm40 182.3 744.0 921.2 Tomm70a 761.1 1607.5 2052.9 Tomm7 477.5 1446.4 2205.5 Nhp2 340.0 1457.9 2315.4 C1qbp 1788.6 8074.8 10490.8 Mrpl12 642.5 2125.4 2684.6 Phb2 1008.1 4307.0 5795.3 Hspe1 283.2 760.5 949.9 CEM 1 + Yars2 226.3 461.3 586.7 Top 10 Genes Rsl1d1 1034.2 2269.3 2810.9 Ccdc58 384.7 846.1 1041.1 Timm13 686.6 3417.1 5229.0 Pno1 1416.1 4729.6 5733.3

Null module Tomm20l GEO Series "GSE19885" 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=GSE19885 Status: Public on Feb 08 2013 Title: Gene expression data from rapamycin resistant and sensitive cell lines Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 23300087 Summary & Design: Summary: The mammalian target of rapamycin (mTOR) is a central regulator of cell proliferation. Inhibitors of mTOR are being evaluated as anti-tumor agents. Given the emerging role of microRNAs (miRNAs) in tumorgenesis we hypothesized that miRNAs could play important roles in the response of tumors to mTOR inhibitors. Rapamycin resistant myogenic cells developed by long-term rapamycin treatment showed extensive reprogramming of miRNAs expression, characterized by up-regulation of the mir-17~92 and related clusters and down-regulation of tumor-suppressor miRNAs. Antagonists of oncogenic miRNA families and mimics of tumor suppressor miRNAs (let-7) restored rapamycin sensitivity in resistant tumor cells. This study identified miRNAs as new downstream components of the mTOR-signaling pathway, which may determine the response of tumors to mTOR inhibitors.

Overall design: Total RNA extraction and hybridization on Affymetrix microarrays of rapamycin sensitive (RS) cells (BC3H1, mouse brain tumor cell line with myogenic properties, ATCC) cultured in Dulbeccos modified essential medium (DMEM) media supplemented with 20% fetal bovine serum (FBS), penicillin (100 U/ml) and streptomycin (100 mg/ml). Rapamycin resistant cells (RR1) were developed by culturing BC3H1 cells in the presence of 1 uM rapamycin for 6 months. Three samples in triplicates: 1) Rapamycin sensitive cells treated with DMSO for 24 h(BC3H1, reference), 2) Rapamycin sensitive cells treated for 24 h with 100 nM rapamycin (BC3H1+R), 3) Rapamycin resistant cells constantly treated with 1uM Rapamycion (RR1+R).

Background corr dist: KL-Divergence = 0.0520, L1-Distance = 0.0558, L2-Distance = 0.0044, Normal std = 0.6110

0.719 Kernel fit Pairwise Correlations Normal fit

Density 0.359

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

RS_DMSO_rep1RS_DMSO_rep2RS_DMSO_rep3 (0.0414992)RS_Rap_rep1 (0.0984919)RS_Rap_rep2 (0.0675685) (0.0879209)RS_Rap_rep3 (0.0665217)RR_Rap_rep-1 (0.0870424)RR_Rap_rep-2 RR_Rap_rep-3(0.190556) (0.147341) (0.213059) [ min ] [ medium ] [ max ] CEM 1 Tomm20 7632.8 9625.8 22214.3 P ( S | Z, I ) = 1.00 Tomm22 3603.5 4177.4 5048.2 Mean Corr = 0.91401Tomm40 1149.0 2406.4 4052.2 Tomm70a 916.3 1382.2 3525.3 Tomm7 1232.2 1904.7 5017.0 Nhp2 2010.4 5294.9 11489.8 C1qbp 4791.4 7126.6 14414.7 Mrpl12 1813.4 4263.3 7422.0 Phb2 3258.3 4371.1 9207.1 Hspe1 2924.6 5700.4 10612.2 CEM 1 + Yars2 287.0 484.1 868.5 Top 10 Genes Rsl1d1 2497.5 3507.5 6523.5 Ccdc58 1125.9 1468.3 3676.6 Timm13 3774.6 5969.4 7239.8 Pno1 2538.9 5054.5 5548.7

Null module Tomm20l GEO Series "GSE13408" 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=GSE13408 Status: Public on Sep 01 2009 Title: Cell cycle exit and terminal differentiation independent of the Rb gene family during embryonic development Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21059851 Summary & Design: Summary: The retinoblastoma cell cycle regulator pRb and the two related proteins p107 and p130 are thought to suppress cancer development both by inhibiting the G1/S transition of the cell cycle in response to growth-arrest signals and by promoting cellular differentiation. Here, we investigated the phenotype of Rb family triple knock-out (TKO) embryonic stem cells as they differentiate in vivo and in culture. Confirming the central role of the Rb gene family in cell cycle progression, TKO mouse embryos did not survive past mid-gestation and differentiating TKO cells displayed increased proliferation and cell death. However, patterning and cell fate determination were largely unaffected in these TKO embryos. Furthermore, a number of TKO cells, including in the neural lineage, were able to exit the cell cycle in G1 and terminally differentiate. This ability of Rb family TKO cells to undergo cell cycle arrest was associated with the repression of target genes for the E2F6 transcription factor, uncovering a pRb-independent control of the G1/S transition of the cell cycle. These results show that the Rb gene family is required for proper embryonic development but is not absolutely essential to induce G1 arrest and differentiation in certain lineages.

Overall design: Genome-wide gene expression was analyzed for wild-type and TKO ESC and EB cells. Three biological replicates were isolated for wild-type ESCs, TKO ESCs, and wild-type EBs, while five biological replicates were isolated for TKO EBs.

Background corr dist: KL-Divergence = 0.0569, L1-Distance = 0.0273, L2-Distance = 0.0013, Normal std = 0.5413

0.737 Kernel fit Pairwise Correlations Normal fit

Density 0.368

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

TKO EBTKO (2-55-2) EBWT (14-14-4) (0.0520606) EB (B21)WT (0.0542284) ESC (0.11016)WT (B21) EB (0.0964996)(J1)WT ESC(0.0590739)WT (J1) EB (0.0463571) (R1)WT ESC (0.0511433)TKO (R1) EB (0.0750264)TKO (7-4-1) ESC TKO(0.086199) (7-4-1) EBTKO (Dutch) (0.0836113) ESCTKO (0.0113798) (Dutch) EBTKO (Ta1-12) (0.0628851) ESC (0.0918078)(Ta1-12) (0.119568) [ min ] [ medium ] [ max ] CEM 1 Tomm20 7907.9 11996.0 14139.7 P ( S | Z, I ) = 1.00 Tomm22 2391.1 3073.1 3701.6 Mean Corr = 0.90499Tomm40 693.0 1740.8 3159.0 Tomm70a 1120.1 2591.7 4218.1 Tomm7 1831.0 3875.9 4090.2 Nhp2 1744.3 7013.6 11302.3 C1qbp 4313.8 8507.5 11386.9 Mrpl12 1878.8 3319.0 5081.0 Phb2 4240.4 5839.6 7164.3 Hspe1 3583.6 6229.9 9111.6 CEM 1 + Yars2 206.5 335.4 758.7 Top 10 Genes Rsl1d1 1873.6 4172.5 6385.4 Ccdc58 1032.4 3237.3 4255.2 Timm13 3464.3 4593.5 5186.1 Pno1 2325.3 4896.9 8550.0

Null module Tomm20l GEO Series "GSE19079" 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=GSE19079 Status: Public on Nov 19 2010 Title: Myocardial expression data from wild-type and akt2-/- mice Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: Wild-type (WT) C57Bl/6 and akt2-/- male mice.

Keywords: RNA Expression Array

Overall design: Left ventricles (LV) from 12-16 week-old male wild type mice and age-matched akt2-/- mice

Background corr dist: KL-Divergence = 0.0153, L1-Distance = 0.0204, L2-Distance = 0.0006, Normal std = 0.7977

0.500 Kernel fit Pairwise Correlations Normal fit

Density 0.250

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 LV,Mouse akt2-/- LV,Mouse 1 WT (0.297344) LV,Mouse1 (0.297715) WT LV,Mouse2 (0.161261) WT LV,Mouse3 (0.092476) akt2-/- LV, 2 akt2-/- (0.0945561) 3 (0.056647)[ min ] [ medium ] [ max ] CEM 1 Tomm20 5955.7 7641.3 8422.3 P ( S | Z, I ) = 1.00 Tomm22 2363.6 4648.7 4841.8 Mean Corr = 0.89797Tomm40 1559.4 1784.1 1851.7 Tomm70a 671.8 1346.7 1395.9 Tomm7 2167.4 3613.8 3907.3 Nhp2 636.8 687.0 781.0 C1qbp 5774.9 8219.4 8389.0 Mrpl12 7544.3 9958.8 10370.7 Phb2 6422.7 7333.3 7622.0 Hspe1 2961.2 3267.6 3928.9 CEM 1 + Yars2 607.5 935.6 979.7 Top 10 Genes Rsl1d1 1320.5 1897.6 2015.9 Ccdc58 1235.2 1659.5 1822.2 Timm13 3227.1 4083.4 4811.6 Pno1 1921.4 3228.0 3385.1

Null module Tomm20l GEO Series "GSE44175" 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=GSE44175 Status: Public on Feb 09 2013 Title: Expression data from mouse embyonic stem cell, neural progenitor and neuron Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 23775126 Summary & Design: Summary: The effect of HMGN1 protein on gene expression of mouse ESC, NP and Neurons were investigated by comparing the transcriptome between Hmgn1+/+ and Hmgn1 -/- cells.

Overall design: three cell types, two genotypes, three reps per sample type

Background corr dist: KL-Divergence = 0.0123, L1-Distance = 0.0320, L2-Distance = 0.0019, Normal std = 0.8462

0.471 Kernel fit Pairwise Correlations Normal fit

Density 0.236

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

EmbyonicEmbyonic stemEmbyonic cell, stem Hmgn1+/+,Neural cell, stem Hmgn1+/+, progenitor,Neural cell, biological Hmgn1+/+, progenitor,Neural biological Hmgn1+/+, rep1 progenitor,Neuron, biological (0.060242) Hmgn1+/+, rep2Neuron, biological Hmgn1+/+, (0.0689714) Hmgn1+/+, rep3Neuron, biological Hmgn1+/+, (0.131136)rep1 biologicalEmbyonic biological(0.00820966)Hmgn1+/+, rep2 biologicalEmbyonic rep1(0.00875806) stem rep3 biological(0.0570982)Embyonic rep2cell,(0.00607638) stem (0.0585468)Hmgn1-/-,Neural rep3cell, stem (0.0589405)Hmgn1-/-, progenitor,Neural cell, biological Hmgn1-/-, progenitor,Neural biological Hmgn1-/-,rep1 progenitor,Neuron, biological(0.076245) Hmgn1-/-,rep2 biologicalNeuron, Hmgn1-/-, (0.117402) Hmgn1-/-,rep3 biologicalNeuron, Hmgn1-/-, (0.0908891)rep1 biological biological(0.0136231) Hmgn1-/-, rep2 biological rep1(0.0173823) rep3 biological(0.0709003) rep2(0.0143587) (0.0718319) rep3[ min (0.0693887) ] [ medium ] [ max ] CEM 1 Tomm20 5657.7 9323.5 14140.3 P ( S | Z, I ) = 1.00 Tomm22 2472.8 3992.2 4699.0 Mean Corr = 0.89229Tomm40 340.5 1220.9 1871.7 Tomm70a 600.0 2074.8 5806.4 Tomm7 3832.6 4322.6 6301.5 Nhp2 802.2 3763.3 7078.3 C1qbp 2763.1 7990.8 11718.0 Mrpl12 1456.0 3284.4 4227.8 Phb2 1919.6 4913.9 5642.6 Hspe1 1493.1 4147.3 6755.3 CEM 1 + Yars2 184.5 879.1 1531.5 Top 10 Genes Rsl1d1 1544.5 4032.2 8141.4 Ccdc58 711.7 1740.5 4078.4 Timm13 4112.2 5134.5 6140.2 Pno1 594.6 3367.8 5643.4

Null module Tomm20l 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 (0.125165) day lung-embryoMouse 14-rep1 (0.122209) day lung-embryoMouse 14-rep2 (0.11405) day lung-embryoMouse 16-rep1 (0.0805392) day lung-embryoMouse 16-rep2 (0.0724277) day lung-postnatalMouse 18-rep1 (0.0490437) day lung-postnatalMouse 18-rep2 (0.0589722) lung-postnatalMouseday (0.0360939) 2-rep1 lung-postnatalMouseday (0.0254518)2-rep2 lung-postnatalMouseday (0.0332849)10-rep1 lung-postnatalday 10-rep2 (0.0574475) day 30-rep1 (0.051875) day 30-rep2 (0.0842504)[ min (0.0891904) ] [ medium ] [ max ] CEM 1 Tomm20 2085.4 3765.3 5733.2 P ( S | Z, I ) = 1.00 Tomm22 1644.1 2237.1 3648.9 Mean Corr = 0.88853Tomm40 518.6 593.4 1355.2 Tomm70a 488.7 709.8 1879.9 Tomm7 1522.7 2496.6 3644.0 Nhp2 405.2 582.5 2655.8 C1qbp 1112.9 1403.9 4761.9 Mrpl12 948.4 1179.5 3759.2 Phb2 1286.6 1983.2 4670.7 Hspe1 887.5 1252.1 4920.6 CEM 1 + Yars2 94.9 161.3 477.7 Top 10 Genes Rsl1d1 783.9 1194.4 3517.0 Ccdc58 310.8 626.7 1580.3 Timm13 1935.1 2721.6 3979.7 Pno1 638.6 1095.1 2723.5

Null module Tomm20l GEO Series "GSE6482" 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=GSE6482 Status: Public on Jan 01 2007 Title: mECK36: a cell and animal model of virally induced Kaposi's sarcoma Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 17349582 Summary & Design: Summary: Transfection of a Kaposi's sarcoma (KS) herpesvirus (KSHV) Bacterial Artificial Chromosome (KSHVBac36) into mouse bone marrow endothelial lineage cells generated a cell (mECK36) that induced KS-like tumors in mice. mECK36 formed KSHV-harboring vascularized spindle-cell sarcomas that were LANA+ and displayed a KSHV and host transcriptomes reminiscent of KS tumors.

Keywords: Cell type comparison

Overall design: There are three biological replicates per sample. Tumors (mKS) were compared the the human KS signature. mECK36 and mEC-V were compared to putative BM lineage cells.

Background corr dist: KL-Divergence = 0.0664, L1-Distance = 0.0251, L2-Distance = 0.0010, Normal std = 0.5172

0.771 Kernel fit Pairwise Correlations Normal fit

Density 0.386

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

mECK36mECK36 1 (0.0374337)mECK36 2 (0.0318353)mEC-V 3 (0.11406) mEC-V1 (0.177882) mEC-V2 (0.17785) mKS13 (0.116927) (0.0702822)mKS2 (0.0501255)mKS3 (0.223605) [ min ] [ medium ] [ max ] CEM 1 Tomm20 2389.8 5090.0 10572.6 P ( S | Z, I ) = 1.00 Tomm22 1282.6 2684.9 3811.1 Mean Corr = 0.88835Tomm40 1471.2 2317.0 3437.5 Tomm70a 641.0 1010.7 2085.0 Tomm7 1056.3 1420.6 2077.4 Nhp2 1515.9 2425.0 2651.6 C1qbp 1470.2 4256.1 5899.0 Mrpl12 929.2 1188.5 2267.1 Phb2 3286.1 4030.6 5795.6 Hspe1 1503.1 1820.7 6009.2 CEM 1 + Yars2 107.9 563.9 693.2 Top 10 Genes Rsl1d1 1331.0 2639.9 3358.5 Ccdc58 438.0 661.2 1848.6 Timm13 1865.8 2326.8 2705.5 Pno1 855.8 2023.6 2629.2

Null module Tomm20l GEO Series "GSE7275" 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=GSE7275 Status: Public on Sep 05 2007 Title: Evaluation of murine mast cells derived exosomal RNA versus their parental cells MC/9. Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 17486113 Summary & Design: Summary: Exosomes are vesicles of endocytic origin released by many types of cells into the extracellular environment. In an attempt to further examine the exosome-mediated cellular communication, we show that exosomes from a mouse mast cell line (MC/9), exosomes from primary bone marrow derived mast cells, and exosomes from a human mast cell line (HMC-1) contain RNA but not DNA.

Microarray assessments of exosome-derived RNA revealed that these vesicles contain mRNA from approximately 1200 genes, many of which are unique and not present in the cytoplasmic RNA pool in the donor cell.

Keywords: Exosomal RNA versus their parental cells, MC/9

Overall design: Exosomes were prepared from the supernatant of MC/9 cells by differential centrifugations and filtration. RNA was isolated from the exosomes and their parental cells using Trizo. The microarray experiments were performed by SweGene (www.swegene.org/) according to Affymetrix microarray DNA chip analysis. The experiment was performed in quadruple samples. ExoRNA1, ExoRNA2, ExoRNA3, and ExoRNA4 for the exosomes samples and Mast_cells1, Mast_cells2, Mast_cells3, and Mast_cells4 for the MC/9 cells.

Background corr dist: KL-Divergence = 0.0228, L1-Distance = 0.0688, L2-Distance = 0.0086, Normal std = 0.8711

0.458 Kernel fit Pairwise Correlations Normal fit

Density 0.229

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

ExosomalExosomal RNA,Exosomal biological RNA,Exosomal biological RNA, rep1Mast biological(0.144079) RNA, rep2 cellsMast biological(0.114165) RNA, rep3 cellsMast biological(0.084019) RNA, rep4 cellsMast biological(0.144722) RNA, rep1 cells biological(0.0780439) RNA, rep2 biological(0.0598313) rep3 (0.207556) rep4[ (0.167583)min ] [ medium ] [ max ] CEM 1 Tomm20 1511.5 10569.9 14674.4 P ( S | Z, I ) = 1.00 Tomm22 904.3 2142.6 2742.7 Mean Corr = 0.88660Tomm40 168.7 686.7 1689.8 Tomm70a 23.8 1348.4 2590.3 Tomm7 298.5 2929.8 4965.5 Nhp2 87.9 3026.6 5699.9 C1qbp 60.1 3195.7 6459.0 Mrpl12 26.3 4460.2 5720.3 Phb2 384.5 3511.3 5067.1 Hspe1 28.1 1283.6 1819.3 CEM 1 + Yars2 39.8 396.6 526.0 Top 10 Genes Rsl1d1 102.5 2876.6 3711.5 Ccdc58 386.3 1166.1 1505.4 Timm13 31.7 3434.4 3900.7 Pno1 31.1 1427.5 1835.7

Null module Tomm20l GEO Series "GSE12518" 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=GSE12518 Status: Public on Apr 15 2009 Title: Differential expression profile between MNV-1 infected and mock-infected RAW 264.7 cells. Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 19211757 Summary & Design: Summary: Noroviruses have been widely recognized for their importance as causative agents of non-bacterial gastroenteritis. Mouse norovirus is the only representative of the norovirus genus, family Caliciviridae, able to grow in cell culture. The aim of this study is to describe the differences in the expression profiles of MNV-1 and mock-infected macrophages (RAW 264.7 cells), in order to better understand the response of the host cell to norovirus infection.

Overall design: This study compares two type of samples (MNV-infected and mock-infected RAW cells) in biological triplicates respectively. The MNV stock used for infection was obtained in the same cell line, and purified with a sucrose cushion in order to account for expression changes caused by virus infection only.

Background corr dist: KL-Divergence = 0.0217, L1-Distance = 0.0741, L2-Distance = 0.0057, Normal std = 0.9739

0.425 Kernel fit Pairwise Correlations Normal fit

Density 0.213

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

Macrophages_MNVinfected_12h_rep1Macrophages_MNVinfected_12h_rep2Macrophages_MNVinfected_12h_rep3Macrophages_mock-infected_12h_rep1Macrophages_mock-infected_12h_rep2Macrophages_mock-infected_12h_rep3 (0.436448) (0.146941) (0.0434967) (0.110405)[ (0.205382)min (0.0573272) ] [ medium ] [ max ] CEM 1 Tomm20 2426.6 6585.3 7580.3 P ( S | Z, I ) = 1.00 Tomm22 1191.5 2307.5 2694.1 Mean Corr = 0.88832Tomm40 1248.7 2306.4 2791.3 Tomm70a 1141.4 3918.0 5603.7 Tomm7 907.5 2684.9 3278.4 Nhp2 2459.6 6859.0 9816.5 C1qbp 3270.2 9813.0 11690.9 Mrpl12 1727.7 4373.0 7083.8 Phb2 5797.5 8440.9 12472.3 Hspe1 4322.9 8086.3 11285.0 CEM 1 + Yars2 564.4 778.7 839.5 Top 10 Genes Rsl1d1 2083.5 3946.7 4649.4 Ccdc58 1304.2 2345.3 2810.7 Timm13 2331.5 4761.0 6591.8 Pno1 1934.4 2829.2 4183.0

Null module Tomm20l GEO Series "GSE8295" 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=GSE8295 Status: Public on Jul 24 2007 Title: Comprehensive analysis of PPARÎ±-dependent regulation of hepatic lipid metabolism by expression profiling - 4 Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 18288265 Summary & Design: Summary: PPARÎ± is a ligand-activated transcription factor involved in the regulation of nutrient metabolism and inflammation. Although much is already known about the function of PPARÎ± in hepatic lipid metabolism, many PPARÎ±-dependent pathways and genes have yet to be discovered. In order to obtain an overview of PPARÎ±-regulated genes relevant to lipid metabolism, and to probe for novel candidate PPARÎ± target genes, livers from several animal studies in which PPARÎ± was activated and/or disabled were analyzed by Affymetrix GeneChips. Numerous novel PPARÎ±-regulated genes relevant to lipid metabolism were identified. Out of this set of genes, eight genes were singled out for study of PPARÎ±-dependent regulation in mouse liver and in mouse, rat, and human primary hepatocytes, including thioredoxin interacting protein (Txnip), electron-transferring-flavoprotein Î² polypeptide (Etfb), electron-transferring-flavoprotein dehydrogenase (Etfdh), phosphatidylcholine transfer protein (Pctp), endothelial lipase (EL, Lipg), adipose triglyceride lipase (Pnpla2), hormone-sensitive lipase (Lipe), and monoglyceride lipase (Mgll). Using an in silico screening approach, one or more PPAR response elements (PPREs) were identified in each of these genes. Since Pnpla2, Lipe, and Mgll contribute to hepatic triglyceride hydrolysis, gene regulation was studied under conditions of elevated hepatic lipids. In wild-type mice fed a high fat diet, the decrease in hepatic lipids following treatment with the PPARÎ± agonist Wy14643 was paralleled by significant up-regulation of Pnpla2, Lipe, and Mgll, suggesting that induction of triglyceride hydrolysis may contribute to the anti-steatotic role of PPARÎ±. Our study illustrates the power of transcriptional profiling to uncover novel PPARÎ±-regulated genes and pathways in liver.

Keywords: identification of target genes

Overall design: Five microgram total RNA was labelled according to the ENZO-protocol, fragmented and hybridized according to Affymetrix's protocols.

Background corr dist: KL-Divergence = 0.1374, L1-Distance = 0.0285, L2-Distance = 0.0011, Normal std = 0.4050

1.003 Kernel fit Pairwise Correlations Normal fit

Density 0.502

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_wildtype_WY14643_5d_rep1liver_wildtype_WY14643_5d_rep2liver_wildtype_WY14643_5d_rep3liver_wildtype_WY14643_5d_rep4liver_PPARa-knockout_WY14643_5d_rep1 (0.129195)liver_PPARa-knockout_WY14643_5d_rep2 (0.154883)liver_PPARa-knockout_WY14643_5d_rep3 (0.208515)liver_PPARa-knockout_WY14643_5d_rep4 (0.159627)liver_wildtype_control_5d_rep1liver_wildtype_control_5d_rep2 (0.0163094)liver_wildtype_control_5d_rep3 (0.0359685)liver_wildtype_control_5d_rep4 (0.0212278)liver_PPARa-knockout_control_5d_rep1 (0.026087) (0.0552015)liver_PPARa-knockout_control_5d_rep2 (0.0108281)liver_PPARa-knockout_control_5d_rep3 (0.0107353)liver_PPARa-knockout_control_5d_rep4 (0.0299902) (0.0417442) (0.0204044)[ min (0.0138136) (0.0654698)] [ medium ] [ max ] CEM 1 Tomm20 3235.9 4055.4 5730.9 P ( S | Z, I ) = 1.00 Tomm22 1891.1 2151.5 3059.3 Mean Corr = 0.88455Tomm40 1752.9 2089.1 4234.6 Tomm70a 1974.6 2749.2 4419.6 Tomm7 1932.8 2391.2 3425.1 Nhp2 1688.8 2035.7 4970.0 C1qbp 6316.9 7179.6 8586.2 Mrpl12 5758.3 6521.0 7758.7 Phb2 12190.2 13959.8 25471.2 Hspe1 1777.2 2100.4 4008.0 CEM 1 + Yars2 439.9 738.2 899.1 Top 10 Genes Rsl1d1 1088.7 1367.1 2409.6 Ccdc58 1633.0 2091.6 3107.3 Timm13 7405.0 8639.7 12004.4 Pno1 2125.2 2554.2 3015.7

Null module Tomm20l GEO Series "GSE7069" 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=GSE7069 Status: Public on Apr 20 2007 Title: Zfx controls the self-renewal of embryonic and hematopoietic stem cells Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 17448993 Summary & Design: Summary: Stem cells (SC) exhibit a unique capacity for self-renewal in an undifferentiated state. It is unclear whether the self-renewal of pluripotent embryonic SC (ESC) and of tissue-specific adult SC such as hematopoietic SC (HSC) is controlled by common mechanisms. The deletion of transcription factor Zfx impaired the self-renewal but not the differentiation capacity of murine ESC; conversely, Zfx overexpression facilitated ESC self-renewal by opposing differentiation. Furthermore, Zfx deletion abolished the maintenance of adult bone marrow HSC, but did not affect erythromyeloid progenitors or fetal HSC. In both ESC and HSC, Zfx activated a common set of direct target genes. In addition, the loss of Zfx resulted in the induction of immediate-early and/or stress-inducible genes in both SC types but not in their differentiated progeny. These studies identify the first shared transcriptional regulator of ESC and HSC, suggesting a common molecular basis of self-renewal in embryonic and adult SC.

Keywords: Global gene expression data analysis in Zfx-deficient murine ESC and HSC

Overall design: arrays (Affymetrix) at the Columbia University Microarray Project core facility according to the manufacturer's instructions. Samples were hybridized in duplicates, with the correlation between duplicate samples calculated at 0.995-0.997. Quality control and normalization were performed using positive and negative hybridization controls (Affymetrix) spiked into the RNA prior to labeling. Linear amplification of RNA was confirmed for every sample. Array scanning and raw data processing were done using GCOS 1.4 software (Affymetrix).

Background corr dist: KL-Divergence = 0.0096, L1-Distance = 0.0136, L2-Distance = 0.0002, Normal std = 0.8717

0.458 Kernel fit Pairwise Correlations Normal fit

Density 0.229

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

ESC_Zfx-flox_Replicate1ESC_Zfx-flox_Replicate2ESC_Zfx-null_Replicate1ESC_Zfx-null_Replicate2 (0.209417)HSC_Zfx-cko_Replicate1 (0.198974)HSC_Zfx-cko_Replicate2 (0.0270603)HSC_Zfx-flox_Replicate1 (0.0936696)HSC_Zfx-flox_Replicate2 (0.141674) (0.198024) (0.0706967) (0.0604846)[ min ] [ medium ] [ max ] CEM 1 Tomm20 3011.7 9333.9 10975.4 P ( S | Z, I ) = 1.00 Tomm22 1293.7 3163.4 3978.2 Mean Corr = 0.87624Tomm40 109.9 2150.7 3438.5 Tomm70a 1451.1 2792.6 4204.6 Tomm7 2716.1 4345.2 5907.2 Nhp2 865.5 4874.7 6339.2 C1qbp 5550.9 6244.2 10277.1 Mrpl12 1150.8 2843.1 3397.2 Phb2 2250.5 4901.0 6664.6 Hspe1 892.1 5418.3 8078.1 CEM 1 + Yars2 213.9 819.1 1370.9 Top 10 Genes Rsl1d1 469.3 4632.6 6026.0 Ccdc58 632.3 2076.0 2823.4 Timm13 2834.0 3973.3 4517.9 Pno1 1784.8 3932.7 4487.2

Null module Tomm20l GEO Series "GSE6998" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 32 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

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

and repair after injury. Whether this response

represents simple hyperplasia of various liver elements

or requires recapitulation of the genetic program of

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

we examined transcriptional programs of

adult liver after partial hepatectomy and contrasted

these with developing embryonic liver. Principal component

analysis demonstrated that the time series of

gene expression during liver regeneration does not segregate

according to developmental transcription patterns.

Gene ontology analysis revealed that liver restoration

after hepatectomy and liver development differ

dramatically with regard to transcription factors

and chromatin structure modification. In contrast, the

tissues are similar with regard to proliferationassociated

genes. Consistent with these findings, realtime

polymerase chain reaction showed transcription

factors known to be important in liver development

are not induced during liver regeneration. These three

lines of evidence suggest that at a transcriptional level,

restoration of liver mass after injury is best described

as hepatocyte hyperplasia and not true regeneration.

We speculate this novel pattern of gene expression may

underlie the unique capacity of the liver to repair itself

after injury.

Keywords: time course

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

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

0.727 Kernel fit Pairwise Correlations Normal fit

Density 0.364

0.000 CEM 1

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

Pre-normalization Quantiles

baselinebaseline sampleregeneration sampleat T0,regeneration rep1 at T0, (0.0245156)sampleregeneration rep2 (0.0296385) sampleatregeneration T1, rep1 sampleatregeneration T1, (0.0180755) rep2 sampleatregeneration T2, (0.0170973) rep1 sampleatregeneration T2, (0.024934) rep2 sampleatregeneration T6, (0.0157998) rep1 sampleatregeneration T6, (0.0133932) rep2 sampleatregeneration T12, (0.0364985) samplerep1atregeneration T12, (0.0148392) samplerep2atregeneration T18, (0.0360262) samplerep1atregeneration T18, (0.00818818) samplerep2atregeneration T24, (0.00568981) samplerep1atregeneration T24, (0.0332569) samplerep2atregeneration T30, (0.00941192) samplerep1atregeneration T30, (0.0190708) samplerep2atregeneration T48, (0.012735) samplerep1atdevelopmental T48, (0.0116431) samplerep2atdevelopmental T72, (0.0489392) rep1at developmentalsample T72, (0.0204336) rep2 developmental sampleat T105,(0.0226172) developmental sampleat rep1 T105, (0.020467) developmental sampleat rep2 T115, (0.0301155) developmental sampleat rep1 T115, (0.0816845) developmental sampleat rep2 T125, (0.138036) developmental sampleat rep1 T125, (0.0470557) developmental sampleat rep2 T135, (0.0787956) developmental sampleat rep1 T135, (0.0420163) developmental sampleat rep2 T145, (0.0498171) sampleat rep1 T145, (0.0250033) sampleat rep2 T165, (0.0282778) at rep1 T165, (0.0211969)[ rep2min (0.0147304) ] [ medium ] [ max ] CEM 1 Tomm20 862.4 2547.2 7057.0 P ( S | Z, I ) = 1.00 Tomm22 677.3 903.7 2219.7 Mean Corr = 0.87271Tomm40 140.4 749.6 2224.3 Tomm70a 896.1 1177.5 2062.1 Tomm7 534.8 1174.3 2118.7 Nhp2 232.0 992.5 3297.1 C1qbp 1203.6 2220.1 6083.2 Mrpl12 1521.5 2938.2 3911.9 Phb2 1545.4 3604.4 6926.4 Hspe1 1215.2 3098.1 6036.9 CEM 1 + Yars2 258.3 327.8 550.9 Top 10 Genes Rsl1d1 397.2 861.4 3131.8 Ccdc58 367.2 739.0 1412.3 Timm13 994.1 2473.4 3669.3 Pno1 804.6 1196.4 2506.1

Null module Tomm20l GEO Series "GSE38257" 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=GSE38257 Status: Public on Dec 21 2012 Title: A Novel Tumor suppressor network in squamous malignancies Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 23145321 Summary & Design: Summary: The specific ablation of Rb1 gene in stratified epithelia (RbF/F;K14cre) promotes proliferation and altered differentiation but is insufficient to produce spontaneous tumors. The pRb relative, p107, compensates some of the functions of pRb in these tissues, however RbF/F;K14cre;p107-/- mice die postnatally. Acute pRb loss in stratified epithelia, using an inducible mouse model (RbF/F;K14creERTM), shows that p107 exerts specific tumor suppressor functions in its absence. After simultaneous absence of pRb and p107, p53 transcriptional function is impaired and Pten expression is reduced. All mutant mice develop spontaneous squamous tumors carcinomas rapidly. Gene expression analysis of mouse tumors, besides supporting the impaired p53 function and the susceptibility to Akt/mTOR inhibitors, also revealed significant overlap with human squamous carcinomas. Thus, RbF/F;K14creERTM;p107-/- may constitute a new mouse model for these malignancies. Collectively, these data demonstrate the existence of a previously unreported functional connection between pRb, Pten and p53 tumor suppressors, through p107, of a particular relevance in squamous tumor development.

Overall design: Gene expression was compared between normal mouse skin and carcinomas arising in the skin of RbF/F;K14creERTM;p107-/- mouse. All mice were treated with tamoxifen.

Background corr dist: KL-Divergence = 0.0326, L1-Distance = 0.0283, L2-Distance = 0.0009, Normal std = 0.6484

0.639 Kernel fit Pairwise Correlations Normal fit

Density 0.320

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

Skin_Normal_1Skin_Normal_2Skin_Normal_3 (0.117423)Skin_Normal_4 (0.140338)Rb_p107_carcinoma_rep1 (0.210214)Rb_p107_carcinoma_rep2 (0.12222)Rb_p107_carcinoma_rep3Rb_p107_carcinoma_rep4 (0.0343515)Rb_p107_carcinoma_rep5 (0.0234658)Rb_p107_carcinoma_rep6 (0.0655077)Rb_p107_carcinoma_rep7 (0.0348842)Rb_p107_carcinoma_rep8 (0.0278028)Rb_p107_carcinoma_rep9 (0.0536858)Rb_p107_carcinoma_rep10 (0.0175283) (0.0290386) (0.0851832) (0.0383569)[ min ] [ medium ] [ max ] CEM 1 Tomm20 2748.3 6354.9 7070.4 P ( S | Z, I ) = 1.00 Tomm22 1505.1 4738.1 5128.5 Mean Corr = 0.86584Tomm40 635.1 1252.9 1444.1 Tomm70a 552.8 1389.6 1728.9 Tomm7 1672.7 3123.0 3455.4 Nhp2 1262.6 5156.0 5784.5 C1qbp 1961.1 3350.4 3945.8 Mrpl12 1398.2 2575.7 3030.6 Phb2 2291.2 3407.6 3947.3 Hspe1 943.2 1644.2 1774.7 CEM 1 + Yars2 103.4 302.1 385.4 Top 10 Genes Rsl1d1 508.6 1530.4 1831.1 Ccdc58 331.2 1044.0 1253.2 Timm13 3439.5 4522.0 5001.2 Pno1 535.4 2050.5 2241.1

Null module Tomm20l GEO Series "GSE27720" 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=GSE27720 Status: Public on Jan 06 2012 Title: AMPK stimulation and PGC-1 alpha suppression in peroxisome deficient hepatocytes favor catabolic over anabolic carbohydrate metabolism Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 22002056 Summary & Design: Summary: These arrays contain data from the livers of 10 week old L-Pex5 -/- male mice

Overall design: 6 arrays, 3 biological replicates

Background corr dist: KL-Divergence = 0.0148, L1-Distance = 0.0326, L2-Distance = 0.0017, Normal std = 0.8076

0.494 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

WT liverL-Pex5 1 (0.305587) WTKnockout liverL-Pex5 2 liver(0.0909479) WTKnockout1 (0.118817) liverL-Pex5 3 liver(0.0777729) Knockout2 (0.350613) liver 3 (0.0562626)[ min ] [ medium ] [ max ] CEM 1 Tomm20 2451.8 3656.9 5258.1 P ( S | Z, I ) = 1.00 Tomm22 2540.7 2692.6 3033.4 Mean Corr = 0.86610Tomm40 1539.4 1730.8 1892.5 Tomm70a 1222.4 1849.3 1967.1 Tomm7 2203.0 2414.9 2626.1 Nhp2 978.9 1878.7 2538.8 C1qbp 3952.7 5301.4 6218.3 Mrpl12 4358.1 5014.5 5351.9 Phb2 4598.8 5367.7 6033.9 Hspe1 2730.9 3765.7 4018.5 CEM 1 + Yars2 565.0 796.3 942.6 Top 10 Genes Rsl1d1 1240.6 1538.0 1838.8 Ccdc58 1297.3 1669.5 1703.3 Timm13 5059.5 6192.4 7649.8 Pno1 1648.1 2464.2 2843.8

Null module Tomm20l GEO Series "GSE13302" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 30 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13302 Status: Public on May 12 2009 Title: Gene expression profiling in the lung and liver of Perfluorooctane sulfonate (PFOS) exposed mouse fetuses Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 19429403 Summary & Design: Summary: Most of the transcriptional changes induced by PFOS in the fetal mouse liver and lung were related to activation of PPARalpha. When compared to the transcript profiles induced by PFOA (Pubmed ID 17681415), few remarkable differences were found other than up-regulation of Cyp3a genes. Because PFOS and PFOA have been shown to differ in their mode of action in the murine neonate, these data suggest that changes related to PFOS-induced neonatal toxicity may not be evident in the fetal transcriptome at term.

Overall design: Thirty timed-pregnant CD-1 mice were orally dosed from gestation day 1-17 with either 0, 5, or 10 mg/kg/day PFOS in 0.5% Tween 20. At term, fetal lung and liver were collected, total RNA prepared, and samples pooled from three fetuses per litter. Five biological replicates consisting of individual litter samples were then evaluated for each treatment group using Affymetrix mouse 430_2 microarrays.

Background corr dist: KL-Divergence = 0.0214, L1-Distance = 0.0694, L2-Distance = 0.0077, Normal std = 0.8465

0.471 Kernel fit Pairwise Correlations Normal fit

Density 0.236

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

0mg/kg/day0mg/kg/day PFOS,0mg/kg/day lungPFOS,0mg/kg/day rep1 liverPFOS, (0.0478847)0mg/kg/day rep1 lungPFOS, (0.0230394)0mg/kg/day rep2 liverPFOS, (0.0232757)0mg/kg/day rep2 lungPFOS, (0.0211981)0mg/kg/day rep3 liverPFOS, (0.0491164)0mg/kg/day rep3 lungPFOS, (0.0112256)0mg/kg/day rep4 liverPFOS, (0.0383331)5mg/kg/day rep4 lungPFOS, (0.0168867)5mg/kg/day rep5 liverPFOS, (0.0660155)5mg/kg/day rep5 lungPFOS, (0.0281779)5mg/kg/day rep1 liverPFOS, (0.0198466)5mg/kg/day rep1 lungPFOS, (0.0396324)5mg/kg/day rep2 liverPFOS, (0.0307362)5mg/kg/day rep2 lungPFOS, (0.0406592)5mg/kg/day rep3 liverPFOS, (0.0408921)5mg/kg/day rep3 lungPFOS, (0.0184662)5mg/kg/day rep4 liverPFOS, (0.0289465)10mg/kg/day rep4 lungPFOS, (0.0426388)10mg/kg/day rep5 liver PFOS, (0.0242726)10mg/kg/day rep5 lungPFOS, (0.0576114)10mg/kg/day rep1 liverPFOS, 10mg/kg/day(0.0352879) rep1 lungPFOS, 10mg/kg/day(0.0180958) rep2 liverPFOS, 10mg/kg/day(0.0163864) rep2 lungPFOS, 10mg/kg/day(0.0370086) rep3 liverPFOS, 10mg/kg/day(0.0354047) rep3 lungPFOS, 10mg/kg/day(0.0506887) rep4 liverPFOS, (0.0280698) rep4 lungPFOS, (0.0560578) rep5 liver (0.0222844) rep5 [(0.0318607) min ] [ medium ] [ max ] CEM 1 Tomm20 3306.8 3792.7 4697.8 P ( S | Z, I ) = 1.00 Tomm22 1432.1 1932.7 2359.5 Mean Corr = 0.86473Tomm40 614.4 1498.3 2151.2 Tomm70a 419.3 1169.1 1772.1 Tomm7 1445.0 2114.5 2638.7 Nhp2 430.6 1309.0 1641.2 C1qbp 1089.4 4024.0 4795.7 Mrpl12 934.9 2904.8 3662.9 Phb2 1919.6 4665.4 5572.7 Hspe1 971.3 2749.8 4763.3 CEM 1 + Yars2 135.2 421.1 630.0 Top 10 Genes Rsl1d1 873.8 1341.1 1692.4 Ccdc58 430.3 1270.8 1844.5 Timm13 1846.4 3492.8 4011.7 Pno1 544.2 1169.6 1579.2

Null module Tomm20l GEO Series "GSE48397" 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=GSE48397 Status: Public on Jul 10 2013 Title: Expression data from (mouse) normal lung fibroblasts and carcinoma-associated fibroblasts Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 22962265 Summary & Design: Summary: Cancer-associated fibroblasts (CAFs) have been reported to support tumor progression by a variety of mechanisms. However, their role in the progression of non-small cell lung cancer (NSCLC) remains poorly defined. In addition, the extent to which specific proteins secreted by CAFs contribute directly to tumor growth is unclear. To study the role of CAFs in NSCLC, a cross-species functional characterization of mouse and human lung CAFs was performed, including gene expression analysis comparing normal mouse lung fibroblasts (NFs) and mouse lung CAFs to seek for differentially-expressed secreted proteins.

Gene expression microarrays were used to identify transcriptomic changes between NFs and CAFs that may contribute to their different tumor-enhancing capacity.

Overall design: NFs and CAFs were grown in vitro for RNA extraction and hybridization on mouse 430_2 Affymetrix microarrays

Background corr dist: KL-Divergence = 0.0594, L1-Distance = 0.0233, L2-Distance = 0.0009, Normal std = 0.5290

0.754 Kernel fit Pairwise Correlations Normal fit

Density 0.377

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

lung fibroblasts,lung fibroblasts,lung biological fibroblasts,lung biological fibroblasts,replicatelung biological fibroblasts,replicate 1carcinoma-asssociated (0.0970422) biological replicate 2carcinoma-asssociated (0.215813) biological replicate 3carcinoma-asssociated (0.263193) replicate 4carcinoma-asssociated (0.186951)fibroblasts, 5carcinoma-asssociated (0.0537331)fibroblasts, biological fibroblasts, biological fibroblasts,replicate biological fibroblasts,replicate 1 (0.0324028) biological[ replicate min2 (0.0213478) biological replicate 3 ](0.026387) replicate 4 (0.0800891) [5 (0.0230411)medium ] [ max ] CEM 1 Tomm20 5857.6 7999.3 12463.0 P ( S | Z, I ) = 1.00 Tomm22 2215.5 2617.7 4239.4 Mean Corr = 0.85520Tomm40 1822.9 2471.0 3056.5 Tomm70a 1176.4 1683.9 2281.7 Tomm7 1642.8 2317.6 4143.6 Nhp2 1218.2 3197.1 7651.1 C1qbp 3192.5 5246.9 6748.2 Mrpl12 1283.2 2643.5 8208.8 Phb2 2242.8 2912.7 5234.0 Hspe1 1943.2 3032.4 5583.5 CEM 1 + Yars2 191.9 432.3 554.7 Top 10 Genes Rsl1d1 1317.5 2368.2 3425.2 Ccdc58 551.1 785.3 1501.6 Timm13 4171.3 5514.8 10386.2 Pno1 1135.2 2653.1 3193.1

Null module Tomm20l GEO Series "GSE42299" 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=GSE42299 Status: Public on Dec 10 2012 Title: Expression profiles of C2C12 myotubes in response to PGC-1Î± (peroxisome proliferator-activated receptor gamma, coactivator 1 alpha) overexpression and/or iron chelation Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 23318259 Summary & Design: Summary: Mitochondria are centers of metabolism and signaling whose content and function must adapt to changing cellular environments. The biological signals that initiate mitochondrial restructuring and the cellular processes that drive this adaptive response are largely obscure. To better define these systems, we performed matched quantitative genomic and proteomic analyses of mouse muscle cells as they performed mitochondrial biogenesis. We find that proteins involved in cellular iron homeostasis are highly coordinated with this process, and that depletion of cellular iron results in a rapid, dose-dependent decrease of select mitochondrial protein levels and oxidative capacity. We further show that this process is universal across a broad range of cell types and fully reversed when iron is reintroduced. Collectively, our work reveals that cellular iron is a key regulator of mitochondrial biogenesis, and provides quantitative datasets that can be leveraged to explore post-transcriptional and post-translational processes that are essential for mitochondrial adaptation.

Overall design: C2C12 mouse myoblasts were differentiated into myotubes for 3 days, at which point they were infected with adenovirus expressing either green fluorescent protein (GFP) or GFP-tagged PGC-1Î± (GFP-PGC-1Î±) Â± treatment with the iron chelator deferoxamine (DFO) (for 4 treatments total). The cells were grown for three more days, then RNA was extracted and applied to Affymetrix Mouse 430 2.0 arrays. Gene expression was measured in biological duplicate (4 treatments ˆ 2 replicates = 8 arrays).

Background corr dist: KL-Divergence = 0.0474, L1-Distance = 0.0332, L2-Distance = 0.0013, Normal std = 0.6028

0.693 Kernel fit Pairwise Correlations Normal fit

Density 0.347

0.000 CEM 1

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

Pre-normalization Quantiles

C2C12_GFP_rep1C2C12_GFP_rep2C2C12_GFP-PGC-1Î±_rep1 (0.101728)C2C12_GFP-PGC-1Î±_rep2 (0.118443)C2C12_GFP-PGC-1Î±+DFO_rep1C2C12_GFP-PGC-1Î±+DFO_rep2 (0.0904976)C2C12_GFP+DFO_rep1 (0.0743478)C2C12_GFP+DFO_rep2 (0.123231) (0.141154) (0.198091) (0.152508)[ min ] [ medium ] [ max ] CEM 1 Tomm20 4545.2 5493.0 5672.4 P ( S | Z, I ) = 1.00 Tomm22 2641.5 3812.4 4183.6 Mean Corr = 0.85021Tomm40 934.2 2328.6 2781.8 Tomm70a 1664.6 2186.8 2508.4 Tomm7 1267.4 1633.9 1752.1 Nhp2 682.0 1299.0 1428.3 C1qbp 2550.9 5515.7 6652.0 Mrpl12 2636.8 6044.7 6609.5 Phb2 3927.6 7730.9 9052.3 Hspe1 1135.6 3103.7 3985.2 CEM 1 + Yars2 327.6 563.3 785.6 Top 10 Genes Rsl1d1 1623.1 2368.5 3102.3 Ccdc58 1022.8 1979.1 2445.2 Timm13 3931.2 5830.4 6373.6 Pno1 1512.5 2984.4 3851.0

Null module Tomm20l GEO Series "GSE26616" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 6 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

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

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

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

0.652 Kernel fit Pairwise Correlations Normal fit

Density 0.326

0.000 CEM 1

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

Pre-normalization Quantiles

Ezh1/2 2KOEzh1/2 FACS 2KOEzh1/2 purified FACS 2KOEzh1/2 purified basalFACS WTEzh1/2 epidermal purifiedFACS matrix WTEzh1/2 purified FACS cellsORS cells WT (0.152486) cellspurified basalFACS(0.10227) (0.249357) epidermal purified matrix cellsORS cells [ (0.368338)cells (0.0480048)min (0.0795441) ] [ medium ] [ max ] CEM 1 Tomm20 6079.9 7686.4 9640.4 P ( S | Z, I ) = 1.00 Tomm22 2558.6 3614.0 5303.0 Mean Corr = 0.84862Tomm40 1443.6 2379.7 3491.2 Tomm70a 1464.2 2139.6 2715.8 Tomm7 3407.2 4864.1 5909.2 Nhp2 2810.3 5081.5 8058.3 C1qbp 4986.6 5968.0 8850.1 Mrpl12 2271.0 4165.2 5682.9 Phb2 4397.2 6163.3 7336.6 Hspe1 4427.8 6804.3 8709.4 CEM 1 + Yars2 389.0 623.5 1066.7 Top 10 Genes Rsl1d1 1799.1 2261.9 4617.7 Ccdc58 703.4 1251.3 1858.5 Timm13 2666.7 3908.4 5233.0 Pno1 1337.0 2172.1 4632.3

Null module Tomm20l GEO Series "GSE6689" 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=GSE6689 Status: Public on Jan 07 2008 Title: Expression data during stem cell differentiation Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 18184438 Summary & Design: Summary: Stem cell development requires selection of specific genetic programs to direct cellular fate. Using microarray technology, we profile expression trends at selected timepoints during stem cell differentiation to characterize these changes.

Keyword(s): timecourse

Overall design: Total RNA was isolated using the Micro-to-Midi isolation kit (Invitrogen), and subjected to comparative gene expression profiling by labelled cRNA hybridization to the mouse genome 430 2.0 microarray (Affymetrix). Data acquired using the GeneChip Scanner 3000 was analyzed with the Genespring GX 7.3 microarray data software bioinformatics suite (Agilent Technologies) restricting the derived gene list to identify differentially expressed genes defined by a >1.5-fold difference and P<0.05. Data population sets were normalized to the undifferentiated phenotype, and quality filtered to eliminate background noise prior to hierarchical clustering.

Background corr dist: KL-Divergence = 0.0505, L1-Distance = 0.0486, L2-Distance = 0.0033, Normal std = 0.5968

0.726 Kernel fit Pairwise Correlations Normal fit

Density 0.363

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_ES-LIF(+)_rep1Timepoint1_ES-LIF(-)_rep1Timepoint2_CM_rep1Control_ES-LIF(+)_rep2 (0.150235)Timepoint1_ES-LIF(-)_rep2 (0.0887892) (0.142403)Timepoint2_CM_rep2Timepoint1b_CP_rep1 (0.0810462)Control_ES-LIF(+)_rep3 (0.0487432) (0.111954)Timepoint1_ES-LIF(-)_rep3 Timepoint2_CM_rep3(0.0396106)Timepoint1b_CP_rep2 (0.0685591)Timepoint1b_CP_rep3 (0.050119) (0.133275) (0.0343509) (0.0509146)[ min ] [ medium ] [ max ] CEM 1 Tomm20 10580.4 14992.6 17775.1 P ( S | Z, I ) = 1.00 Tomm22 2799.2 3398.5 4400.8 Mean Corr = 0.84503Tomm40 3277.0 4555.6 5087.3 Tomm70a 1817.5 3405.6 3708.7 Tomm7 1881.5 3477.0 4132.0 Nhp2 4205.9 10727.0 11916.2 C1qbp 7197.3 12242.7 15392.6 Mrpl12 3687.9 5817.6 6430.8 Phb2 5693.2 7616.6 9067.3 Hspe1 2794.2 5089.2 5490.6 CEM 1 + Yars2 466.3 1120.4 1441.8 Top 10 Genes Rsl1d1 2743.6 5188.7 6506.8 Ccdc58 1086.0 2899.1 3803.1 Timm13 2973.4 3797.3 4557.8 Pno1 3710.0 5636.9 6947.8

Null module Tomm20l GEO Series "GSE27114" 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=GSE27114 Status: Public on Sep 04 2012 Title: Expression data from REST knock-out versus REST wild type cells during in vitro neurogenesis Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 22964890 Summary & Design: Summary: While changes in chromatin are integral to transcriptional reprogramming during cellular differentiation, it is currently unclear how chromatin modifications are targeted to specific loci. We developed a computational model on the premise that transcription factors (TFs) direct dynamic chromatin changes during cell fate decisions. When applied to a neurogenesis paradigm, this approach predicted the TF REST as a determinant of gain of Polycomb-mediated H3K27me3 in neuronal progenitor cells. We prove this prediction experimentally by showing that the absence of REST causes loss of H3K27me3 at target promoters in trans at the same cellular state. Moreover, promoter fragments containing a REST binding site are sufficient to recruit H3K27me3 in cis, while deletion of their REST site results in loss of H3K27me3. These findings illustrate that computational modeling can systematically identify TFs that regulate chromatin dynamics genome-wide. Local determination of Polycomb activity by REST exemplifies such TF based regulation of chromatin.

Overall design: Expression profiling of REST knock-out (RESTko) versus REST wildtype (RESTwt) or REST heterozygous knock-out (RESThet) cells at three stages of in vitro neuronal differentiation. RESTko and RESTwt/RESThet embryonic stem (ES) cells were differentiated to terminal neurons (TN) via a defined neuronal progenitor (NP) state. Three biological replicates (suffixes a to c).

Background corr dist: KL-Divergence = 0.0155, L1-Distance = 0.0419, L2-Distance = 0.0020, Normal std = 0.8997

0.478 Kernel fit Pairwise Correlations Normal fit

Density 0.239

0.000 CEM 1

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

Pre-normalization Quantiles

2_ESwt_a2_ESwt_b (0.184535)2_NPwt_a (0.233197)2_NPwt_b (0.0663767)2_TNwt_a (0.0335525)2_TNwt_b (0.291107) (0.191232) [ min ] [ medium ] [ max ] CEM 1 Tomm20 3465.2 10559.4 14636.8 P ( S | Z, I ) = 1.00 Tomm22 1811.1 3045.8 3226.9 Mean Corr = 0.84943Tomm40 1564.0 1971.1 2924.9 Tomm70a 436.5 1157.6 2119.6 Tomm7 1821.7 6003.4 7811.9 Nhp2 665.5 5361.0 12032.0 C1qbp 2332.0 6117.7 8865.8 Mrpl12 2127.2 4119.1 4664.1 Phb2 3769.5 7927.0 8527.4 Hspe1 1283.1 4754.6 9218.7 CEM 1 + Yars2 318.8 541.0 733.8 Top 10 Genes Rsl1d1 1205.6 5500.2 6634.8 Ccdc58 176.6 3330.5 4439.8 Timm13 3954.9 6990.2 7401.8 Pno1 495.1 1841.2 3693.6

Null module Tomm20l GEO Series "GSE46090" 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=GSE46090 Status: Public on Apr 17 2013 Title: Gene expression in WT and Ikaros-deficient DN3, DN4 and DP thymocyte populations Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 24643801 Summary & Design: Summary: DN3, DN4 and DP cells were sorted from 3-4 week old WT and mice and subjected to transcriptome analysis

Overall design: Cells from 3 mice were pooled for sorting.

Background corr dist: KL-Divergence = 0.0692, L1-Distance = 0.0334, L2-Distance = 0.0015, Normal std = 0.5233

0.791 Kernel fit Pairwise Correlations Normal fit

Density 0.396

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 DN3WT cells DN3 repWT cells 1 DN4 (0.0206691) repWT cells 2 DN4 (0.0443113) repWT cells 1 DP (0.23191) rep cellsWT 2 DP (0.0809757)rep cellsDN3 1 (0.170713) cellsrepDN3 2 rep (0.145377) cells 1DN4 (0.0259516) rep cells 2DN4 (0.0320474) rep cells 1DP (0.0781034) rep cells 2DP (0.0196032)rep cells 1 (0.0726536) rep 2 (0.077684) [ min ] [ medium ] [ max ] CEM 1 Tomm20 3493.7 6823.1 7953.1 P ( S | Z, I ) = 1.00 Tomm22 1384.7 2210.1 2773.2 Mean Corr = 0.82608Tomm40 254.7 890.8 1338.7 Tomm70a 717.2 1859.7 2276.8 Tomm7 2328.3 4044.7 5284.4 Nhp2 215.8 2168.6 3760.4 C1qbp 1396.5 10295.5 11383.1 Mrpl12 1198.4 3742.1 5370.2 Phb2 1872.3 5753.9 7269.5 Hspe1 140.9 741.3 964.6 CEM 1 + Yars2 119.3 403.4 590.6 Top 10 Genes Rsl1d1 562.0 1972.6 3021.5 Ccdc58 312.1 901.7 1322.3 Timm13 2074.9 4455.1 5365.1 Pno1 440.2 2651.9 3128.8

Null module Tomm20l 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 (0.092685)ctrl_rep3 (0.0723357)ctrl_rep4 (0.255347)irr_rep1 (0.151836)irr_rep2 (0.170261)irr_rep3 (0.0887339)irr_rep4 (0.0667343) (0.102067) [ min ] [ medium ] [ max ] CEM 1 Tomm20 7813.4 9993.5 11414.2 P ( S | Z, I ) = 1.00 Tomm22 3887.4 5507.9 6286.7 Mean Corr = 0.82603Tomm40 1080.2 2308.9 2373.6 Tomm70a 1461.6 2590.8 2829.8 Tomm7 4742.6 4963.5 5608.7 Nhp2 2124.2 5952.1 6716.7 C1qbp 4332.4 7670.8 8335.3 Mrpl12 2377.3 5251.9 5750.9 Phb2 2759.0 5657.4 6105.5 Hspe1 3300.4 5185.9 5958.2 CEM 1 + Yars2 442.4 1007.1 1125.9 Top 10 Genes Rsl1d1 2161.1 3359.4 3886.6 Ccdc58 940.8 1603.5 1739.2 Timm13 5304.9 7898.0 8167.6 Pno1 1239.7 1925.3 2130.3

Null module Tomm20l GEO Series "GSE31013" 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=GSE31013 Status: Public on Jun 22 2012 Title: Global Differential Gene Expression Analysis of Spontaneous Lung Tumors in B6C3F1 Mice: Comparison to Human Non-Small Cell Lung Cancer Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 22688403 Summary & Design: Summary: Introduction: Lung cancer is the leading cause of cancer-related death in people. There are several chemically induced and genetically modified mouse models used to study lung cancer. We hypothesized that spontaneous murine (B6C3F1) lung tumors can serve as a model to study human non-small cell lung cancer (NSCLC). Methods: RNA was extracted from untreated 2-year-old B6C3F1 mouse spontaneous lung (SL) tumors and age-matched normal lung tissue from a chronic inhalation NTP study. Global gene expression analysis was performed using Affymetrix Mouse Genome 430 2.0 GeneChipÂ® arrays. After data normalization, for each probe set, pairwise comparisons between groups were made using a bootstrap t-test while controlling the mixed directional false discovery rate (mdFDR) to generate a differential gene expression list. IPA, KEGG, and EASE software tools were used to evaluate the overrepresented cancer genes and pathways. Results: MAPK and TGF-beta pathways were overrepresented within the dataset. Almost all of the validated genes by quantitative real time RT-PCR had comparable directional fold changes with the microarray data. The candidate oncogenes included Kras, Braf, Raf1, Id2, Hmga1, Cks1b, and Foxf1. The candidate tumor suppressor genes included Rb1, Cdkn2a, Hnf4a, Tcf21, Ptprd, Hpgd, Hopx, Ogn, Id4, Hoxa5, Smad6, Smad7, Zbtb16, Cyr61, Dusp4, and Ifi16. In addition, several genes important in lung development were also differentially expressed, such as Smad6, Hopx, Sox4, Sox9 and Mycn. Conclusion: In this study, we have demonstrated that several cancer genes and signaling pathways relevant for human NSCLC were similarly altered in spontaneous murine lung tumors.

Overall design: Six spontaneous lung tumors and six normal lungs (as controls) from 2-year-old B6C3F1 mice.

Background corr dist: KL-Divergence = 0.0937, L1-Distance = 0.0321, L2-Distance = 0.0018, Normal std = 0.4603

0.871 Kernel fit Pairwise Correlations Normal fit

Density 0.436

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

Lung_normal_1Lung_normal_2Lung_normal_3 (0.0365138)Lung_normal_4 (0.0518336)Lung_normal_5 (0.0543435)Lung_normal_6 (0.0910251)Spontaneous_lung_tumor_1 (0.0555163)Spontaneous_lung_tumor_2 (0.0486843)Spontaneous_lung_tumor_3Spontaneous_lung_tumor_4 (0.0286909)Spontaneous_lung_tumor_5 (0.219589)Spontaneous_lung_tumor_6 (0.00766726) (0.0217106) (0.181945) (0.202481)[ min ] [ medium ] [ max ] CEM 1 Tomm20 2073.5 3334.5 6415.8 P ( S | Z, I ) = 1.00 Tomm22 1234.1 1570.0 2265.8 Mean Corr = 0.82033Tomm40 636.2 784.9 1409.2 Tomm70a 431.8 592.2 1480.7 Tomm7 1383.7 1642.3 2286.0 Nhp2 483.6 992.4 2298.1 C1qbp 1212.9 1664.9 2999.2 Mrpl12 795.6 1403.8 2684.6 Phb2 1092.1 2141.6 4909.6 Hspe1 1005.6 1352.8 2724.3 CEM 1 + Yars2 115.6 227.6 377.9 Top 10 Genes Rsl1d1 906.2 1321.9 2059.3 Ccdc58 184.2 563.9 961.6 Timm13 1456.6 2036.9 3470.5 Pno1 879.2 1126.1 1825.4

Null module Tomm20l GEO Series "GSE46606" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 30 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE46606 Status: Public on May 04 2013 Title: Transcriptional regulation of germinal center B and plasma cell fates by dynamical control of IRF4 (expression) Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 23684984 Summary & Design: Summary: Temporal analysis of B cell activation in vitro using CD40L and IL-2/4/5 cytokines in wild type Irf4+/+ B cells or in mutant Irf4-/- B cells harboring a tet-inducible allele of Irf4. IRF4 expression was restored, or not, in the Irf4-/- background by culturing in the presence of low or high concentrations of doxycycline. The results provide insight in the role of IRF4 expression levels in coordinating different programs of B cell differentiation.

Overall design: Resting mature peripheral primary B cells were enriched from the spleens of Irf4+/+ or Irf4-inducible mice on the Irf4-/- background. We sought to compare gene expression profiles of wild type and Irf4 mutant B cells in response to mitogens that promote the differentiation of the B cells into plasma cells and cells that have undergone class switch recombination. Day 0 samples represent RNA analysis of unstimulated cells, whereas Day 1 and Day 3 samples represent analysis of stimulated cells in culture. For stimulation, cells were cultured with insect cell purified CD40L and IL-2/4/5 cytokines for the indicated days. In the case of doxycycline-mediated rescue of IRF4 expression, doxycycline was added at predefined low and high concentrations that yield low or high numbers of plasma cells, respectively (see Molecular Systems Biology 7:495). Each replicate represents analysis of B cells from an individual mouse. Of the three replicates in each group, two were performed in parallel and one was performed at a different time. All cells were lysed using Trizol and total RNA was purified according to manufacturer's suggestions. The high quality of the RNA was confirmed using Agilent Bioanalyzer 2100 system. 250ng of RNA was then processed into biotinylated cRNA according to standard procedures and used to hybridize to Affymetrix 430 2.0 arrays. Signal intensities were normalized using the D-Chip algorithm (PM-only model) and the output was used to quantify differential gene expression between groups.

Background corr dist: KL-Divergence = 0.0934, L1-Distance = 0.0402, L2-Distance = 0.0024, Normal std = 0.4712

0.897 Kernel fit Pairwise Correlations Normal fit

Density 0.448

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

4KO-hiD14KO-hiD3 rep1 4KO-loD1(0.0410624) rep1 4KO-loD3(0.0106848) rep1 4KO-zeroD0(0.0370825) rep1 4KO-zeroD1(0.00993873) rep14KO-zeroD3 (0.0590924) rep14KO-hiD1 (0.0206069) rep14KO-hiD3 rep2(0.00713565) 4KO-loD1(0.0270863) rep2 4KO-loD3(0.00775821) rep2 4KO-zeroD0(0.028152) rep2 4KO-zeroD1(0.00591632) rep24KO-zeroD3 (0.0861104) rep24KO-hiD1 (0.0291165) rep24KO-hiD3 rep3(0.00923009) 4KO-loD1(0.0292396) rep3 4KO-loD3(0.0038766) rep3 4KO-zeroD0(0.0220555) rep3 4KO-zeroD1(0.0165452) rep34KO-zeroD3 (0.0806016) rep3WT-D0 (0.0194651) rep3 rep1WT-D1 (0.0226155) (0.081587) rep1WT-D3 (0.0436987) rep1WT-D0 (0.0080957) rep2WT-D1 (0.101631) rep2WT-D3 (0.0433407) rep2WT-D0 (0.00760694) rep3WT-D1 (0.105792) rep3WT-D3 (0.0286724) rep3 (0.00620244) [ min ] [ medium ] [ max ] CEM 1 Tomm20 4951.3 6454.9 7671.0 P ( S | Z, I ) = 1.00 Tomm22 2380.9 3934.2 4665.7 Mean Corr = 0.81361Tomm40 657.5 1303.7 2299.4 Tomm70a 1980.8 3335.7 3928.8 Tomm7 2066.7 2870.3 3264.0 Nhp2 1214.3 3017.1 7028.0 C1qbp 2818.4 5940.6 9561.4 Mrpl12 1068.9 2804.1 5217.8 Phb2 3278.2 5427.5 7515.7 Hspe1 2139.9 4289.6 6838.9 CEM 1 + Yars2 216.0 477.6 1057.5 Top 10 Genes Rsl1d1 1566.9 2787.1 5584.0 Ccdc58 248.6 1066.7 1582.8 Timm13 2137.5 4092.2 5349.3 Pno1 1290.1 3664.4 8723.7

Null module Tomm20l GEO Series "GSE31313" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 22 -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=GSE31313 Status: Public on Aug 08 2012 Title: Expression data from anti-EpCAM treated and untreated SP cells compared to lung tissue Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: Targeted therapies against cancer stem cells which are enriched in side populations (SP) involves interruption of Wnt-signalling. Furthermore, EpCAM is a SP marker and modulator of Wnt-signalling. Therefore, the effects of an anti-EpCAM treatment on SP-cells and WNT/Î²-catenin signalling was studied.

SP of the murine lung adenocarcinoma cell line A2C12 was obtained by fluorescence activated cell sorting and whole genome scans helped to define their molecular phenotype after anti-EpCAM antibody treatment.

Overall design: Anti-EpCAM treated and untreated A2C12 cells were subjected to Hoechst 33342 dye exclusion assay and sorted to SP fractions by FACS. Gene expression of SP cells was compared to non-transgenic lung tissue.

Background corr dist: KL-Divergence = 0.0208, L1-Distance = 0.0491, L2-Distance = 0.0029, Normal std = 0.7902

0.505 Kernel fit Pairwise Correlations Normal fit

Density 0.252

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

A2C12 SPA2C12 cells SPA2C12 biological cells SPA2C12 biological cells replicate anti-EpCAMA2C12 biological replicate 1 anti-EpCAM(0.161342)A2C12 replicate treated 2 anti-EpCAM(0.0754041)Male treatedSP lung,3 (0.0604904)Male cells biological treatedSPlung, biologicalMale cells biological SPlung, biologicalreplicateMale cells replicate biological lung, biologicalreplicateMale 1 replicate (0.0166525) biological1 (0.134257)lung, replicateMale 2 replicate (0.0233547) biological2 (0.0904537)lung, replicateMale 3 (0.0137417) biological3 (0.175671)lung, replicateMale 4 (0.0106104) biological lung, replicateFemale 5 (0.011094) biological replicate Female lung,6 (0.0119377) biologicalreplicate Female lung,7 (0.0159263) biological Female lung,8 replicate (0.0120827) biological Femalelung, replicate 1 (0.0173128) biological Femalelung, replicate 2 (0.0324104) biological Femalelung, replicate 3 (0.0184786) biological Femalelung, replicate 4 (0.0269077) biological lung, replicate 5 (0.0256522) biological replicate 6 (0.02345) replicate 7 (0.0255108)[ min8 (0.0172588) ] [ medium ] [ max ] CEM 1 Tomm20 2199.2 2718.5 7467.1 P ( S | Z, I ) = 1.00 Tomm22 1458.8 1825.9 5499.6 Mean Corr = 0.81925Tomm40 447.8 597.7 1882.6 Tomm70a 216.6 429.7 2548.0 Tomm7 1186.5 2151.6 3567.0 Nhp2 459.0 948.5 4932.1 C1qbp 1195.6 1617.3 8373.3 Mrpl12 917.7 1252.9 5144.0 Phb2 1804.4 2389.3 6721.6 Hspe1 993.2 1957.5 4320.3 CEM 1 + Yars2 104.0 178.2 829.2 Top 10 Genes Rsl1d1 339.0 699.8 7250.3 Ccdc58 110.5 298.6 1865.0 Timm13 1721.1 2224.8 6478.3 Pno1 881.0 1185.9 4963.3

Null module Tomm20l GEO Series "GSE16675" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 72 -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=GSE16675 Status: Public on Nov 17 2010 Title: The influence of segmental copy number variation on tissue transcriptomes through development Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21084671 Summary & Design: Summary: A preliminary understanding of the phenotypic effect of copy number variation (CNV) of DNA segments is emerging. These rearrangements were demonstrated to influence, in a somewhat dose-dependent manner, the expression of genes mapping within. They were shown to also affect the expression of genes located on their flanks, sometimes at great distance. Here, we show by monitoring these effects at multiple life stages, that these controls over expression are effective throughout mouse development. Similarly, we observe that the more specific spatial expression patterns of CNV genes are maintained throughout life. However, we find that some brain-expressed genes appear to be under compensatory loops only at specific time-points, indicating that the influence of CNVs on these genes is modulated through development. We also observe that CNV genes are significantly enriched upon transcripts that show variable time-course of expression in different strains. Thus modifying the number of copy of a gene not only potentially alters its expression level, but possibly also its time of expression.

Keywords: comparative genomic

Overall design: Expression from brain and liver tissues from C57BL/6J, DBA2/J and 129S2 mouse strains at different developmental time points.

Background corr dist: KL-Divergence = 0.0580, L1-Distance = 0.0593, L2-Distance = 0.0060, Normal std = 0.5608

0.711 Kernel fit Pairwise Correlations Normal fit

Density 0.356

0.000 CEM 1

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

Pre-normalization Quantiles

129_E14.5_brain_rep1129_E14.5_brain_rep2129_E14.5_brain_rep3 B6_E14.5_brain_rep1(0.00797621) B6_E14.5_brain_rep2(0.00791661) B6_E14.5_brain_rep3(0.00458635) (0.00751894)D2_E14.5_brain_rep1 (0.00903762)D2_E14.5_brain_rep2 (0.0259121)D2_E14.5_brain_rep3 (0.00686858)129_E14.5_liver_rep1 (0.00659483)129_E14.5_liver_rep2 (0.00271669)129_E14.5_liver_rep3 (0.0360803)B6_E14.5_liver_rep1 (0.0707874)B6_E14.5_liver_rep2 (0.0697882)B6_E14.5_liver_rep3 (0.0624893)D2_E14.5_liver_rep1 (0.0649113)D2_E14.5_liver_rep2 (0.0311623)D2_E14.5_liver_rep3 (0.0612716)129_P1_brain_rep1 (0.0883334)129_P1_brain_rep2 (0.116932)129_P1_brain_rep3 (0.00717896)B6_P1_brain_rep1 (0.00531527)B6_P1_brain_rep2 (0.00834891)B6_P1_brain_rep3 (0.0066004)D2_P1_brain_rep1 (0.00550991)D2_P1_brain_rep2 (0.0069226)D2_P1_brain_rep3 (0.00305498)129_P1_liver_rep1 (0.00614822)129_P1_liver_rep2 (0.00685131)129_P1_liver_rep3 (0.00812329)B6_P1_liver_rep1 (0.00601446)B6_P1_liver_rep2 (0.0033991)B6_P1_liver_rep3 (0.0121307)D2_P1_liver_rep1 (0.00188041)D2_P1_liver_rep2 (0.00463827)D2_P1_liver_rep3 (0.0141041)129_P7_brain_rep1 (0.00963129)129_P7_brain_rep2 (0.00871515)129_P7_brain_rep3 (0.0049787)B6_P7_brain_rep1 (0.00882749)B6_P7_brain_rep2 (0.00411852)B6_P7_brain_rep3 (0.00357721)D2_P7_brain_rep1 (0.00500901)D2_P7_brain_rep2 (0.00782979)D2_P7_brain_rep3 (0.00310852)129_P7_liver_rep1 (0.00623736)129_P7_liver_rep2 (0.00785221)129_P7_liver_rep3 (0.00041648)B6_P7_liver_rep1 (0.00166834)B6_P7_liver_rep2 (0.00237588)B6_P7_liver_rep3 (0.0107911)D2_P7_liver_rep1 (0.00162413)D2_P7_liver_rep2 (0.00198374)D2_P7_liver_rep3 (0.00161038)129_P90_brain_rep1 (0.0050716)129_P90_brain_rep2 (0.00152637)129_P90_brain_rep3 (0.00452463)B6_P90_brain_rep1 (0.00291513)B6_P90_brain_rep2 (0.00306473)B6_P90_brain_rep3 (0.00206516)D2_P90_brain_rep1 (0.00197329)D2_P90_brain_rep2 (0.00286621)D2_P90_brain_rep3 (0.00320044)129_P90_liver_rep1 (0.00253526)129_P90_liver_rep2 (0.00326935)129_P90_liver_rep3 (0.00726561)B6_P90_liver_rep1 (0.0134313)B6_P90_liver_rep2 (0.0114478)B6_P90_liver_rep3 (0.0103282)D2_P90_liver_rep1 (0.00313908)D2_P90_liver_rep2 (0.00979488)D2_P90_liver_rep3 (0.0136023) (0.00419431) (0.0163238)[ min ] [ medium ] [ max ] CEM 1 Tomm20 2155.3 3354.1 9133.0 P ( S | Z, I ) = 1.00 Tomm22 1622.8 2238.1 4473.9 Mean Corr = 0.80223Tomm40 569.5 1105.5 2705.6 Tomm70a 861.2 1193.5 2911.9 Tomm7 287.0 2003.4 4103.9 Nhp2 324.3 884.3 4501.1 C1qbp 1980.3 2873.7 8494.6 Mrpl12 1159.6 3922.6 6871.1 Phb2 1651.5 3138.2 8008.5 Hspe1 368.6 1373.4 4263.9 CEM 1 + Yars2 227.6 369.4 1202.0 Top 10 Genes Rsl1d1 721.4 1299.5 3053.3 Ccdc58 173.2 779.2 1654.3 Timm13 1288.6 4291.2 6593.5 Pno1 595.9 1021.1 2811.1

Null module Tomm20l 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 (0.28427)line, rep2Wild-type, biological (0.320284)line,Wild-type, biological biological rep Gtf2i1 (0.0411397) biological rep Mutant rep1 Gtf2i2 (0.0451749) (0.0662344) Mutantline, rep2 biological (0.105999) line, biological rep 1 (0.0496795) rep[ 2min (0.0872181) ] [ medium ] [ max ] CEM 1 Tomm20 12794.3 15161.6 18322.4 P ( S | Z, I ) = 1.00 Tomm22 5208.5 5996.4 6791.1 Mean Corr = 0.80672Tomm40 2067.0 2228.6 3030.9 Tomm70a 3560.2 4264.8 5503.8 Tomm7 3898.1 5713.0 7974.2 Nhp2 6068.7 6929.5 11046.0 C1qbp 7958.9 8744.7 11695.0 Mrpl12 2857.9 3310.7 4032.9 Phb2 5987.8 6781.2 8500.3 Hspe1 6387.1 6911.9 8291.0 CEM 1 + Yars2 788.7 981.1 1097.2 Top 10 Genes Rsl1d1 4528.8 4916.1 6535.1 Ccdc58 2075.7 3414.6 3555.8 Timm13 4186.9 4671.3 5010.9 Pno1 3178.3 4140.4 5205.0

Null module Tomm20l GEO Series "GSE18396" 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=GSE18396 Status: Public on Jun 30 2010 Title: Dmrt1 (doublesex and mab-3 related transcription factor 1) knockout expression analyses in E13.5 testes in S6 background Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 20007774 Summary & Design: Summary: Dmrt1 (doublesex and mab-3 related transcription factor 1) is a conserved transcriptional regulator of male differentiation required for testicular development in vertebrates. In mice of the 129Sv strain, loss of Dmrt1 causes a high incidence of teratomas. Mutant 129Sv germ cells undergo apparently normal differentiation up to embryonic day 13.5 (E13.5), but some cells fail to arrest mitosis and ectopically express pluripotency markers. Expression analysis and chromatin immunoprecipitation identified DMRT1 target genes whose misexpression may underly teratoma formation.

Overall design: Comparison of E13.5 testes gene expression between Dmrt1(+/-) and Dmrt1(-,-) animals that show high incidence of teratoma formation.

Background corr dist: KL-Divergence = 0.0394, L1-Distance = 0.0172, L2-Distance = 0.0003, Normal std = 0.6150

0.654 Kernel fit Pairwise Correlations Normal fit

Density 0.327

0.000 CEM 1

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

Pre-normalization Quantiles

E13.5 testes,E13.5 wt,testes,E13.5 biological wt,testes,E13.5 biological rep3 wt,testes,E13.5 biological(0.194766) rep2 Dmrt(-,-),testes,E13.5 (0.10722) rep1 Dmrt(-,-),testes, biological (0.141982) Dmrt(-,-), biological rep2 biological(0.0513283) rep3[ (0.0574605) minrep1 (0.447243) ] [ medium ] [ max ] CEM 1 Tomm20 6659.3 7527.3 9144.0 P ( S | Z, I ) = 1.00 Tomm22 3164.1 3542.5 4075.4 Mean Corr = 0.79998Tomm40 97.4 114.7 157.0 Tomm70a 2513.5 2957.8 3390.5 Tomm7 1539.1 1856.1 2157.6 Nhp2 303.9 399.2 479.5 C1qbp 7308.1 7979.6 8541.3 Mrpl12 2885.7 3836.2 4435.0 Phb2 5606.0 6164.1 6946.7 Hspe1 5158.9 5595.0 6644.0 CEM 1 + Yars2 1089.4 1446.2 1917.8 Top 10 Genes Rsl1d1 2579.4 2800.3 3150.7 Ccdc58 3995.6 4760.4 5941.9 Timm13 1210.2 1453.1 1589.8 Pno1 1374.5 1542.5 1815.1

Null module Tomm20l GEO Series "GSE17709" 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=GSE17709 Status: Public on Aug 19 2009 Title: Gene expression analysis of a podocyte specific PTIP deletion in mouse glomerular preparations at 1 month of age Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21060806 Summary & Design: Summary: Glomerular RNA comparison between wild-type and podocyte specific deletion of the PTIP gene in 1 month old kidneys. The PTIP gene was deleted using a floxed allele and a Podocin-Cre driver strain.

These mice develop protein urea by 3 months of age. This study was designed to find gene expression differences prior to the onset of the phenotype.

Overall design: Kidneys were excised at 1 month of age. Glomeruli enriched fractions were generated by sieving of the tissue homogenates. RNA was prepared from glomerular enriched fractions.

Background corr dist: KL-Divergence = 0.0391, L1-Distance = 0.0385, L2-Distance = 0.0021, Normal std = 0.6195

0.644 Kernel fit Pairwise Correlations Normal fit

Density 0.322

0.000 CEM 1

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

Pre-normalization Quantiles

wild-type,wild-type, PTIP+,wild-type, rep1PTIP+, wild-type,(0.0233218) rep2PTIP+, wild-type,(0.0272486) rep3PTIP+, wild-type,(0.0176995) rep4PTIP+, wild-type,(0.0984109) rep5PTIP+, wild-type,(0.0722446) rep6PTIP+, Pod-Cre,(0.0465595) rep7PTIP+, Pod-Cre,(0.0676483) PTIP-,rep8 Pod-Cre,(0.0878827) rep1 PTIP-, (0.0130622)Pod-Cre, rep2 PTIP-, (0.0370876)Pod-Cre, rep3 PTIP-, (0.0118982)Pod-Cre, rep4 PTIP-, (0.012639)Pod-Cre, rep5 PTIP-, (0.120033)Pod-Cre, rep6 PTIP-, (0.171127)Pod-Cre, rep7 PTIP-, (0.0232194)Pod-Cre, rep8 PTIP-, (0.0520714) rep9 PTIP-, (0.0940369) rep10 (0.0238094)[ min ] [ medium ] [ max ] CEM 1 Tomm20 2244.5 3337.1 5867.6 P ( S | Z, I ) = 1.00 Tomm22 531.5 1210.7 2282.8 Mean Corr = 0.79438Tomm40 68.6 314.9 400.3 Tomm70a 228.4 859.5 1017.4 Tomm7 1852.1 2534.7 3246.8 Nhp2 30.6 213.6 367.1 C1qbp 2247.3 3439.2 4703.8 Mrpl12 2796.6 4747.1 6796.9 Phb2 1971.0 3386.1 6268.2 Hspe1 793.6 1667.1 2456.0 CEM 1 + Yars2 463.2 1113.3 1401.9 Top 10 Genes Rsl1d1 256.8 708.5 974.5 Ccdc58 948.3 1688.5 2648.7 Timm13 509.4 2034.2 4298.5 Pno1 585.5 960.0 1400.3

Null module Tomm20l 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 (0.0786879)3T3-L1_t2_rep2 (0.0366919)3T3-L1_t3_rep1 (0.105003)3T3-L1_t3_rep2 (0.224396)3T3-L1_t4_rep1 (0.258298)3T3-L1_t4_rep2 (0.205094) (0.0603984) (0.0314311) [ min ] [ medium ] [ max ] CEM 1 Tomm20 5972.6 7769.7 11553.8 P ( S | Z, I ) = 1.00 Tomm22 2819.8 3995.7 5560.6 Mean Corr = 0.78457Tomm40 648.8 1945.8 2545.5 Tomm70a 735.0 1622.9 2285.3 Tomm7 3722.6 5006.0 5326.2 Nhp2 672.3 1950.5 3560.5 C1qbp 2852.7 4977.0 7967.5 Mrpl12 831.2 3762.2 4641.7 Phb2 3210.6 6164.8 7632.8 Hspe1 3210.9 4727.4 8266.5 CEM 1 + Yars2 175.4 530.7 716.4 Top 10 Genes Rsl1d1 2179.6 3215.1 6142.6 Ccdc58 1629.5 2100.5 2343.5 Timm13 2363.6 4308.9 6016.3 Pno1 1671.1 2686.7 4057.3

Null module Tomm20l GEO Series "GSE55356" 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=GSE55356 Status: Public on Jul 01 2014 Title: p38a-dependent gene expression in the colonic mucosa Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: Gene expression in the colonic mucosa of wild-type and p38a-knockout intestinal epithelial cells (IECs) were compared.

C57BL/6 wild-type mice, and intestinal epithelial cell-specific p38a-knockout mice on a C57BL/6 background were used for isolation of colonic mucosa

Overall design: Gene expression in each genotype was analyzed in triplicate.

Background corr dist: KL-Divergence = 0.0251, L1-Distance = 0.0199, L2-Distance = 0.0005, Normal std = 0.7025

0.576 Kernel fit Pairwise Correlations Normal fit

Density 0.288

0.000 CEM 1

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

Pre-normalization Quantiles

KO-A (0.18282)KO-B (0.0501895)KO-C (0.104171)WT-A (0.20392)WT-B (0.131099)WT-C (0.3278) [ min ] [ medium ] [ max ] CEM 1 Tomm20 2300.3 4317.7 4717.4 P ( S | Z, I ) = 1.00 Tomm22 2570.1 3246.5 3506.7 Mean Corr = 0.78726Tomm40 308.1 457.3 592.5 Tomm70a 634.1 1403.9 1978.8 Tomm7 3376.3 4152.4 4599.2 Nhp2 527.7 1363.4 1561.9 C1qbp 1509.3 3312.7 4597.0 Mrpl12 4055.8 5993.5 6346.7 Phb2 2606.7 3216.6 3816.6 Hspe1 1022.0 1779.3 2864.7 CEM 1 + Yars2 153.6 347.5 503.3 Top 10 Genes Rsl1d1 583.9 1104.6 1446.2 Ccdc58 609.0 1054.2 1215.1 Timm13 2879.0 3478.2 3786.5 Pno1 614.2 1259.6 1924.0

Null module Tomm20l GEO Series "GSE17553" 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=GSE17553 Status: Public on Dec 31 2009 Title: Estradiol or Testosterone treated efferent duct and caput epididymis Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 19553595 Summary & Design: Summary: The role of estrogen and testosterone in the regulation of gene expression in the proximal reproductive tract is not completely understood. To address this question, mice were treated with testosterone or estradiol and RNA from the efferent ducts and caput epididymis was processed and hybridized to Affymetrix MOE 430 2.0 microarrays. Analysis of array output identified probe sets in each tissue with altered levels in hormone treated versus control animals. Hormone treatment efficacy was confirmed by determination of serum hormone levels pre- and post-treatment and observed changes in transcript levels of previously reported hormone-responsive genes. Tissue-specific hormone sensitivity was observed with 2867 and 3197 probe sets changing significantly in the efferent ducts after estrogen and testosterone treatment, respectively. In the caput epididymis, 117 and 268 probe sets changed after estrogen and testosterone treatment, respectively, demonstrating a greater response to hormone in the efferent ducts than the caput epididymis. Transcripts sharing similar profiles in the intact and hormone-treated animals compared with castrated controls were also identified. Ontological analysis of probe sets revealed a significant number of hormone-regulated transcripts encode proteins associated with lipid metabolism, transcription and steroid metabolism in both tissues. Real-time RT-PCR was employed to confirm array data and investigate other potential hormone-responsive regulators of proximal reproductive tract function. The results of this work reveal previously unknown responses to estrogen in the caput epididymis and to testosterone in the efferent ducts as well as tissue specific hormone sensitivity in the proximal reproductive tract.

Overall design: Adult animals were castrated or sham-castrated, allowed to recover for 14 days, and then treated with 0.015 mg estradiol (castrated), 0.015 mg testosterone propionate (castrated), or vehicle (castrated and sham-castrated as biological controls) in duplicate. Efferent duct and caput epididymis was collected from each sample and analyzed. Duplicates are included in the provided data and numbered 1 or 2 for each treatment regimen.

Background corr dist: KL-Divergence = 0.0449, L1-Distance = 0.0261, L2-Distance = 0.0011, Normal std = 0.5797

0.688 Kernel fit Pairwise Correlations Normal fit

Density 0.344

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

EfferentCaput duct castratedepididymisCaput epididymisCaput 1 (0.140479)castrated epididymisCaput castrated 1 epididymis Caput(0.0304182) sham-castrated 2 epididymis Caput(0.0484986) sham-castrated epididymisCaput TP 1 (0.0810122)treatedepididymisEfferent TP 2 (0.0803183)treated1Efferent (0.0255061)duct E2 sham-castratedtreated2Efferent (0.0273743)duct sham-castrated1Efferent (0.0251834)duct castrated 1Efferent duct (0.0961737) TP 2Efferent duct 2(0.119587)treated (0.132837) TPEfferent duct treated1 (0.0445364) E2Caput duct treated2 (0.0840624) E2epididymis treated1 (0.018642) 2 E2(0.0254007) treated 2[ (0.0199705) min ] [ medium ] [ max ] CEM 1 Tomm20 1165.4 4000.1 5259.7 P ( S | Z, I ) = 1.00 Tomm22 569.3 1764.9 2293.3 Mean Corr = 0.78237Tomm40 34.6 793.1 1324.9 Tomm70a 300.9 973.2 1254.2 Tomm7 1014.2 2307.8 2935.7 Nhp2 41.7 1477.8 2280.6 C1qbp 1565.7 2306.1 4416.3 Mrpl12 432.3 1707.9 2710.3 Phb2 1019.5 2584.9 3734.1 Hspe1 820.5 1270.2 2819.6 CEM 1 + Yars2 204.7 306.7 482.0 Top 10 Genes Rsl1d1 577.5 1235.4 1555.3 Ccdc58 434.7 893.2 2031.6 Timm13 251.1 2554.1 3438.8 Pno1 328.0 836.2 1823.3

Null module Tomm20l GEO Series "GSE28408" 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=GSE28408 Status: Public on Feb 01 2013 Title: Expression data from Ly6G+ and Ly6G- dendritic cells (DC) Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 23305731 Summary & Design: Summary: To investigate the functional properties of Ly6G+ DC, we employed GeneChip analysis to compare the gene expression profiles between Ly6G+ DC and Ly6C- DC.

Overall design: Crude bone marrow (BM) cells prepared from C57BL/6 mice were cultured in the presence of GM-CSF. On day 6, CD11c+/MHC II+/Ly6G+ cells and CD11c+/MHC II+/Ly6G- cells were simultaneously sorted from the same cultures by FACSAria. Total RNA were extracted and hybridized on Affymetrix microarrays.

Background corr dist: KL-Divergence = 0.0392, L1-Distance = 0.0299, L2-Distance = 0.0012, Normal std = 0.6277

0.644 Kernel fit Pairwise Correlations Normal fit

Density 0.322

0.000 CEM 1

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

Pre-normalization Quantiles

T_SHG001-Mouse430_2_2,T_SHG002-Mouse430_2_2,T_SHG003-Mouse430_2,T_SHG004-Mouse430_2, Ly6G+DC1T_SHG007-Mouse430_2, Ly6G-DC1T_SHG006-Mouse430_2, (0.25772) Ly6G+DC2 (0.146281) Ly6G-DC2 (0.130562) Ly6G+DC3 (0.123775) Ly6G-DC3 (0.135907)[ min (0.205755) ] [ medium ] [ max ] CEM 1 Tomm20 3017.4 7330.7 8252.3 P ( S | Z, I ) = 1.00 Tomm22 1324.2 3888.9 4234.7 Mean Corr = 0.78001Tomm40 372.2 535.1 1173.6 Tomm70a 695.4 1009.6 1401.1 Tomm7 795.6 3543.3 6079.3 Nhp2 646.2 830.7 1403.6 C1qbp 2233.4 3085.6 4570.2 Mrpl12 639.6 1021.6 1448.6 Phb2 1751.1 2272.8 3392.4 Hspe1 751.1 2270.1 3057.6 CEM 1 + Yars2 114.0 199.3 221.3 Top 10 Genes Rsl1d1 817.6 1324.0 2046.7 Ccdc58 397.5 840.4 1732.1 Timm13 593.3 2420.3 2711.8 Pno1 689.5 934.6 1334.9

Null module Tomm20l GEO Series "GSE20177" 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=GSE20177 Status: Public on Sep 03 2010 Title: Expression data from mouse wild-type and Dnmt1-/-Dnmt3a-/-Dnmt3b-/- embryonic stem(ES) cells and nuclear transfer-trophoblastic stem(ntTS) cells, and wild-type trophoblastic stem(TS) cells, primitive endoderm cells, and extra-embryonic endoderm(XEN) cells Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 20637626 Summary & Design: Summary: To investigate the role of DNA methylation in early embryogenesis, we created Dnmt1-/-Dnmt3a-/-Dnmt3b-/- triple knockout (TKO) embryos by the nuclear transfer (NT) technique using TKO ES cells as the nucleus donor, and found that the TKO NT embryos could develop into blastocysts. From the TKO NT blastocysts, we successfully established trophoblastic stem cells (ntTS cells), and these TKO ntTS cells could self-renew and contribute to the placenta in vivo. Expression profile analysis using microarray revealed that, although many genes were aberrantly expressed, the fundamental gene expression patterns of stem cells were retained in these TKO ntTS cells.

Overall design: To investigate the properties of the TKO ntTS cells from their expression profiles, we compared the microarray data from the TKO ntTS cells with data from wild-type (WT) ntTS cells and other cell types that represent the three blastocyst-derived lineages: the epiblast (EPI), trophectoderm (TE), and primitive endoderm (PE). WT and TKO ES cells were used as EPI, TS cells derived from wild-type blastocysts were used as TE, and extra-embryonic endoderm (XEN) cells derived from wild-type blastocysts were used as PE. We also treated WT ES cells with Gata4 to induce parietal endoderm cells as PE. The total RNA was extracted from these cell lines, and microarray data were obtained using mouse expression microarrays.

Background corr dist: KL-Divergence = 0.0923, L1-Distance = 0.0382, L2-Distance = 0.0028, Normal std = 0.4674

0.871 Kernel fit Pairwise Correlations Normal fit

Density 0.435

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

TKO ES,TKO biological ES,WT biological ES, repeat1 WTbiological ES, repeat2 (0.117528) WTbiological repeat1ES+GATA4, (0.0625995)WT repeat2ES+GATA4,(0.155981)WT biological ntTS,(0.0886458)WT biological biological ntTS,repeat1TKO biological repeat2 (0.0180215)ntTS,repeat1TKO biological (0.0440726)ntTS,repeat2 (0.0158681)WT biologicalTS, (0.0108579)repeat1 WTbiological TS, repeat2 (0.0273296) WTbiological repeat1 XEN, (0.0202459)WT biological repeat2 XEN,(0.126034) biological (0.145294) repeat1 repeat2 (0.0750853) (0.0924361)[ min ] [ medium ] [ max ] CEM 1 Tomm20 11030.2 14401.5 17308.3 P ( S | Z, I ) = 1.00 Tomm22 2022.1 3267.1 4955.3 Mean Corr = 0.77872Tomm40 2370.8 3411.7 4911.8 Tomm70a 2319.6 4333.7 7200.2 Tomm7 2027.0 3502.2 4519.1 Nhp2 3990.6 5785.7 11303.8 C1qbp 7278.2 11086.4 12562.1 Mrpl12 2084.6 3700.3 5696.2 Phb2 4067.8 5714.0 7467.8 Hspe1 3552.3 5792.8 7896.6 CEM 1 + Yars2 443.3 788.9 1150.2 Top 10 Genes Rsl1d1 3756.8 5406.6 7785.7 Ccdc58 2234.7 3253.8 4389.2 Timm13 2974.1 3970.0 4527.1 Pno1 2602.6 3669.1 7331.4

Null module Tomm20l GEO Series "GSE26568" 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=GSE26568 Status: Public on May 31 2013 Title: Impact of KLF2 expression on T cell genetic program Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 24155966 Summary & Design: Summary: On triggering of the T cell receptor CD8 T lymphocytes downregulate expression of the transcription factor KLF2. KLF2 expression remains low as these cells differentiate to Cytotoxic T lymphocytes (CTL) but may be re-expressed depending on the local environmental signals.

We used retroviral transduction to enforce KLF2 expression in CTL to determine the impact of it re-expression on the CTL genetic program.

Overall design: T lymphocytes with a transgenic T cell receptor (P14 LCMV) isolated from murine spleens were activated with gp33-41 peptide for 2 days and transduced with empty vector (evGFP) or GFP-KLF2. After differentiation to CTL in culture with Interleukin-2 for 2 further days, cells positive for GFP were isolated by Fluorescence Activated Cell Sorting and the RNA extracted for microarray analysis.

Background corr dist: KL-Divergence = 0.0293, L1-Distance = 0.0215, L2-Distance = 0.0005, Normal std = 0.6816

0.600 Kernel fit Pairwise Correlations Normal fit

Density 0.300

0.000 CEM 1

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

Pre-normalization Quantiles

evGFP transducedevGFP transducedevGFP CTL, transducedGFP-KLF2 biological CTL,GFP-KLF2 biological transduced CTL, rep.GFP-KLF2 1biological transduced(0.168669) rep. CTL, 2 transduced(0.32948) rep. biological CTL, 3 (0.105063) biological CTL, rep. 1biological (0.0822305)[ rep. min 2 (0.146722) rep. ] 3 (0.167835)[ medium ] [ max ] CEM 1 Tomm20 11429.1 12420.9 13719.2 P ( S | Z, I ) = 1.00 Tomm22 6310.6 6599.6 6907.8 Mean Corr = 0.77849Tomm40 1800.6 2481.1 3129.8 Tomm70a 2325.8 3141.3 3382.0 Tomm7 5560.1 6038.4 6373.7 Nhp2 9201.7 10421.6 11073.8 C1qbp 5859.1 8112.0 9089.3 Mrpl12 4209.7 5335.6 5925.7 Phb2 5984.5 6781.7 8335.1 Hspe1 4310.1 6113.3 6933.8 CEM 1 + Yars2 591.7 795.3 978.2 Top 10 Genes Rsl1d1 3984.0 5020.0 6072.9 Ccdc58 1227.4 2077.3 2540.3 Timm13 6364.8 7582.8 7965.1 Pno1 2402.4 3023.5 3707.6

Null module Tomm20l GEO Series "GSE45619" 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=GSE45619 Status: Public on Mar 29 2013 Title: Expression analysis of GATA1s murine megakaryocyte progenitors from bone marrow and fetal Liver Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: About 10% of Down syndrome (DS) infants are born with a myeloproliferative disorder (DS-TMD) that spontaneously resolves within the first few months of life. About 20-30% of these infants subsequently develop acute megakaryoblastic leukemia (DS-AMKL). In order to understand differences that may exist between fetal and bone marrow megakaryocyte progenitor cell populations we flow sorted megakaryocyte progenitor cells and performed microarray expression analysis.

kewywords: Mouse megakaryocyte progenitors

Overall design: Expression data of flow cytometrically isolated murine megakaryocyte progenitor cells (lin-, Sca-1-, c-kit+, CD150+, CD41+) from GATA1s fetal liver and bone marrow

Background corr dist: KL-Divergence = 0.0282, L1-Distance = 0.0322, L2-Distance = 0.0012, Normal std = 0.7067

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

Gs_MKP_BM_1Gs_MKP_BM_2Gs_MKP_BM_3 (0.168576)Gs_MKP_FL_1 (0.124643)Gs_MKP_FL_2 (0.162917) Gs_MKP_FL_3(0.097566) (0.30393) (0.142368) [ min ] [ medium ] [ max ] CEM 1 Tomm20 4535.8 5019.7 5666.6 P ( S | Z, I ) = 1.00 Tomm22 2457.8 3017.0 3665.8 Mean Corr = 0.77399Tomm40 237.3 348.0 387.6 Tomm70a 1279.5 1473.7 1613.7 Tomm7 2079.7 2892.4 3946.4 Nhp2 933.9 1585.2 1847.7 C1qbp 6141.1 6856.6 7572.4 Mrpl12 3282.7 4262.6 5922.7 Phb2 4667.0 5266.0 6848.1 Hspe1 4448.4 5105.4 6029.1 CEM 1 + Yars2 758.7 1112.4 1403.5 Top 10 Genes Rsl1d1 2968.8 3611.4 3722.6 Ccdc58 2182.5 3148.1 3959.7 Timm13 1877.8 2432.3 3385.3 Pno1 1070.9 1239.8 1600.6

Null module Tomm20l GEO Series "GSE7897" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 60 -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=GSE7897 Status: Public on Aug 09 2008 Title: Expression data from Mouse Lymphoma Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 18922927 Summary & Design: Summary: We have made use of the EÎ¼-myc transgenic mouse, a model for the study of B-cell lymphoma development that is initiated through a defined genetic alteration, to explore the contributions of additional somatic alterations that contribute to the heterogeneity of the resulting tumors. As one example of such heterogeneity, we have focused on the observation that lymphomas develop in EÎ¼-myc mice with a variable time of onset. Twenty-five early-onset, 25 late-onset lymphomas and 10 normal samples were each assayed on an Affymetrix Mouse Genome 430 2.0 array.

Keywords: Myc induced lymphomas with various time-of-onset

Overall design: To focus on events that might distinguish early and late onset tumors, we performed genome-wide expression analyses of early- and late-onset lymphomas from E´-myc transgenic mice using expression microarray techniques. Total RNA was prepared from 25 early-onset (32-76 days, 62.6+/-11.0 days, median 65 days), 25 late-onset tumors (253-649 days, 391.5+/-101.8 days, median 398 days) and 10 normal tissues (lymph nodes or spleen, 38-438 days, 181.0+/-175.2 days, median 62.5 days) and subjected to Affymetrix GeneChip analyses.

Background corr dist: KL-Divergence = 0.3081, L1-Distance = 0.0449, L2-Distance = 0.0038, Normal std = 0.2815

1.417 Kernel fit Pairwise Correlations Normal fit

Density 0.709

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 Myc-inducedMouse Myc-inducedMouse lymphoma Myc-inducedMouse lymphoma Myc-inducedMouse 1 (0.00293099) lymphoma Myc-inducedMouse 2 (0.0620922) lymphoma Myc-inducedMouse 3 (0.00433228) lymphoma Myc-inducedMouse 4 (0.00774872) lymphoma Myc-inducedMouse 5 (0.00839449) lymphoma Myc-inducedMouse 6 (0.0108226) lymphoma Myc-inducedMouse 8 (0.00398601) lymphoma Myc-inducedMouse 9 (0.022983) lymphoma Myc-inducedMouse 10 (0.0136581) lymphoma Myc-inducedMouse 11 (0.00597475) lymphoma Myc-inducedMouse 12 (0.00472963) lymphoma Myc-inducedMouse 13 (0.0075293) lymphoma Myc-inducedMouse 14 (0.00605788) lymphoma Myc-inducedMouse 15 (0.00311079) lymphoma Myc-inducedMouse 16 (0.0043615) lymphoma Myc-inducedMouse 17 (0.00884784) lymphoma Myc-inducedMouse 19 (0.022291) lymphoma Myc-inducedMouse 20 (0.0138331) lymphoma Myc-inducedMouse 21 (0.0161519) lymphoma Myc-inducedMouse 22 (0.011234) lymphoma Myc-inducedMouse 23 (0.00535903) lymphoma Myc-inducedMouse 24 (0.00933961) lymphoma Myc-inducedMouse 26 (0.0177737) lymphoma Myc-inducedMouse 28 (0.0130156) lymphoma Myc-inducedMouse 29 (0.0126957) lymphoma Myc-inducedMouse 111 lymphoma(0.0119902) Myc-inducedMouse 112 lymphoma(0.0112489) Myc-inducedMouse 113 lymphoma(0.00753438) Myc-inducedMouse 114 lymphoma(0.0102215) Myc-inducedMouse 116 lymphoma(0.0116063) Myc-inducedMouse 117 lymphoma(0.00400354) Myc-inducedMouse 118 lymphoma(0.0209994) Myc-inducedMouse 119 lymphoma(0.00818605) Myc-inducedMouse 120 lymphoma(0.00899617) Myc-inducedMouse 121 lymphoma(0.00952215) Myc-inducedMouse 123 lymphoma(0.0136674) Myc-inducedMouse 124 lymphoma(0.00548534) Myc-inducedMouse 125 lymphoma(0.00332305) Myc-inducedMouse 126 lymphoma(0.0127019) Myc-inducedMouse 127 lymphoma(0.00538937) Myc-inducedMouse 128 lymphoma(0.0108341) Myc-inducedMouse 129 lymphoma(0.00907736) Myc-inducedMouse 130 lymphoma(0.0265581) Myc-inducedMouse 131 lymphoma(0.00409526) Myc-inducedMouse 133 lymphoma(0.00843499) Myc-inducedMouse 135 lymphoma(0.00609349) Myc-inducedMouse 136 lymphoma(0.0184025) WildtypeMouse 137 lymphoma(0.0192449) WildtypeMouse Normal138 (0.0084374) WildtypeMouse Normal141Lymph (0.00543968) WildtypeMouse NormalLymphNode Wildtype Mouse1 NormalLymphNode(0.0355157) Wildtype Mouse2 NormalLymphNode(0.049595) Wildtype Mouse3 NormalLymphNode(0.0443237) Wildtype Mouse4 NormalLymphNode(0.0394105) Wildtype Mouse5 NormalSpleenNode(0.0414266) Wildtype 6 NormalLymph7(0.0399393) (0.0544902) NormalLymphNode 8 LymphNode(0.0489653) [9 Node(0.0468758)min 10 (0.0387106)] [ medium ] [ max ] CEM 1 Tomm20 3118.8 8777.8 11710.3 P ( S | Z, I ) = 1.00 Tomm22 1335.8 2840.5 4831.9 Mean Corr = 0.76812Tomm40 798.1 3104.5 4109.4 Tomm70a 535.1 1721.5 2545.3 Tomm7 728.1 2034.3 3172.8 Nhp2 812.3 5155.6 7324.3 C1qbp 1658.8 8970.1 12719.2 Mrpl12 658.7 3181.0 4436.3 Phb2 2165.9 6363.5 8263.7 Hspe1 1204.9 2728.8 4952.7 CEM 1 + Yars2 128.3 491.1 722.4 Top 10 Genes Rsl1d1 1522.7 4193.8 5652.5 Ccdc58 227.0 958.2 1680.8 Timm13 1261.6 3854.7 6213.2 Pno1 820.2 2635.7 3713.7

Null module Tomm20l GEO Series "GSE28389" 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=GSE28389 Status: Public on Apr 05 2011 Title: [E-MTAB-368] Transcription profiling by array of mouse embryos at 8 different stages Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21427719 Summary & Design: Summary: Transcription profiling of mouse development

The experiment were perfomed as a part of our Vertebrate Evo-Devo project. The aim of the project is to compare transcription profiles of normal (unmanipulated, wild-type, whole embryo) vertebrate embryos.

Overall design: Total RNA was collected from wild type C57BL/6 mice, whole embryos at 8 different stages (Stages:E7.5, E8.5, E9.5, E10.5, E12.5, E14.5, E16.5, E18.5), and hybridized to Affymetrix Mouse Genome 430 2.0 Array. All the stages contains data from 2 to 3 biological replications. Each staged-samples consists of pooled total RNA from several whole embryos.

Background corr dist: KL-Divergence = 0.0441, L1-Distance = 0.0355, L2-Distance = 0.0018, Normal std = 0.5966

0.705 Kernel fit Pairwise Correlations Normal fit

Density 0.353

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

[E-MTAB-368][E-MTAB-368] Mouse[E-MTAB-368] developmentalMouse[E-MTAB-368] developmentalMouse[E-MTAB-368] developmentalMousestage[E-MTAB-368] E7.5 developmentalMousestage[E-MTAB-368] 1 (0.0682983) E7.5 developmentalMousestage[E-MTAB-368] 2 (0.120019) E7.5 developmentalMousestage[E-MTAB-368] 3 (0.133423) E8.5 developmentalMousestage[E-MTAB-368] 1 (0.0562923) E8.5 developmentalMousestage[E-MTAB-368] 2 (0.0333674) E8.5 developmentalMousestage[E-MTAB-368] 3 (0.0229817) E9.5 developmentalMousestage[E-MTAB-368] 1 (0.0266641) E9.5 developmentalMousestage[E-MTAB-368] 2 (0.0291232) E9.5 developmentalMousestage[E-MTAB-368] 3 (0.00961977) E10.5 developmentalMousestage[E-MTAB-368] 1 E10.5 (0.0324509) developmentalMousestage[E-MTAB-368] 2 E10.5 (0.0150951) developmentalMousestage[E-MTAB-368] 3 E12.5 (0.0133218) developmentalMousestage[E-MTAB-368] 1 E12.5 (0.0367454) developmentalMousestage[E-MTAB-368] 2 E14.5 (0.0444256) developmentalMousestage 1 E14.5 (0.0483659) developmentalMousestage 2 E16.5 (0.0702125) developmentalstage 1 E16.5(0.0342416) stage[ min 2 E18.5(0.0814462) stage 1] E18.5(0.062328) 2 (0.0615777)[ medium ] [ max ] CEM 1 Tomm20 4527.3 9035.7 18618.6 P ( S | Z, I ) = 1.00 Tomm22 2300.0 3704.4 4726.7 Mean Corr = 0.76492Tomm40 827.1 2362.7 4871.9 Tomm70a 1125.3 1814.6 3680.2 Tomm7 1638.8 2636.8 3690.0 Nhp2 1350.0 4558.9 11860.8 C1qbp 2964.9 7912.0 13305.5 Mrpl12 2602.8 4857.0 8997.4 Phb2 3059.5 7758.1 10860.2 Hspe1 2160.1 3513.3 7267.6 CEM 1 + Yars2 329.7 746.2 1514.0 Top 10 Genes Rsl1d1 1841.1 5830.4 9933.4 Ccdc58 1113.9 2079.8 3812.6 Timm13 2432.8 5650.6 8101.7 Pno1 1715.1 4266.6 7648.8

Null module Tomm20l GEO Series "GSE31598" 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=GSE31598 Status: Public on Apr 01 2012 Title: Expression data from directly induced neural stem cells Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 22467474 Summary & Design: Summary: Induced pluripotent stem (iPS) cells give rise to neural stem cells, which are applicable for therapeutic transplantation in treatment of neural diseases. However, generation of neural stem cells from iPS cells requires a careful selection of safe iPS clones. We sought to determine whether direct induction of neural stem cells from partially reprogrammed somatic cells is able to generate safer cells rapidly. We have successfully established direct induction system from fibroblast to neural stem cells. To characterize these directly induced neural stem cells, Gene expression profiles were compared with iPS cell or ES cell-derived neurosphere. We used affymetrix microarrays to compare the global gene expression of neurospheres prepared several method.

Overall design: The mouse strain used in this study except ES/iPS cells was C57BL/6.

Background corr dist: KL-Divergence = 0.1105, L1-Distance = 0.0565, L2-Distance = 0.0068, Normal std = 0.4455

0.907 Kernel fit Pairwise Correlations Normal fit

Density 0.454

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

E14_NeurosphereMouse_adult_fibroblast38C2_iPSC (0.0544494)iPSC_PNS (0.309294)iPSC_SNS (0.0496157) (0.0496969)iNSC_1 (0.0436353) iNSC_2(0.0336824) EB3_ESC(0.00377207)ESC_PNS (0.345148)ESC_SNS (0.00350036)iNSC_3_embryo (0.0579025)iNSC_4_embryo (0.00751358) (0.0417898) [ min ] [ medium ] [ max ] CEM 1 Tomm20 4290.9 8568.1 23412.6 P ( S | Z, I ) = 1.00 Tomm22 2337.7 3020.3 5042.0 Mean Corr = 0.76446Tomm40 1204.6 2320.0 4812.6 Tomm70a 1415.0 3172.8 8477.4 Tomm7 1915.1 3535.0 5675.7 Nhp2 1787.7 4842.4 14288.4 C1qbp 3620.7 6994.6 13501.7 Mrpl12 2431.7 4290.7 7891.9 Phb2 2960.9 4419.0 10651.3 Hspe1 2955.0 5289.5 11924.4 CEM 1 + Yars2 481.7 723.8 1783.6 Top 10 Genes Rsl1d1 1689.8 4049.0 8818.9 Ccdc58 1013.5 1976.2 5257.7 Timm13 3283.0 4258.2 5060.0 Pno1 1187.2 2851.2 7548.9

Null module Tomm20l GEO Series "GSE27429" 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=GSE27429 Status: Public on Feb 22 2011 Title: Expression data at 24 hours after the blocking of Shh signaling in tooth germs at embryonic day 14 Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21447550 Summary & Design: Summary: The genetic mechanism governing the spatial patterning of teeth still remains to be elucidated. Sonic hedgehog (Shh) is one of key signaling molecules involved in the spatial patterning of teeth. By utilizing maternal transfer of 5E1 (an IgG1 monoclonal antibody against Shh protein) through the placenta to block Shh signaling, we investigated the changes in tooth patterning and in gene expression.

We used microarrays to detect specific genes related with Shh signaling in tooth germs and identified some specific genes up- or down-regulated after blocking of Shh signaling activity.

Overall design: Gene-chip expression analysis was performed with RNA from mandibular tooth germs from embryos of pregnant mice at one´day after injection of 5E1 (an IgG1 monoclonal antibody against Shh protein; number of replicates =2), 40-1a (an IgG1 monoclonal antibody against Î²-galactosidase; number of replicates=2), cyclopamine (a specific Smo antagonist; number of replicates=2) or PBS (Phosphate buffered saline; number of replicates=2), using a Affymetrix mouse gene microarray.

Background corr dist: KL-Divergence = 0.0607, L1-Distance = 0.0181, L2-Distance = 0.0004, Normal std = 0.5258

0.759 Kernel fit Pairwise Correlations Normal fit

Density 0.379

0.000 CEM 1

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

Pre-normalization Quantiles

tooth germstooth treatedgermstooth treatedbygermstooth 5E1, treatedbygermsbiologicaltooth 5E1, treatedbygermsbiologicaltooth 40-1a,rep1 treatedbygerms (0.0952761) toothbiological 40-1a,rep2 treatedbygerms (0.186331) toothbiological cyclopamine, rep1 treatedbygerms (0.247931)cyclopamine, rep2 treatedby biological (0.119387)PBS, by biological biological PBS, rep1 biological [(0.0883511) rep1 minrep2 (0.180903) (0.0319691) rep2 ] (0.0498522)[ medium ] [ max ] CEM 1 Tomm20 5199.0 6454.4 8833.2 P ( S | Z, I ) = 1.00 Tomm22 1939.1 2629.6 3192.1 Mean Corr = 0.75844Tomm40 1324.4 2395.9 2693.8 Tomm70a 1497.6 2270.7 2916.6 Tomm7 2101.1 2961.6 3821.2 Nhp2 2178.8 3023.4 4042.2 C1qbp 4603.0 6698.6 7333.6 Mrpl12 2865.7 4502.7 4684.6 Phb2 3523.8 4689.9 5925.8 Hspe1 3674.6 5282.3 7723.0 CEM 1 + Yars2 445.1 669.7 806.7 Top 10 Genes Rsl1d1 2345.4 3404.0 3778.9 Ccdc58 1535.1 1659.7 2091.4 Timm13 3357.8 4316.3 4870.1 Pno1 1372.3 2060.0 2249.2

Null module Tomm20l GEO Series "GSE53077" 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=GSE53077 Status: Public on Jan 15 2014 Title: High Runx1 levels promote a reversible more differentiated cell-state in hair follicle stem cells during quiescence Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 24462289 Summary & Design: Summary: Quiescent hair follicle (HF) bulge stem cells (SCs) differentiate to early progenitor (EP) hair germ (HG) cells, which divide to produce transit-amplifying (TA) matrix cells. EPs can revert to SCs upon injury, but whether this de-differentiation occurs in normal HF homeostasis (hair cycle), and the mechanisms regulating both differentiation and de-differentiation are unclear. Here we use lineage tracing, gain of function, transcriptional profiling, and functional assays to examine the role of observed endogenous Runx1 level changes in the hair cycle. We find that forced Runx1 expression implements hair degeneration (catagen) and simultaneously promotes changes in the quiescent bulge SC transcriptome towards a cell-state resembling the EP HG fate. This cell-state transition is functionally reversible. We propose that SC differentiation and de-differentiation are likely to occur during normal HF degeneration and niche restructuring in response to changes in endogenous Runx1 levels associated with SC location with respect to the niche.

Overall design: Freshly isolated skin cells were FACS sorted based on K15-GFP+/a6-integrin+/CD34- as hair germ and K15-GFP+/a6-integrin+/CD34+ bulge cells. Duplicate samlpes from mice at PD20 that showed telogen morphology throughout skin were used for RNA prepartion and Affymetrix analysis. Wild and transgenic samples after 1-day of doxycycline treatement were compared.

Background corr dist: KL-Divergence = 0.0588, L1-Distance = 0.0239, L2-Distance = 0.0009, Normal std = 0.5355

0.745 Kernel fit Pairwise Correlations Normal fit

Density 0.373

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, sortedWT, bulgesortedWT, cells, bulgesortedWT, biological cells, hairsortedRunx1 germbiological hairrep1 cells,iTG,Runx1 germ (0.049174) rep2sorted biological cells,iTG,Runx1 (0.185869) bulgesorted biological iTG,Runx1 rep1 cells, bulgesorted (0.0544004) iTG, rep2biological cells, hairsorted (0.112633) germbiological hairrep1 cells, germ (0.138458) rep2 biological cells,[ (0.0947014) min biological rep1 ] (0.186899) rep2 (0.177866)[ medium ] [ max ] CEM 1 Tomm20 2020.3 3467.2 5337.6 P ( S | Z, I ) = 1.00 Tomm22 1163.2 2578.8 3076.1 Mean Corr = 0.75906Tomm40 885.8 1317.3 3175.1 Tomm70a 696.2 1377.8 2459.3 Tomm7 882.7 1499.9 2364.0 Nhp2 368.3 1079.3 1382.7 C1qbp 3073.4 7149.0 9782.8 Mrpl12 907.2 2321.9 3807.7 Phb2 2837.0 5296.8 7673.4 Hspe1 1120.3 5055.7 5281.9 CEM 1 + Yars2 247.7 516.7 562.9 Top 10 Genes Rsl1d1 1803.8 2890.8 3468.1 Ccdc58 754.2 1597.8 2570.6 Timm13 974.7 2181.0 2972.1 Pno1 206.5 501.0 651.5

Null module Tomm20l GEO Series "GSE16002" 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=GSE16002 Status: Public on Sep 30 2010 Title: Molecular Events Initiating B Cell Fate Specification Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 20971928 Summary & Design: Summary: Functional genomics comparison of EBFko, Pax5ko, and RAG2ko cell lines.

Identify gene signatures associated with specfication and commitment to the B cell fate.

Overall design: Cultured cells harvested and for RNA extraction and hybridization to Affymetrix 430 2.0 Arrays.

Background corr dist: KL-Divergence = 0.0727, L1-Distance = 0.0236, L2-Distance = 0.0008, Normal std = 0.5007

0.797 Kernel fit Pairwise Correlations Normal fit

Density 0.398

0.000 CEM 1

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

Pre-normalization Quantiles

EBFko-1EBFko-2 (0.0461879)EBFko-3 (0.072893)Pax5ko-1 (0.0685344)Pax5ko-2 (0.0294962)Pax5ko-3 (0.0479467)RAG2ko-1 (0.0503833)RAG2ko-2 (0.33509)RAG2ko-3 (0.258667) (0.0908022) [ min ] [ medium ] [ max ] CEM 1 Tomm20 9573.6 10268.3 15338.1 P ( S | Z, I ) = 1.00 Tomm22 3656.2 3841.2 4713.8 Mean Corr = 0.75609Tomm40 1724.9 2217.6 3055.9 Tomm70a 2093.2 2910.3 3391.2 Tomm7 2252.4 2636.7 3126.0 Nhp2 4784.4 5733.6 8584.5 C1qbp 6624.0 8694.2 11758.6 Mrpl12 4480.1 6395.9 7960.6 Phb2 4850.4 7133.0 8734.7 Hspe1 2907.3 3783.6 9784.1 CEM 1 + Yars2 537.4 662.3 877.5 Top 10 Genes Rsl1d1 4302.1 5926.3 8264.1 Ccdc58 1599.8 1984.1 3944.1 Timm13 4310.1 4972.4 6286.7 Pno1 2311.6 3695.1 6004.3

Null module Tomm20l GEO Series "GSE10587" 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=GSE10587 Status: Public on Feb 19 2009 Title: Gene expression in stria vascularis of mice lacking Slc26a4 and heterzygous controls before the onset of hearing. Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: Determination of differential expression of genes in the stria vascularis of pendrin (Slc26a4) heterozygous and knockout mice before the onset of hearing at postnatal day 10 (P10).

Keywords: differential expression under disease state

Overall design: A total of Six samples of stria vascularis RNA obtained from P10 mice were analyzed. Triplicates from pendrin (Slc26a4) heterozygous and knockout mice were run and analyzed.

Background corr dist: KL-Divergence = 0.0370, L1-Distance = 0.0201, L2-Distance = 0.0004, Normal std = 0.6322

0.642 Kernel fit Pairwise Correlations Normal fit

Density 0.321

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

PostnatalPostnatal day 10Postnatal (P10)day 10Postnatal stria (P10)day vascularis 10Postnatal stria (P10)day vascularis 10Postnatal stria Slc26a4 (P10)day vascularis 10 stria Slc26a4 (P10)(heterozygote)day vascularis 10 stria Slc26a4 (P10)(knockout) vascularis stria Slc26a4 (heterozygote)mice vascularis mice[ (sample1) Slc26a4 (knockout)min (sample2) Slc26a4 (heterozygote)mice (0.204293)] mice (0.243452) (sample3) (knockout) (sample4) mice[ (0.0643468) medium mice (0.324585) (sample5) (sample6) (0.0548529) (0.108469) ] [ max ] CEM 1 Tomm20 1775.0 2182.9 3122.0 P ( S | Z, I ) = 1.00 Tomm22 1020.4 1217.0 1591.4 Mean Corr = 0.78402Tomm40 223.0 280.9 328.7 Tomm70a 403.1 522.5 543.1 Tomm7 1546.3 1970.3 2292.8 Nhp2 97.6 125.0 161.7 C1qbp 1873.7 2690.1 3104.4 Mrpl12 1644.0 1849.9 2453.5 Phb2 2142.5 2368.2 2908.9 Hspe1 1133.9 1432.3 1893.2 CEM 1 + Yars2 270.0 348.9 360.2 Top 10 Genes Rsl1d1 753.0 825.8 892.8 Ccdc58 930.8 1033.2 1096.3 Timm13 899.5 1149.4 1359.6 Pno1 437.3 703.2 876.5

Null module Tomm20l GEO Series "GSE18042" 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=GSE18042 Status: Public on Sep 10 2009 Title: Erythroid differentiation: G1E model Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 19887574 Summary & Design: Summary: Analysis of erythroid differentiation using Gata1 gene-disrupted G1E ER4 clone cells. Estradiol addition activates an ectopically expressed Gata-1-estrogen receptor fusion protein, triggering synchronous differentiation. 30 hour time course corresponds roughly to late burst-forming unit-erythroid stage (t=0 hrs) through orthochromatic erythroblast stage (t=30 hrs).

Overall design: G1E ER4 cells cultured in G1E medium were treated at 6 time points with estradiol to initiate erythroid differentiation by activating Gata1 transcription factor and total RNAs from treated cells were extracted for microarray experiment. The erythroid differentiation status was confirmed by cell pellet color and expression of microRNA miR451. The design was similar to an earlier studies (Welch, J. J., Watts, J. A., Vakoc, C. R., Yao, Y., Wang, H., Hardison, R. C., Blobel, G. A., Chodosh, L. A., and Weiss, M. J. (2004)). Global regulation of erythroid gene expression by transcription factor GATA-1. Blood 104, 3136-3147), except that a more recent version of Affymetric chip was used to acheive greater transcriptome coverage.

Background corr dist: KL-Divergence = 0.0901, L1-Distance = 0.0663, L2-Distance = 0.0070, Normal std = 0.5071

0.884 Kernel fit Pairwise Correlations Normal fit

Density 0.442

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

pre-estradiol,pre-estradiol, biologicalpre-estradiol, biological3 hrep1 post-estradiol,biological biological(0.0658536)3 hrep2 post-estradiol,biological (0.0877264)3 hrep3 post-estradiol,biological (0.0782345)7 h post-estradiol,biological rep17 h post-estradiol,biological(0.030504) rep27 h post-estradiol,biological(0.039607) rep314 h (0.0482793) post-estradiol,biological rep114 h (0.0152755) post-estradiol,biological rep214 h (0.0534066) post-estradiol,biological rep321 h (0.0143838) post-estradiol,biological rep121 h post-estradiol,biological(0.0421388) rep221 h post-estradiol,biological(0.00310972) rep330 h post-estradiol,biological(0.0456864) rep130 h post-estradiol,biological(0.072584) rep230 h post-estradiol,biological(0.0421148) rep3 (0.0200306) rep1 (0.12911) rep2 (0.0976731) rep3[ min (0.114281) ] [ medium ] [ max ] CEM 1 Tomm20 4354.6 5702.9 6331.9 P ( S | Z, I ) = 1.00 Tomm22 1461.1 2112.7 2433.2 Mean Corr = 0.75477Tomm40 256.0 983.8 1561.9 Tomm70a 1179.9 1972.9 2512.1 Tomm7 4186.0 5223.0 6064.3 Nhp2 261.4 901.9 1331.4 C1qbp 2913.1 9576.0 11170.3 Mrpl12 1142.7 4365.7 7186.4 Phb2 2470.0 6167.9 7580.0 Hspe1 3956.5 7735.3 8590.9 CEM 1 + Yars2 441.3 1725.4 2499.2 Top 10 Genes Rsl1d1 805.2 3168.4 4524.7 Ccdc58 2028.3 4285.9 4865.4 Timm13 2500.1 3883.8 4877.0 Pno1 1030.8 1486.6 1846.8

Null module Tomm20l