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: 23 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. Fam161a Cep290 Topors Myo7a Nphp1 Wdr19 Gnat1 Cetn2 Cetn3 Cetn1 Rp1l1 Iqcb1 Ift140 Ift122 Whrn Num ofGenesinQueryGeneset:23.CEMs:1. Overview ofCo-ExpressionModules(CEMs)withDatasetWeighting Kif3a Tbcc Ift52 Ttc8 Ift57 Ift88 Arl3 Rp1

Cep290 Ift88 Ift122 Nphp1 Wdr19 Arl3 Ift57 Rp1 Tbcc Ttc8 Ift140 Iqcb1 Cetn1 Fam161a Cetn3 Myo7a Kif3a Topors Ift52 Gnat1 Cetn2 Whrn Rp1l1 CEM 1(6datasets) 0.0 Scale ofaveragePearsoncorrelations 0.2 0.4 0.6 0.8 1.0 Symbol Num ofCEMGenes:23.Predicted1161.SelectedDatasets:6.Strength:0.2 CEM 1,Geneset"[G]photoreceptorconnectingcilium",Page1 AK129341 Tmem107 Fam161a Ccdc157 Dync2li1 Katnal2 Cep290 Ccdc39 Ccdc96 Dyx1c1 Topors Cluap1 Map10 Myo7a Nphp1 Lrrc48 Lrrc73 Wdr60 Wdr31 Wdr34 Wdr19 Enkd1 Gnat1 Cetn2 Cetn3 Cetn1 Nme5 Rp1l1 Ttc26 Iqcb1 Ift140 Ift122 Whrn Dpcd Eno4 Bbs1 Bbs9 Bbs2 Kif3a Tbcc Lca5 Mtor Ift80 Ift52 Ttc8 Ift57 Ift88 Gtl3 Arl3 Rp1 0.0 1.0

GSE13106 [10] GSE29318 [9]

GSE9338 [42] Only showingfirst200datasets-Seetxtoutputforfulldetails. GSE54056 [12] GSE49346 [6] GSE39391 [21] GSE24207 [73] GSE27630 [8] GSE36833 [49] GSE26299 [108] GSE23200 [6] GSE24512 [29] GSE39458 [6] GSE48338 [8] GSE10246 [182] GSE31797 [6] GSE42601 [6] GSE1986 [17] GSE27261 [8] GSE12769 [20] GSE16585 [31] GSE31972 [6] GSE34423 [40] GSE9954 [70] GSE24813 [10] GSE49128 [17] GSE37431 [6] GSE32095 [24] GSE1871 [12] GSE11443 [6] GSE23895 [18] GSE27568 [16] GSE21193 [10] GSE15315 [6] GSE21900 [12] GSE4193 [8] GSE2197 [6] GSE32529 [224] GSE17263 [6] GSE26568 [6] GSE27713 [7] GSE15872 [18] GSE25737 [6] GSE46942 [7] GSE20696 [8] GSE42061 [12] GSE9441 [36] GSE8660 [6] GSE40087 [15] GSE11898 [9] GSE47414 [18] GSE25423 [10] GSE6383 [6] GSE51365 [28] GSE27605 [8] GSE14891 [8] GSE33308 [10] GSE23925 [6] GSE33770 [8] GSE47196 [6] GSE23833 [12] GSE23002 [8] GSE6933 [15] GSE1074 [12] GSE43620 [8] GSE13874 [14] GSE23408 [39] GSE14004 [9] GSE3463 [12] GSE41759 [14] GSE43635 [9] GSE13526 [6] GSE27675 [14] GSE57543 [6] GSE27799 [6] GSE6196 [9] GSE10528 [6] GSE4734 [61] GSE20954 [14] GSE47421 [24] GSE40286 [10] GSE45820 [6] GSE27114 [6] GSE22824 [24] GSE39082 [6] GSE19299 [6] GSE15794 [6] GSE7348 [6] GSE34863 [8] GSE15871 [18] GSE31561 [36] GSE21568 [12] GSE47425 [7] GSE7020 [8] GSE40856 [8] GSE13692 [8] GSE13753 [10] GSE13611 [8] GSE38044 [6] GSE26476 [6] GSE29648 [10] GSE25257 [6] GSE13635 [6] GSE5891 [6] GSE5127 [18] GSE50122 [10] GSE39030 [6] GSE11201 [18] GSE10113 [12] GSE27195 [6] GSE5309 [7] GSE12986 [10] GSE32963 [6] GSE14243 [6] GSE36665 [6] GSE17553 [16] GSE13302 [30] GSE8434 [6] GSE27546 [51] GSE23600 [10] GSE38672 [6] GSE33942 [12] GSE45968 [6] GSE24695 [9] GSE10813 [12] GSE11165 [6] GSE21711 [6] GSE24061 [88] GSE26616 [6] GSE24289 [6] GSE26290 [12] GSE23398 [7] GSE5298 [8] GSE28664 [17] GSE23016 [9] GSE56482 [8] GSE18907 [12] GSE41925 [8] GSE11333 [6] GSE39469 [6] GSE20968 [6] GSE8969 [6] GSE56135 [8] GSE39273 [6] GSE22527 [6] GSE30684 [6] GSE7141 [6] GSE15379 [12] GSE22448 [6] GSE17923 [6] GSE54285 [12] GSE13693 [9] GSE52101 [17] GSE17886 [16] CEM+ CEM GSE13103 [8] GSE4928 [8] GSE30488 [52] GSE4260 [6] GSE10589 [6] GSE43713 [16] 0.0 GSE35396 [24] GSE31940 [8]

GSE4765 [6] Scale ofaveragePearsoncorrelations GSE5332 [12] GSE22140 [13] GSE5497 [6] GSE6540 [12] GSE21861 [8] GSE24291 [6] 0.2 GSE5861 [6] GSE2557 [6] GSE20390 [6] GSE44118 [6] GSE31849 [18] GSE25029 [56] GSE17097 [20] GSE53951 [10] GSE8621 [12] 0.4 GSE5425 [6] GSE10902 [6] GSE19204 [6] GSE43059 [8] GSE5313 [6] GSE7767 [6] GSE46500 [6] GSE22251 [9] GSE30855 [6] 0.6 GSE27159 [8] GSE15772 [8] GSE15610 [12] GSE6285 [24] GSE47065 [8] GSE50729 [6] GSE12498 [12] GSE55809 [8] GSE32277 [33] 0.8 GSE3100 [23] GSE13873 [27] GSE24614 [6] GSE10989 [6] Score 2.57 2.58 2.59 2.59 2.59 2.61 2.61 2.62 2.63 2.63 2.63 2.64 2.64 2.65 2.68 2.73 2.74 2.82 2.83 2.87 2.89 2.92 2.94 2.95 3.12 3.18 3.20 1.0 Notes D430042O09Rik 1110051M20Rik A330021E22Rik E230008N13Rik 1700003M02Rik 2300009A05Rik 1700088E04Rik 1700029J07Rik Symbol Num ofCEMGenes:23.Predicted1161.SelectedDatasets:6.Strength:0.2 CEM 1,Geneset"[G]photoreceptorconnectingcilium",Page2 BC022687 Fam154b Fam229b Ccpg1os Dync2h1 Ccdc113 Ccdc103 Ccdc173 Psmc3ip Ankrd42 Ppp1r42 Psmd13 Zswim3 Ubxn10 Ccdc65 Ccdc57 Vps13a Dnajb2 Klhdc1 Dixdc1 Pih1d2 Plk1s1 Wdr78 Bbs10 Cep41 Tcp11 Tsacc Meig1 Pacrg Amn1 Lrguk Stim1 Rabl2 Tctn2 Ttc25 Lztfl1 Birc2 Bbs5 Ppil6 Rpgr Iqcd Iqcg 0.0 1.0

GSE13106 [10] GSE29318 [9]

GSE4765 [6] Scale ofaveragePearsoncorrelations GSE5332 [12] GSE22140 [13] GSE5497 [6] GSE6540 [12] GSE21861 [8] GSE24291 [6] 0.2 GSE5861 [6] GSE2557 [6] GSE20390 [6] GSE44118 [6] GSE31849 [18] GSE25029 [56] GSE17097 [20] GSE53951 [10] GSE8621 [12] 0.4 GSE5425 [6] GSE10902 [6] GSE19204 [6] GSE43059 [8] GSE5313 [6] GSE7767 [6] GSE46500 [6] GSE22251 [9] GSE30855 [6] 0.6 GSE27159 [8] GSE15772 [8] GSE15610 [12] GSE6285 [24] GSE47065 [8] GSE50729 [6] GSE12498 [12] GSE55809 [8] GSE32277 [33] 0.8 GSE3100 [23] GSE13873 [27] GSE24614 [6] GSE10989 [6] Score 2.08 2.09 2.09 2.10 2.10 2.11 2.12 2.13 2.16 2.16 2.16 2.17 2.17 2.17 2.18 2.19 2.19 2.20 2.20 2.22 2.23 2.25 2.25 2.26 2.28 2.28 2.30 2.31 2.32 2.34 2.35 2.37 2.38 2.38 2.39 2.43 2.44 2.45 2.46 2.47 2.49 2.49 2.49 2.50 2.52 2.53 2.54 2.54 2.55 2.57 1.0 Notes Symbol Num ofCEMGenes:23.Predicted1161.SelectedDatasets:6.Strength:0.2 CEM 1,Geneset"[G]photoreceptorconnectingcilium",Page3 Ppp1r16a Fam151b Fam194a Ccdc163 Ccdc181 Tmem80 Znrd1as Rpgrip1 Ttc30a1 Ndufaf3 C1qtnf4 Chchd6 Mterfd2 Akap10 Cep104 Spice1 Zfp523 Rangrf Mdh1b Glt8d1 Lrrc46 Wdr63 Wdr35 Wdr66 Pde6d Morn5 Morn2 Znhit2 Pde8a Fank1 Cetn4 Chd1l Dnal4 Stk30 Stk36 Zfp54 Ift172 Mks1 Triqk B9d1 Cds1 Nek4 Ulk4 Svip Ift74 Ift43 Carf Mak Arl6 Pifo 0.0 1.0

GSE13106 [10] GSE29318 [9]

GSE4765 [6] Scale ofaveragePearsoncorrelations GSE5332 [12] GSE22140 [13] GSE5497 [6] GSE6540 [12] GSE21861 [8] GSE24291 [6] 0.2 GSE5861 [6] GSE2557 [6] GSE20390 [6] GSE44118 [6] GSE31849 [18] GSE25029 [56] GSE17097 [20] GSE53951 [10] GSE8621 [12] 0.4 GSE5425 [6] GSE10902 [6] GSE19204 [6] GSE43059 [8] GSE5313 [6] GSE7767 [6] GSE46500 [6] GSE22251 [9] GSE30855 [6] 0.6 GSE27159 [8] GSE15772 [8] GSE15610 [12] GSE6285 [24] GSE47065 [8] GSE50729 [6] GSE12498 [12] GSE55809 [8] GSE32277 [33] 0.8 GSE3100 [23] GSE13873 [27] GSE24614 [6] GSE10989 [6] Score 1.72 1.73 1.74 1.74 1.74 1.75 1.75 1.76 1.76 1.77 1.77 1.77 1.79 1.79 1.79 1.79 1.79 1.80 1.80 1.80 1.82 1.82 1.83 1.83 1.84 1.85 1.85 1.88 1.88 1.90 1.91 1.91 1.92 1.95 1.96 1.97 1.98 1.98 1.98 1.99 2.00 2.00 2.01 2.01 2.03 2.04 2.04 2.05 2.06 2.07 1.0 Notes 8430427H17Rik 1700019L03Rik 2310061I04Rik Symbol Num ofCEMGenes:23.Predicted1161.SelectedDatasets:6.Strength:0.2 CEM 1,Geneset"[G]photoreceptorconnectingcilium",Page4 Tmem230 Camsap1 AI429214 Tctex1d2 Fam188b Arhgef33 Mycbpap Fam216a Ccdc104 Ankrd54 Dynlrb2 Cops7a Ccdc87 Ccdc79 Ccdc66 Pex11a Chrac1 Ptpmt1 Dnajb1 Wdpcp Smim8 Hspa4l Nupr1l Med16 Wdr47 Wdr38 Rsph9 Ap4b1 Spag1 Ddx20 Susd3 Riiad1 Spa17 Thap4 Fyco1 Mcts2 Acot7 Dnm3 Kctd7 Stag3 Rabl5 Coq4 Usp2 Radil Lyar Icmt Kif9 0.0 1.0

GSE13106 [10] GSE29318 [9]

GSE4765 [6] Scale ofaveragePearsoncorrelations GSE5332 [12] GSE22140 [13] GSE5497 [6] GSE6540 [12] GSE21861 [8] GSE24291 [6] 0.2 GSE5861 [6] GSE2557 [6] GSE20390 [6] GSE44118 [6] GSE31849 [18] GSE25029 [56] GSE17097 [20] GSE53951 [10] GSE8621 [12] 0.4 GSE5425 [6] GSE10902 [6] GSE19204 [6] GSE43059 [8] GSE5313 [6] GSE7767 [6] GSE46500 [6] GSE22251 [9] GSE30855 [6] 0.6 GSE27159 [8] GSE15772 [8] GSE15610 [12] GSE6285 [24] GSE47065 [8] GSE50729 [6] GSE12498 [12] GSE55809 [8] GSE32277 [33] 0.8 GSE3100 [23] GSE13873 [27] GSE24614 [6] GSE10989 [6] Score 1.52 1.52 1.52 1.53 1.53 1.54 1.54 1.54 1.56 1.57 1.57 1.57 1.57 1.57 1.58 1.58 1.58 1.58 1.58 1.58 1.58 1.59 1.60 1.60 1.60 1.61 1.61 1.62 1.62 1.63 1.63 1.63 1.65 1.65 1.65 1.66 1.66 1.67 1.67 1.67 1.67 1.68 1.68 1.69 1.69 1.70 1.70 1.70 1.71 1.71 1.0 Notes 4932438A13Rik 2610301B20Rik 1700007K13Rik 2210408I21Rik D3Ertd751e Symbol Num ofCEMGenes:23.Predicted1161.SelectedDatasets:6.Strength:0.2 CEM 1,Geneset"[G]photoreceptorconnectingcilium",Page5 BC030307 Tmem231 Rnf138rt1 Tsnaxip1 Slc25a19 Slc25a33 Fam221a Fam227a Hsbp1l1 Efcab10 Ppip5k1 Stard10 Zswim7 Ccdc11 Arfgef2 Gm166 Ptpn20 Spata1 Fem1c Qrich1 Dalrd3 Med31 Nup35 Cep63 Spag8 Acyp1 Cep19 Naa25 Tpgs2 Strip2 Hirip3 Pfdn5 Tcf20 Odf2l Map9 Nipbl Gas8 Tchp Mlh3 Cerk Rnf6 Kat5 Phf1 Mlf1 Poli 0.0 1.0

GSE13106 [10] GSE29318 [9]

GSE4765 [6] Scale ofaveragePearsoncorrelations GSE5332 [12] GSE22140 [13] GSE5497 [6] GSE6540 [12] GSE21861 [8] GSE24291 [6] 0.2 GSE5861 [6] GSE2557 [6] GSE20390 [6] GSE44118 [6] GSE31849 [18] GSE25029 [56] GSE17097 [20] GSE53951 [10] GSE8621 [12] 0.4 GSE5425 [6] GSE10902 [6] GSE19204 [6] GSE43059 [8] GSE5313 [6] GSE7767 [6] GSE46500 [6] GSE22251 [9] GSE30855 [6] 0.6 GSE27159 [8] GSE15772 [8] GSE15610 [12] GSE6285 [24] GSE47065 [8] GSE50729 [6] GSE12498 [12] GSE55809 [8] GSE32277 [33] 0.8 GSE3100 [23] GSE13873 [27] GSE24614 [6] GSE10989 [6] Score 1.34 1.34 1.35 1.35 1.35 1.36 1.36 1.36 1.37 1.37 1.37 1.38 1.39 1.39 1.39 1.40 1.40 1.41 1.42 1.42 1.42 1.42 1.43 1.43 1.43 1.43 1.43 1.44 1.45 1.45 1.45 1.46 1.46 1.46 1.47 1.47 1.48 1.48 1.49 1.49 1.49 1.50 1.50 1.51 1.51 1.51 1.51 1.52 1.52 1.52 1.0 Notes Symbol Num ofCEMGenes:23.Predicted1161.SelectedDatasets:6.Strength:0.2 CEM 1,Geneset"[G]photoreceptorconnectingcilium",Page6 Hsp90aa1 Ccnb1ip1 Slc25a35 Ccdc90b Epb4.1l5 Gm5617 Pde4dip Spata33 Fam58b Fam45a Fam98c Nup188 Zc3h14 Mettl25 Golga4 Scaper Tarbp2 Dnaic1 Ssx2ip Prom1 Mesp1 Ahctf1 Lrrc23 Wdr17 Wdr27 Sugp2 Cops3 Rad9b Wdr16 Ube2u Mrgbp Usp47 Mkrn1 Gpr62 Gtf2f2 Tdrd7 Rfesd Xrcc4 Pias1 Tescl Actr8 Actr6 Lrrc6 Dgkd Cog6 Ddx1 Insl5 Nat9 Fbf1 Ctr9 0.0 1.0

GSE13106 [10] GSE29318 [9]

GSE4765 [6] Scale ofaveragePearsoncorrelations GSE5332 [12] GSE22140 [13] GSE5497 [6] GSE6540 [12] GSE21861 [8] GSE24291 [6] 0.2 GSE5861 [6] GSE2557 [6] GSE20390 [6] GSE44118 [6] GSE31849 [18] GSE25029 [56] GSE17097 [20] GSE53951 [10] GSE8621 [12] 0.4 GSE5425 [6] GSE10902 [6] GSE19204 [6] GSE43059 [8] GSE5313 [6] GSE7767 [6] GSE46500 [6] GSE22251 [9] GSE30855 [6] 0.6 GSE27159 [8] GSE15772 [8] GSE15610 [12] GSE6285 [24] GSE47065 [8] GSE50729 [6] GSE12498 [12] GSE55809 [8] GSE32277 [33] 0.8 GSE3100 [23] GSE13873 [27] GSE24614 [6] GSE10989 [6] Score 1.20 1.20 1.20 1.21 1.21 1.21 1.22 1.23 1.23 1.24 1.25 1.25 1.25 1.25 1.25 1.25 1.25 1.26 1.26 1.26 1.27 1.27 1.28 1.28 1.28 1.28 1.28 1.28 1.28 1.28 1.28 1.29 1.30 1.30 1.30 1.30 1.31 1.31 1.32 1.32 1.32 1.32 1.32 1.33 1.33 1.33 1.33 1.33 1.33 1.34 1.0 Notes 2700049A03Rik 1700020D05Rik 1110004E09Rik Symbol Num ofCEMGenes:23.Predicted1161.SelectedDatasets:6.Strength:0.2 CEM 1,Geneset"[G]photoreceptorconnectingcilium",Page7 Cdc42ep3 Sh3bgrl2 Mov10l1 Traf3ip1 Clec11a Pla2g2c Mageb3 Dnah7a Ccdc13 Bcap29 Vps37c Golga5 Sympk Efcab2 Trim39 Ccl27a Zfp956 Zfp784 Zfp672 Ttc30b Mif4gd Galnt3 Armc4 Heatr2 Lrrc61 Lrrc36 Wdr65 Kifap3 Dnah8 Hspb6 Cep95 Sox30 Letm2 Oser1 Dcaf8 Acsl1 Tnni3 Ttc12 Mypn Btaf1 Ybx3 Itgae Sirt1 Styx Iqch Iqck Ak7 0.0 1.0

GSE13106 [10] GSE29318 [9]

GSE4765 [6] Scale ofaveragePearsoncorrelations GSE5332 [12] GSE22140 [13] GSE5497 [6] GSE6540 [12] GSE21861 [8] GSE24291 [6] 0.2 GSE5861 [6] GSE2557 [6] GSE20390 [6] GSE44118 [6] GSE31849 [18] GSE25029 [56] GSE17097 [20] GSE53951 [10] GSE8621 [12] 0.4 GSE5425 [6] GSE10902 [6] GSE19204 [6] GSE43059 [8] GSE5313 [6] GSE7767 [6] GSE46500 [6] GSE22251 [9] GSE30855 [6] 0.6 GSE27159 [8] GSE15772 [8] GSE15610 [12] GSE6285 [24] GSE47065 [8] GSE50729 [6] GSE12498 [12] GSE55809 [8] GSE32277 [33] 0.8 GSE3100 [23] GSE13873 [27] GSE24614 [6] GSE10989 [6] Score 1.06 1.06 1.06 1.06 1.06 1.06 1.07 1.07 1.07 1.07 1.08 1.09 1.09 1.09 1.09 1.10 1.10 1.10 1.10 1.11 1.12 1.12 1.12 1.12 1.13 1.13 1.13 1.14 1.14 1.14 1.14 1.14 1.15 1.15 1.15 1.15 1.16 1.16 1.16 1.17 1.17 1.17 1.18 1.18 1.18 1.18 1.19 1.19 1.19 1.19 1.0 Notes 5730508B09Rik 4931406P16Rik Symbol Num ofCEMGenes:23.Predicted1161.SelectedDatasets:6.Strength:0.2 CEM 1,Geneset"[G]photoreceptorconnectingcilium",Page8 Hist2h2aa2 Zmynd12 Slc4a1ap Shroom3 Ccdc136 Ccdc117 Snrnp27 Dnajc27 Slc26a8 Slc38a9 Mapk15 Ccdc89 Scube2 Zdhhc5 Zcchc7 Btbd10 Zranb1 Mrpl39 Mplkip Mfsd6l Isyna1 Myo1a Med19 Neurl4 Strada Spire2 Qsox2 Trafd1 Wdr48 Rad17 Alms1 Acrbp Tex15 Prr15l Cdkl4 Ribc1 Spef1 Efhc1 Ttbk2 Ttc16 Lca5l Msh5 Ago4 Celf6 Rnls Clp1 Cul3 Ift46 0.0 1.0

GSE13106 [10] GSE29318 [9]

GSE4765 [6] Scale ofaveragePearsoncorrelations GSE5332 [12] GSE22140 [13] GSE5497 [6] GSE6540 [12] GSE21861 [8] GSE24291 [6] 0.2 GSE5861 [6] GSE2557 [6] GSE20390 [6] GSE44118 [6] GSE31849 [18] GSE25029 [56] GSE17097 [20] GSE53951 [10] GSE8621 [12] 0.4 GSE5425 [6] GSE10902 [6] GSE19204 [6] GSE43059 [8] GSE5313 [6] GSE7767 [6] GSE46500 [6] GSE22251 [9] GSE30855 [6] 0.6 GSE27159 [8] GSE15772 [8] GSE15610 [12] GSE6285 [24] GSE47065 [8] GSE50729 [6] GSE12498 [12] GSE55809 [8] GSE32277 [33] 0.8 GSE3100 [23] GSE13873 [27] GSE24614 [6] GSE10989 [6] Score 0.95 0.95 0.96 0.96 0.96 0.96 0.96 0.96 0.97 0.97 0.97 0.97 0.97 0.98 0.99 0.99 0.99 0.99 0.99 0.99 1.00 1.00 1.00 1.00 1.01 1.01 1.01 1.01 1.01 1.02 1.02 1.03 1.03 1.03 1.03 1.03 1.03 1.03 1.03 1.04 1.04 1.04 1.04 1.04 1.05 1.05 1.05 1.05 1.05 1.05 1.0 Notes 4833427G06Rik 9230110C19Rik 0610009B22Rik 5330417C22Rik 1700009P17Rik Symbol Num ofCEMGenes:23.Predicted1161.SelectedDatasets:6.Strength:0.2 CEM 1,Geneset"[G]photoreceptorconnectingcilium",Page9 Hist2h2be Tmem129 Mapk1ip1 Trappc12 Fam107b Macrod2 Tbc1d32 Phyhipl Zmym5 Kdm5b Rmnd1 Dnaja4 Spata7 Sh3gl2 Pdcd2l Zfp653 Zfp654 Gtf2e1 Cops5 Hilpda Atp5sl Usp54 Rab28 Esco1 Styxl1 Tceb2 Piwil2 Tex14 Lrriq3 Krcc1 Atp5s Supt3 Cldn7 Nupl2 Ercc3 Pmp2 Spef2 Zbtb3 Fbxl5 Eno3 Swt1 Pkig Taf5 Me1 Dlat 0.0 1.0

GSE13106 [10] GSE29318 [9]

GSE4765 [6] Scale ofaveragePearsoncorrelations GSE5332 [12] GSE22140 [13] GSE5497 [6] GSE6540 [12] GSE21861 [8] GSE24291 [6] 0.2 GSE5861 [6] GSE2557 [6] GSE20390 [6] GSE44118 [6] GSE31849 [18] GSE25029 [56] GSE17097 [20] GSE53951 [10] GSE8621 [12] 0.4 GSE5425 [6] GSE10902 [6] GSE19204 [6] GSE43059 [8] GSE5313 [6] GSE7767 [6] GSE46500 [6] GSE22251 [9] GSE30855 [6] 0.6 GSE27159 [8] GSE15772 [8] GSE15610 [12] GSE6285 [24] GSE47065 [8] GSE50729 [6] GSE12498 [12] GSE55809 [8] GSE32277 [33] 0.8 GSE3100 [23] GSE13873 [27] GSE24614 [6] GSE10989 [6] Score 0.84 0.84 0.84 0.84 0.84 0.84 0.85 0.85 0.85 0.85 0.85 0.86 0.87 0.87 0.87 0.87 0.87 0.87 0.88 0.88 0.88 0.88 0.88 0.88 0.89 0.89 0.89 0.89 0.89 0.90 0.90 0.91 0.91 0.91 0.91 0.91 0.91 0.91 0.92 0.92 0.92 0.93 0.93 0.93 0.94 0.94 0.94 0.94 0.94 0.95 1.0 Notes 1700012B09Rik Symbol Num ofCEMGenes:23.Predicted1161.SelectedDatasets:6.Strength:0.2 CEM 1,Geneset"[G]photoreceptorconnectingcilium",Page10 Tmem232 Slc25a18 Abhd14a Suv39h2 Ccdc101 Sdr39u1 Fgfr1op Sccpdh Unc13b Katnal1 Ccdc62 Cep120 Ccdc19 Mapre3 Dnttip1 Hmox2 Dmap1 Suclg1 Mrpl55 Zfp446 Ttc21b Gkap1 Kpna2 Nup98 Cdk20 Bbs12 Lyrm9 Usp34 Naa38 Fancg Ndrg3 Enkur Cntd1 Ngly1 Nme6 Gpx4 Phtf1 Sun1 Phc1 Nae1 Nek1 Rec8 Mfn2 Ly6k Slirp Setx Faf1 Oit1 Me2 0.0 1.0

GSE13106 [10] GSE29318 [9]

GSE4765 [6] Scale ofaveragePearsoncorrelations GSE5332 [12] GSE22140 [13] GSE5497 [6] GSE6540 [12] GSE21861 [8] GSE24291 [6] 0.2 GSE5861 [6] GSE2557 [6] GSE20390 [6] GSE44118 [6] GSE31849 [18] GSE25029 [56] GSE17097 [20] GSE53951 [10] GSE8621 [12] 0.4 GSE5425 [6] GSE10902 [6] GSE19204 [6] GSE43059 [8] GSE5313 [6] GSE7767 [6] GSE46500 [6] GSE22251 [9] GSE30855 [6] 0.6 GSE27159 [8] GSE15772 [8] GSE15610 [12] GSE6285 [24] GSE47065 [8] GSE50729 [6] GSE12498 [12] GSE55809 [8] GSE32277 [33] 0.8 GSE3100 [23] GSE13873 [27] GSE24614 [6] GSE10989 [6] Score 0.76 0.76 0.76 0.76 0.76 0.76 0.76 0.76 0.76 0.77 0.77 0.77 0.77 0.77 0.77 0.78 0.78 0.78 0.78 0.78 0.79 0.79 0.79 0.79 0.79 0.79 0.80 0.80 0.80 0.81 0.81 0.81 0.81 0.81 0.81 0.81 0.82 0.82 0.82 0.82 0.82 0.82 0.83 0.83 0.83 0.83 0.83 0.83 0.83 0.83 1.0 Notes 4933427G17Rik 1700016K19Rik 4930444P10Rik 1700011I03Rik Symbol Num ofCEMGenes:23.Predicted1161.SelectedDatasets:6.Strength:0.2 CEM 1,Geneset"[G]photoreceptorconnectingcilium",Page11 Tmem216 Tmem237 Arhgap19 Gm11992 Slc25a31 Smarca2 Epb4.1l2 Spata24 Timm8b Rasgrf2 Tubb4b Ccdc77 Immp1l Dnttip2 Tecpr2 Sept14 Zfp839 Osbp2 Mmel1 Rhpn1 Glb1l3 Hook1 Cited1 Ubac1 Mtmr6 Vps4a Jarid2 Sycp3 Mrp63 Tex11 Dctn2 Stx17 Fars2 Wnk4 Arid2 Kif3b Mtfr1 Zpbp Daxx Gnl2 Cry1 Mxi1 Sirt3 Nol8 Slx4 Eed 0.0 1.0

GSE13106 [10] GSE29318 [9]

GSE4765 [6] Scale ofaveragePearsoncorrelations GSE5332 [12] GSE22140 [13] GSE5497 [6] GSE6540 [12] GSE21861 [8] GSE24291 [6] 0.2 GSE5861 [6] GSE2557 [6] GSE20390 [6] GSE44118 [6] GSE31849 [18] GSE25029 [56] GSE17097 [20] GSE53951 [10] GSE8621 [12] 0.4 GSE5425 [6] GSE10902 [6] GSE19204 [6] GSE43059 [8] GSE5313 [6] GSE7767 [6] GSE46500 [6] GSE22251 [9] GSE30855 [6] 0.6 GSE27159 [8] GSE15772 [8] GSE15610 [12] GSE6285 [24] GSE47065 [8] GSE50729 [6] GSE12498 [12] GSE55809 [8] GSE32277 [33] 0.8 GSE3100 [23] GSE13873 [27] GSE24614 [6] GSE10989 [6] Score 0.67 0.67 0.67 0.67 0.67 0.67 0.67 0.67 0.67 0.67 0.67 0.67 0.67 0.68 0.68 0.68 0.68 0.68 0.68 0.69 0.69 0.69 0.69 0.70 0.70 0.70 0.70 0.71 0.71 0.71 0.71 0.71 0.72 0.72 0.72 0.73 0.73 0.73 0.73 0.73 0.74 0.74 0.74 0.75 0.75 0.75 0.75 0.75 0.75 0.75 1.0 Notes 4933411K20Rik Symbol Num ofCEMGenes:23.Predicted1161.SelectedDatasets:6.Strength:0.2 CEM 1,Geneset"[G]photoreceptorconnectingcilium",Page12 Fam174a Ccdc169 Khdrbs3 Dpy19l2 Ldhal6b Ppp1cc Ccdc63 Ccdc14 Ndufs4 Katnb1 Lmbr1l Rbm11 Trim37 Efcab7 Smco2 Zfp318 Mrpl54 Gltpd1 Gtf2e2 Dnah2 Nup85 Noxo1 Trpm4 Cdk19 Znhit6 Znhit3 Prok2 Park2 Pcgf1 Hipk3 Hcfc2 Pcgf6 Zfp62 Tekt2 Glmn Hagh Cog8 Ddit3 Cbx7 Ldhc Asz1 Gbf1 Rtca Sbf2 Taf6 Ift27 Ufl1 Ak8 Igj 0.0 1.0

GSE13106 [10] GSE29318 [9]

GSE4765 [6] Scale ofaveragePearsoncorrelations GSE5332 [12] GSE22140 [13] GSE5497 [6] GSE6540 [12] GSE21861 [8] GSE24291 [6] 0.2 GSE5861 [6] GSE2557 [6] GSE20390 [6] GSE44118 [6] GSE31849 [18] GSE25029 [56] GSE17097 [20] GSE53951 [10] GSE8621 [12] 0.4 GSE5425 [6] GSE10902 [6] GSE19204 [6] GSE43059 [8] GSE5313 [6] GSE7767 [6] GSE46500 [6] GSE22251 [9] GSE30855 [6] 0.6 GSE27159 [8] GSE15772 [8] GSE15610 [12] GSE6285 [24] GSE47065 [8] GSE50729 [6] GSE12498 [12] GSE55809 [8] GSE32277 [33] 0.8 GSE3100 [23] GSE13873 [27] GSE24614 [6] GSE10989 [6] Score 0.61 0.62 0.62 0.62 0.62 0.62 0.62 0.62 0.62 0.62 0.63 0.63 0.63 0.63 0.63 0.63 0.63 0.63 0.63 0.63 0.63 0.63 0.64 0.64 0.64 0.64 0.64 0.64 0.64 0.65 0.65 0.65 0.65 0.65 0.65 0.65 0.65 0.65 0.65 0.65 0.66 0.66 0.66 0.66 0.66 0.66 0.66 0.66 0.67 0.67 1.0 Notes 4930404A10Rik 4930550C14Rik 1700074P13Rik Symbol Num ofCEMGenes:23.Predicted1161.SelectedDatasets:6.Strength:0.2 CEM 1,Geneset"[G]photoreceptorconnectingcilium",Page13 Mphosph8 Fam160a2 BC051142 AA467197 Tmem86b Trp53bp1 Mapkbp1 Slc22a21 Fam135a Ube2d2b Ppp2r5e Plekhg4 Zfp280d Zfp518a Dbndd1 D1Pas1 Dnah12 Gpr180 Ankrd9 Ndufc1 Papolb Smc1b Dcaf17 Zbtb26 Zfp612 Slc5a5 Med17 Lrrc27 Ubxn6 Hook2 Pcbp3 Ncoa6 Dnali1 Fyttd1 Sycp1 Mdm1 Mtch2 Prps1 Ptpn2 Stk33 Mdc1 Sbds Mreg Taf7l Lrif1 Ttll1 Jrk 0.0 1.0

GSE13106 [10] GSE29318 [9]

GSE4765 [6] Scale ofaveragePearsoncorrelations GSE5332 [12] GSE22140 [13] GSE5497 [6] GSE6540 [12] GSE21861 [8] GSE24291 [6] 0.2 GSE5861 [6] GSE2557 [6] GSE20390 [6] GSE44118 [6] GSE31849 [18] GSE25029 [56] GSE17097 [20] GSE53951 [10] GSE8621 [12] 0.4 GSE5425 [6] GSE10902 [6] GSE19204 [6] GSE43059 [8] GSE5313 [6] GSE7767 [6] GSE46500 [6] GSE22251 [9] GSE30855 [6] 0.6 GSE27159 [8] GSE15772 [8] GSE15610 [12] GSE6285 [24] GSE47065 [8] GSE50729 [6] GSE12498 [12] GSE55809 [8] GSE32277 [33] 0.8 GSE3100 [23] GSE13873 [27] GSE24614 [6] GSE10989 [6] Score 0.55 0.55 0.55 0.55 0.55 0.56 0.56 0.56 0.56 0.56 0.56 0.56 0.56 0.56 0.56 0.57 0.57 0.57 0.58 0.58 0.58 0.58 0.58 0.58 0.58 0.58 0.59 0.59 0.59 0.59 0.59 0.59 0.59 0.60 0.60 0.60 0.60 0.60 0.60 0.60 0.60 0.60 0.60 0.61 0.61 0.61 0.61 0.61 0.61 0.61 1.0 Notes Symbol Num ofCEMGenes:23.Predicted1161.SelectedDatasets:6.Strength:0.2 CEM 1,Geneset"[G]photoreceptorconnectingcilium",Page14 Trappc11 Zmynd10 Fam179b Rsph10b Ccdc176 Ccdc108 Ccdc160 Tbc1d12 Rmnd5b Nfatc2ip Gm4871 Shcbp1l Scamp1 Tmbim7 Sec22a Golga3 Atp11a Spata6 Pam16 Zfp110 Inpp5k Mrpl47 Slc4a7 Slc9a5 Actr10 Abhd4 Prame Hspb9 Rims2 Stam2 Vdac2 Sel1l2 Crtam Tex12 Gsto2 Nudt9 Smpx Capsl Aste1 Prr14 Prepl Dgke Rce1 Blzf1 Pex7 Grk4 Ttll3 Lig4 Cir1 Acr 0.0 1.0

GSE13106 [10] GSE29318 [9]

GSE4765 [6] Scale ofaveragePearsoncorrelations GSE5332 [12] GSE22140 [13] GSE5497 [6] GSE6540 [12] GSE21861 [8] GSE24291 [6] 0.2 GSE5861 [6] GSE2557 [6] GSE20390 [6] GSE44118 [6] GSE31849 [18] GSE25029 [56] GSE17097 [20] GSE53951 [10] GSE8621 [12] 0.4 GSE5425 [6] GSE10902 [6] GSE19204 [6] GSE43059 [8] GSE5313 [6] GSE7767 [6] GSE46500 [6] GSE22251 [9] GSE30855 [6] 0.6 GSE27159 [8] GSE15772 [8] GSE15610 [12] GSE6285 [24] GSE47065 [8] GSE50729 [6] GSE12498 [12] GSE55809 [8] GSE32277 [33] 0.8 GSE3100 [23] GSE13873 [27] GSE24614 [6] GSE10989 [6] Score 0.48 0.48 0.48 0.48 0.48 0.48 0.49 0.49 0.49 0.49 0.49 0.49 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.51 0.51 0.51 0.51 0.51 0.51 0.51 0.51 0.51 0.51 0.51 0.51 0.51 0.51 0.51 0.52 0.52 0.52 0.53 0.53 0.53 0.53 0.54 0.54 0.54 0.54 1.0 Notes 1810043G02Rik 4930504O13Rik 1700026D08Rik 4930453N24Rik 4930505A04Rik Symbol Num ofCEMGenes:23.Predicted1161.SelectedDatasets:6.Strength:0.2 CEM 1,Geneset"[G]photoreceptorconnectingcilium",Page15 Tmem55b Loh12cr1 Fam221b Laptm4b Aldh1a7 Zfp385a Prpf40b Map7d2 Zswim1 Ranbp2 Spag17 Gm626 Rbm44 Pnma1 Dcaf10 Zfp800 Zfp438 Zfp541 Creld2 Arl13b Dnhd1 Cspp1 Wdr96 Senp2 Hdac6 Dpy30 Dhx40 Thoc5 Fscn2 Cyth2 Bnip1 Nkapl Pick1 Flad1 Tekt5 Nmbr Adgb Nt5m Snx1 Ppil4 Pex3 Cutc Pigo Frs3 Ttc4 0.0 1.0

GSE13106 [10] GSE29318 [9]

GSE4765 [6] Scale ofaveragePearsoncorrelations GSE5332 [12] GSE22140 [13] GSE5497 [6] GSE6540 [12] GSE21861 [8] GSE24291 [6] 0.2 GSE5861 [6] GSE2557 [6] GSE20390 [6] GSE44118 [6] GSE31849 [18] GSE25029 [56] GSE17097 [20] GSE53951 [10] GSE8621 [12] 0.4 GSE5425 [6] GSE10902 [6] GSE19204 [6] GSE43059 [8] GSE5313 [6] GSE7767 [6] GSE46500 [6] GSE22251 [9] GSE30855 [6] 0.6 GSE27159 [8] GSE15772 [8] GSE15610 [12] GSE6285 [24] GSE47065 [8] GSE50729 [6] GSE12498 [12] GSE55809 [8] GSE32277 [33] 0.8 GSE3100 [23] GSE13873 [27] GSE24614 [6] GSE10989 [6] Score 0.41 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.42 0.43 0.43 0.43 0.43 0.43 0.43 0.44 0.44 0.44 0.44 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.45 0.46 0.46 0.46 0.47 0.47 0.47 0.47 0.47 0.47 0.47 0.48 0.48 0.48 0.48 0.48 0.48 1.0 Notes Symbol Num ofCEMGenes:23.Predicted1161.SelectedDatasets:6.Strength:0.2 CEM 1,Geneset"[G]photoreceptorconnectingcilium",Page16 Fam178b Als2cr11 Ccdc126 Ccdc158 Trmt10a Ccdc64 Sephs2 Exosc8 Fabp12 Crybg3 Prdx6b Chmp6 Setdb1 Psmd8 Dcaf15 Sgsm3 Pla2g7 Pcnxl4 Zfp212 Lancl1 Gtf2h1 As3mt Rpap2 Pinlyp Cep89 Klhl28 Ascc1 Tcaim Tex13 Herc2 Herc4 Tdrkh Rnf17 Smg9 Mns1 Tprgl Hint3 Ddb2 Elof1 Uba2 Elfn1 Heca Pan2 Zbbx Cpt2 Efhb Clgn Poln Taf7 Sp2 0.0 1.0

GSE13106 [10] GSE29318 [9]

GSE4765 [6] Scale ofaveragePearsoncorrelations GSE5332 [12] GSE22140 [13] GSE5497 [6] GSE6540 [12] GSE21861 [8] GSE24291 [6] 0.2 GSE5861 [6] GSE2557 [6] GSE20390 [6] GSE44118 [6] GSE31849 [18] GSE25029 [56] GSE17097 [20] GSE53951 [10] GSE8621 [12] 0.4 GSE5425 [6] GSE10902 [6] GSE19204 [6] GSE43059 [8] GSE5313 [6] GSE7767 [6] GSE46500 [6] GSE22251 [9] GSE30855 [6] 0.6 GSE27159 [8] GSE15772 [8] GSE15610 [12] GSE6285 [24] GSE47065 [8] GSE50729 [6] GSE12498 [12] GSE55809 [8] GSE32277 [33] 0.8 GSE3100 [23] GSE13873 [27] GSE24614 [6] GSE10989 [6] Score 0.35 0.35 0.36 0.36 0.36 0.36 0.36 0.36 0.37 0.37 0.37 0.37 0.37 0.37 0.38 0.38 0.38 0.38 0.38 0.38 0.38 0.38 0.38 0.39 0.39 0.39 0.39 0.39 0.39 0.39 0.40 0.40 0.40 0.40 0.40 0.40 0.40 0.40 0.40 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 0.41 1.0 Notes 9530077C05Rik 1700040L02Rik 4930503L19Rik Symbol Num ofCEMGenes:23.Predicted1161.SelectedDatasets:6.Strength:0.2 CEM 1,Geneset"[G]photoreceptorconnectingcilium",Page17 BC016423 Ammecr1 Gm10044 Fam193a Trpd52l3 Ankrd12 Plekha5 Dopey1 Dusp22 Nup205 Plekhf2 Fbxo36 Cnnm2 Ndufv2 Ptpdc1 Angel1 Ttc39a Fbxw5 Polr2a Atxn2l Pebp4 Syce3 Gpr98 Otub2 Atpif1 Nupl1 Nxnl2 Zdbf2 Dkkl1 Grip1 Mpp5 M1ap Mea1 Napg Cby1 Exd1 Tc2n Ica1l Gin1 Rfx2 Pigk Tcta Dazl Tln2 Mtf1 Rho Flt3 0.0 1.0

GSE13106 [10] GSE29318 [9]

GSE4765 [6] Scale ofaveragePearsoncorrelations GSE5332 [12] GSE22140 [13] GSE5497 [6] GSE6540 [12] GSE21861 [8] GSE24291 [6] 0.2 GSE5861 [6] GSE2557 [6] GSE20390 [6] GSE44118 [6] GSE31849 [18] GSE25029 [56] GSE17097 [20] GSE53951 [10] GSE8621 [12] 0.4 GSE5425 [6] GSE10902 [6] GSE19204 [6] GSE43059 [8] GSE5313 [6] GSE7767 [6] GSE46500 [6] GSE22251 [9] GSE30855 [6] 0.6 GSE27159 [8] GSE15772 [8] GSE15610 [12] GSE6285 [24] GSE47065 [8] GSE50729 [6] GSE12498 [12] GSE55809 [8] GSE32277 [33] 0.8 GSE3100 [23] GSE13873 [27] GSE24614 [6] GSE10989 [6] Score 0.30 0.30 0.30 0.30 0.30 0.31 0.31 0.31 0.31 0.31 0.31 0.31 0.31 0.32 0.32 0.32 0.32 0.32 0.32 0.32 0.32 0.32 0.32 0.32 0.32 0.33 0.33 0.33 0.33 0.33 0.33 0.33 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.34 0.35 0.35 0.35 0.35 0.35 0.35 0.35 0.35 0.35 0.35 1.0 Notes 4933427D14Rik 1700094D03Rik 1700102P08Rik 9630033F20Rik 9530057J20Rik Symbol Num ofCEMGenes:23.Predicted1161.SelectedDatasets:6.Strength:0.2 CEM 1,Geneset"[G]photoreceptorconnectingcilium",Page18 Tmem242 Gramd1b Fam179a Commd1 Itgb1bp1 Pwwp2b R3hcc1l Slco6c1 Zfyve19 Gnpda2 Rhbdd3 Rimbp3 Ccp110 Akirin2 Cchcr1 Ankef1 Dnajc4 Trim11 Trim23 Cbwd1 Rasal2 Gtf3c3 Atpaf2 Dnah6 Cdan1 Glcci1 Slmap Dynll2 Wfdc3 Naa35 Socs7 Mkrn3 Tusc2 Bcar3 Ndst4 Crls1 Sgcg Shc4 Pes1 Pigp Rfx4 Naf1 Ing2 Brf1 Atr 0.0 1.0

GSE13106 [10] GSE29318 [9]

GSE4765 [6] Scale ofaveragePearsoncorrelations GSE5332 [12] GSE22140 [13] GSE5497 [6] GSE6540 [12] GSE21861 [8] GSE24291 [6] 0.2 GSE5861 [6] GSE2557 [6] GSE20390 [6] GSE44118 [6] GSE31849 [18] GSE25029 [56] GSE17097 [20] GSE53951 [10] GSE8621 [12] 0.4 GSE5425 [6] GSE10902 [6] GSE19204 [6] GSE43059 [8] GSE5313 [6] GSE7767 [6] GSE46500 [6] GSE22251 [9] GSE30855 [6] 0.6 GSE27159 [8] GSE15772 [8] GSE15610 [12] GSE6285 [24] GSE47065 [8] GSE50729 [6] GSE12498 [12] GSE55809 [8] GSE32277 [33] 0.8 GSE3100 [23] GSE13873 [27] GSE24614 [6] GSE10989 [6] Score 0.24 0.24 0.24 0.24 0.24 0.24 0.24 0.24 0.24 0.25 0.25 0.25 0.25 0.25 0.25 0.25 0.25 0.26 0.26 0.26 0.26 0.26 0.26 0.26 0.27 0.27 0.27 0.27 0.27 0.27 0.27 0.27 0.28 0.28 0.28 0.28 0.28 0.28 0.28 0.28 0.28 0.28 0.29 0.29 0.29 0.29 0.30 0.30 0.30 0.30 1.0 Notes 1700029P11Rik 1700003E16Rik 1110058L19Rik 5830415F09Rik Symbol Num ofCEMGenes:23.Predicted1161.SelectedDatasets:6.Strength:0.2 CEM 1,Geneset"[G]photoreceptorconnectingcilium",Page19 Thumpd3 Slc22a16 Fam167a Cdk2ap2 Ccdc175 Tmem60 Ppp1r36 Dnajb13 Atp13a4 Smim13 Slco6b1 Dnajc28 Tex19.1 Ppp3cc Tada2b Hsf2bp Cmtm1 Dnajb6 Dcaf11 Zbtb49 Tatdn3 Lsm10 Lgals8 Gpbp1 Armc2 Cngb1 Hoxa4 Ddx17 Cep44 Ghitm Herc1 Nme7 Lrp11 Asxl2 Ttbk1 Tctn3 Efr3a Add3 Eno2 Sufu Cpvl Kat8 Ttll9 Inha Lias Atl1 0.0 1.0

GSE13106 [10] GSE29318 [9]

GSE4765 [6] Scale ofaveragePearsoncorrelations GSE5332 [12] GSE22140 [13] GSE5497 [6] GSE6540 [12] GSE21861 [8] GSE24291 [6] 0.2 GSE5861 [6] GSE2557 [6] GSE20390 [6] GSE44118 [6] GSE31849 [18] GSE25029 [56] GSE17097 [20] GSE53951 [10] GSE8621 [12] 0.4 GSE5425 [6] GSE10902 [6] GSE19204 [6] GSE43059 [8] GSE5313 [6] GSE7767 [6] GSE46500 [6] GSE22251 [9] GSE30855 [6] 0.6 GSE27159 [8] GSE15772 [8] GSE15610 [12] GSE6285 [24] GSE47065 [8] GSE50729 [6] GSE12498 [12] GSE55809 [8] GSE32277 [33] 0.8 GSE3100 [23] GSE13873 [27] GSE24614 [6] GSE10989 [6] Score 0.19 0.19 0.19 0.19 0.19 0.20 0.20 0.20 0.20 0.20 0.20 0.20 0.20 0.20 0.20 0.20 0.20 0.20 0.21 0.21 0.21 0.21 0.21 0.21 0.21 0.21 0.21 0.21 0.21 0.21 0.21 0.22 0.22 0.22 0.22 0.22 0.22 0.22 0.22 0.22 0.22 0.22 0.23 0.23 0.23 0.23 0.23 0.23 0.24 0.24 1.0 Notes 4930430A15Rik 1700028P14Rik Symbol Num ofCEMGenes:23.Predicted1161.SelectedDatasets:6.Strength:0.2 CEM 1,Geneset"[G]photoreceptorconnectingcilium",Page20 Camsap3 Fam184a Atxn7l3b Ccdc64b Ccdc122 Tbc1d31 Camkmt Slc30a4 Stxbp5l Capn10 Cep112 Acad11 Dzank1 Gtpbp1 Nudt18 Rnf166 Eefsec Ttc39d Tspyl4 Garnl3 Myo9a Got1l1 Gmcl1 Lrrc63 Rsph1 Nsun7 Dhx16 Wdtc1 Fbxo8 Pdzd9 Cstf2t Tdrd9 Upf3a Dcaf6 Tulp2 Map7 Derl3 Clip4 Akna Suco Espn Tbca Ofd1 Mib1 Cdr2 Stx8 Hdc Tti1 0.0 1.0

GSE13106 [10] GSE29318 [9]

GSE4765 [6] Scale ofaveragePearsoncorrelations GSE5332 [12] GSE22140 [13] GSE5497 [6] GSE6540 [12] GSE21861 [8] GSE24291 [6] 0.2 GSE5861 [6] GSE2557 [6] GSE20390 [6] GSE44118 [6] GSE31849 [18] GSE25029 [56] GSE17097 [20] GSE53951 [10] GSE8621 [12] 0.4 GSE5425 [6] GSE10902 [6] GSE19204 [6] GSE43059 [8] GSE5313 [6] GSE7767 [6] GSE46500 [6] GSE22251 [9] GSE30855 [6] 0.6 GSE27159 [8] GSE15772 [8] GSE15610 [12] GSE6285 [24] GSE47065 [8] GSE50729 [6] GSE12498 [12] GSE55809 [8] GSE32277 [33] 0.8 GSE3100 [23] GSE13873 [27] GSE24614 [6] GSE10989 [6] Score 0.15 0.15 0.16 0.16 0.16 0.16 0.16 0.16 0.16 0.16 0.16 0.16 0.16 0.16 0.16 0.16 0.16 0.17 0.17 0.17 0.17 0.17 0.17 0.17 0.17 0.17 0.17 0.17 0.18 0.18 0.18 0.18 0.18 0.18 0.18 0.18 0.18 0.18 0.18 0.18 0.18 0.18 0.19 0.19 0.19 0.19 0.19 0.19 0.19 0.19 1.0 Notes 2210018M11Rik 1700030K09Rik 4930526D03Rik 1700001L19Rik Symbol Num ofCEMGenes:23.Predicted1161.SelectedDatasets:6.Strength:0.2 CEM 1,Geneset"[G]photoreceptorconnectingcilium",Page21 Tmem184a Rab3gap1 Mageb16 Sepsecs Ankrd39 Chmp2b Donson Ccdc40 Fbxo15 Mettl22 Izumo4 Tex101 Rbm48 H2afb1 Snapin Sh3gl3 Smek2 Zfp949 Stard6 Crebzf Cand1 Usp9y Dmxl2 Reep6 Fhad1 Gpr65 Zc3h8 Mipep Gtf2f1 Appl2 Lekr1 Pcf11 Grtp1 Zfp41 Gcc2 Ccnk Terf1 Kif27 Xpo6 Ssh2 Itpkc Optn Nuf2 Phf7 Klc3 Pgp 0.0 1.0

GSE13106 [10] GSE29318 [9]

GSE4765 [6] Scale ofaveragePearsoncorrelations GSE5332 [12] GSE22140 [13] GSE5497 [6] GSE6540 [12] GSE21861 [8] GSE24291 [6] 0.2 GSE5861 [6] GSE2557 [6] GSE20390 [6] GSE44118 [6] GSE31849 [18] GSE25029 [56] GSE17097 [20] GSE53951 [10] GSE8621 [12] 0.4 GSE5425 [6] GSE10902 [6] GSE19204 [6] GSE43059 [8] GSE5313 [6] GSE7767 [6] GSE46500 [6] GSE22251 [9] GSE30855 [6] 0.6 GSE27159 [8] GSE15772 [8] GSE15610 [12] GSE6285 [24] GSE47065 [8] GSE50729 [6] GSE12498 [12] GSE55809 [8] GSE32277 [33] 0.8 GSE3100 [23] GSE13873 [27] GSE24614 [6] GSE10989 [6] Score 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.11 0.12 0.12 0.12 0.12 0.12 0.12 0.12 0.12 0.13 0.13 0.13 0.13 0.13 0.13 0.13 0.13 0.13 0.13 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.14 0.15 0.15 0.15 0.15 0.15 0.15 0.15 1.0 Notes Symbol Num ofCEMGenes:23.Predicted1161.SelectedDatasets:6.Strength:0.2 CEM 1,Geneset"[G]photoreceptorconnectingcilium",Page22 Tmem150c BC030336 Tmem217 Arhgap39 Cdkn2aip Fam117a Ccndbp1 Abhd17a Ccdc114 Wfdc15a Zdhhc12 Tbc1d20 Cmtm2b Ppp1r26 Gm5142 Dync1i2 C77080 Gpr108 Cnot10 Ap1m1 Aamdc Zfp830 Med28 Ero1lb Abhd8 Usp37 Trip12 Nim1k Fbxo7 Tex40 Tesk2 Wwc2 Polr2i Ptpn4 Gstz1 Fkbpl Gtsf1 Msh4 Jazf1 Hhatl Asns Eml5 Ybx2 Tob1 Tbx1 Ahi1 Clpx Clk3 Elp5 Lig3 0.0 1.0

GSE13106 [10] GSE29318 [9]

GSE4765 [6] Scale ofaveragePearsoncorrelations GSE5332 [12] GSE22140 [13] GSE5497 [6] GSE6540 [12] GSE21861 [8] GSE24291 [6] 0.2 GSE5861 [6] GSE2557 [6] GSE20390 [6] GSE44118 [6] GSE31849 [18] GSE25029 [56] GSE17097 [20] GSE53951 [10] GSE8621 [12] 0.4 GSE5425 [6] GSE10902 [6] GSE19204 [6] GSE43059 [8] GSE5313 [6] GSE7767 [6] GSE46500 [6] GSE22251 [9] GSE30855 [6] 0.6 GSE27159 [8] GSE15772 [8] GSE15610 [12] GSE6285 [24] GSE47065 [8] GSE50729 [6] GSE12498 [12] GSE55809 [8] GSE32277 [33] 0.8 GSE3100 [23] GSE13873 [27] GSE24614 [6] GSE10989 [6] Score 0.06 0.06 0.06 0.06 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.07 0.08 0.08 0.08 0.08 0.08 0.08 0.08 0.08 0.08 0.08 0.08 0.09 0.09 0.09 0.09 0.09 0.09 0.09 0.09 0.09 0.09 0.09 0.09 0.09 0.10 0.10 0.10 0.10 0.10 0.10 0.10 0.11 0.11 0.11 1.0 Notes 4933425L06Rik 1700026L06Rik 4430402I18Rik Symbol Num ofCEMGenes:23.Predicted1161.SelectedDatasets:6.Strength:0.2 CEM 1,Geneset"[G]photoreceptorconnectingcilium",Page23 BC049762 Tmem135 Atp6v1g1 Fam118a Fam219a Epb4.1l3 Dmrtc1a Ankrd32 Pyroxd1 Sec23ip Sec14l3 Lrrc10b Lrrc16a Necap2 Sipa1l3 Saysd1 Fbxo38 Skiv2l2 Kbtbd7 Akr1e1 Micalcl Supt20 Cadm1 Tcam1 Abhd3 Pfkfb2 Cpeb3 Dhx32 Kank3 Bcl2l1 Spcs1 Fbxo6 Jade3 Drap1 Psip1 Pi4ka Elac1 Lrrc9 Cdc7 Elfn2 Pmel Poc5 Helz Crat Bad Klf9 Fryl 0.0 1.0

GSE13106 [10] GSE29318 [9]

GSE4765 [6] Scale ofaveragePearsoncorrelations GSE5332 [12] GSE22140 [13] GSE5497 [6] GSE6540 [12] GSE21861 [8] GSE24291 [6] 0.2 GSE5861 [6] GSE2557 [6] GSE20390 [6] GSE44118 [6] GSE31849 [18] GSE25029 [56] GSE17097 [20] GSE53951 [10] GSE8621 [12] 0.4 GSE5425 [6] GSE10902 [6] GSE19204 [6] GSE43059 [8] GSE5313 [6] GSE7767 [6] GSE46500 [6] GSE22251 [9] GSE30855 [6] 0.6 GSE27159 [8] GSE15772 [8] GSE15610 [12] GSE6285 [24] GSE47065 [8] GSE50729 [6] GSE12498 [12] GSE55809 [8] GSE32277 [33] 0.8 GSE3100 [23] GSE13873 [27] GSE24614 [6] GSE10989 [6] Score 0.02 0.02 0.02 0.03 0.03 0.03 0.03 0.03 0.03 0.03 0.03 0.03 0.03 0.03 0.04 0.04 0.04 0.04 0.04 0.04 0.04 0.04 0.04 0.04 0.04 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.05 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 0.06 1.0 Notes 4930447C04Rik 1700010I14Rik Symbol Num ofCEMGenes:23.Predicted1161.SelectedDatasets:6.Strength:0.2 CEM 1,Geneset"[G]photoreceptorconnectingcilium",Page24 Slc25a28 Dcun1d2 Ccdc74a Mrps18a Zscan10 Zkscan5 Slc31a2 Rad51c Ccdc30 Tmem8 Pou6f1 Ruvbl2 Ccnyl1 Med26 Armc3 Zpbp2 Vprbp Tex38 Mllt10 Mmaa Bpnt1 Ovol1 Rilpl2 Lats1 Gstt2 Ago3 Ppa2 Sav1 Ints8 Nxf2 Tln1 Boll 0.0 1.0

GSE13106 [10] GSE29318 [9]

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13106 Status: Public on Sep 09 2009 Title: Regulated SMAD signalling in development Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 19517569 Summary & Design: Summary: Phosphorylation and subsequent nuclear translocation of SMAD proteins determine the cellular response to activin. Here we identify a novel means by which activin signalling is regulated to enable developmental stage-specific SMAD gene transcription. In response to activin A, immature proliferating mouse Sertoli cells exhibit nuclear accumulation of SMAD3, but not SMAD2, although both proteins are phosphorylated. In post-mitotic differentiating cells, both SMAD2 and SMAD3 accumulate in the nucleus. Furthermore, immature Sertoli cells are sensitive to activin dosage; at higher concentrations maximal SMAD3 nuclear accumulation is observed, accompanied by a small, but significant, increase in nuclear SMAD2. Microarray analysis confirmed that differential SMAD utilization correlated with altered transcriptional outcomes and identified new activin target genes, Gja1 and Serpina5, which are known to be required for Sertoli cell development and male fertility. In immature Sertoli cells, genetic or transient knockdown of SMAD3 enhanced SMAD2 nuclear accumulation in response to activin, with increased Serpina5 mRNA levels associated with nuclear localized SMAD2. In transgenic mice with altered activin bioactivity that display male fertility phenotypes, testicular Gja1 and Serpina5 mRNA levels reflected altered in vivo activin levels. We conclude that regulated nuclear accumulation of phosphorylated SMAD2 is a novel determinant of developmentally regulated activin signalling.

Overall design: Murine 15dpp Sertoli Cell treated with 0ng, 5ng activin (duplicates). Total 10 samples.

Background corr dist: KL-Divergence = 0.0442, L1-Distance = 0.0746, L2-Distance = 0.0079, Normal std = 0.6871

0.677 Kernel fit Pairwise Correlations Normal fit

Density 0.339

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

mus-6dpp-0ng_activin-rep1mus-6dpp-0ng_activin-rep2mus-6dpp-5ng_activin-rep1mus-6dpp-5ng_activin-rep2 (0.0786588)mus-6dpp-50ng_activin-rep1 (0.0496605)mus-6dpp-50ng_activin-rep2 (0.0848788)mus-15dpp-0ng_activin-rep1 (0.0887057)mus-15dpp-0ng_activin-rep2 (0.0900037)mus-15dpp-5ng_activin-rep1 (0.138786)mus-15dpp-5ng_activin-rep2 (0.161271) (0.0794695) (0.126382) (0.102184)[ min ] [ medium ] [ max ] CEM 1 Cep290 173.2 399.9 1311.4 P ( S | Z, I ) = 1.00 Ift88 394.0 634.7 1265.7 Mean Corr = 0.41381 Ift122 208.2 269.0 1092.9 Nphp1 400.8 573.5 3539.6 Wdr19 207.3 334.2 770.5 Arl3 2580.9 3254.9 5160.5 Ift57 496.8 770.2 1144.9 Rp1 4.0 14.0 26.7 Tbcc 736.5 932.3 1070.9 Ttc8 473.3 625.6 816.2 Ift140 951.8 1070.8 1985.0 Iqcb1 682.3 777.1 4747.1 Cetn1 4.0 14.7 1519.3 Fam161a 30.4 107.2 180.0 Cetn3 2881.3 3523.9 3691.7 Myo7a 835.9 1129.4 2941.2 Kif3a 758.4 982.4 1198.2 Topors 317.4 468.4 645.6 Ift52 694.5 892.1 1123.7 Gnat1 4.0 5.4 66.0 Cetn2 772.0 888.5 1081.0 Whrn 78.4 141.0 219.3 Rp1l1 4.0 15.3 36.1 Wdr34 313.3 365.9 840.5 Tmem107 1956.2 2468.4 6316.5 AK129341 79.7 123.9 793.5 Ttc26 180.3 276.2 866.7 Ift80 271.4 432.2 1526.9 CEM 1 + Katnal2 71.6 177.9 562.3 Top 10 Genes Dync2li1 956.5 1114.8 1545.7 Bbs2 235.8 340.0 817.8 Dyx1c1 55.3 109.5 643.8 Wdr31 100.7 173.6 548.8

Null module GEO Series "GSE29318" 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=GSE29318 Status: Public on Jul 12 2011 Title: Expression profile of FAC-sorted murine retinal cells Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21743009 Summary & Design: Summary: Microarray experiments were performed using FAC-sorted young photoreceptors to analyze their transcriptome in comparison to remaining retinal cells at same developmental stage and retinal progenitors.

Overall design: For each replicate, retinae of 6 to 8 postnatal day 0 pNestin-GFP or postnatal day 4 rhoEGFP mice were dissected and FAC-sorted based on GFP expression. RNA of fractions was isolated and subsequently analyzed with microarray experiment.

Background corr dist: KL-Divergence = 0.0360, L1-Distance = 0.0199, L2-Distance = 0.0006, Normal std = 0.6174

0.646 Kernel fit Pairwise Correlations Normal fit

Density 0.323

0.000 CEM 1

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

Pre-normalization Quantiles

rhoGFPrhoGFP PN4 retinalrhoGFP PN4 cellsretinalrhoGFP PN4 positive cellsretinalrhoGFP PN4 positive FAC cellsretinalrhoGFP PN4sorted positive FAC cellsretinalnestinGFP PN4biologicalsorted negative FAC cellsretinalnestinGFP biologicalsorted negative PN0 repliacte FACcellsnestinGFP retinalbiological sorted negative PN0 repliacteFAC 1 (0.271616) cellsretinal biologicalsorted PN0 repliacteFAC positive2 (0.170498) cellsretinal biologicalsorted repliacte positive3 FAC (0.130204)cells biological sortedrepliacte positive 1FAC [(0.0824028) min biological sortedrepliacte 2FAC (0.0658802) biologicalsorted] 3repliacte (0.0593989) biological repliacte 1 (0.0874064)[ medium repliacte 2 (0.0569482) 3 (0.0756457) ] [ max ] CEM 1 Cep290 223.2 398.2 1755.9 P ( S | Z, I ) = 1.00 Ift88 417.0 568.4 935.7 Mean Corr = 0.39182 Ift122 257.0 361.0 831.9 Nphp1 661.1 806.0 1123.6 Wdr19 418.9 494.9 957.1 Arl3 2861.4 3845.8 5922.7 Ift57 547.3 633.9 1105.9 Rp1 121.9 602.3 10386.8 Tbcc 668.7 780.7 1474.3 Ttc8 602.4 1202.1 3884.7 Ift140 1018.8 1380.0 2150.0 Iqcb1 621.1 725.5 827.1 Cetn1 16.0 19.2 23.4 Fam161a 173.8 210.5 800.3 Cetn3 2314.3 2807.6 4173.3 Myo7a 198.4 534.8 877.4 Kif3a 756.3 1060.5 1445.6 Topors 379.4 538.7 862.3 Ift52 710.1 807.1 1010.6 Gnat1 82.2 90.9 1772.9 Cetn2 1333.1 1681.1 2620.3 Whrn 274.7 444.1 758.5 Rp1l1 147.0 252.6 4897.0 Wdr34 475.9 625.8 1231.2 Tmem107 2685.3 3846.6 7186.7 AK129341 198.3 334.4 558.5 Ttc26 346.6 483.2 598.7 Ift80 566.6 759.4 1212.3 CEM 1 + Katnal2 152.1 305.9 517.1 Top 10 Genes Dync2li1 972.4 1204.0 3052.1 Bbs2 703.4 946.9 2068.0 Dyx1c1 124.7 165.0 630.4 Wdr31 196.1 278.5 1097.0

Null module GEO Series "GSE9338" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 42 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9338 Status: Public on Jan 19 2008 Title: Expression data from Mus musculus subspecies and their F1 hybrids for 3 tissues (brain, liver, testis) Organism: Mus musculus domesticus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 17947435 Summary & Design: Summary: We have studied different subspecies of the house mouse (M. m. musculus, M. m. domesticus and M. m. castaneus) and their reciprocal F1 hybrids to estimate the within-locus mode of inheritance for subspecies differences in gene expression in three tissues (brain, liver, testis) of male mice. This study investigates mode of inheritance in crosses at a larger taxonomic distance than have been previously systematically investigated. We found the vast majority of transcripts to be additively expressed with only a few transcripts showing dominance or overdominance in expression, except for one direction of one cross, which showed large mis-expression in the testis.

Keywords: comparative whole transcripome analysis

Overall design: Wild-derived inbred lines of M. m. musculus, M. m. domesticus and M. m. castaneus were used to generate reciprocal crosses of M. m. musculus x M. m. domesticus and M. m. musculus x M. m. castaeneus. The gene expression profile of 2 males each of the hybrids and the pure parental subspecies were analyzed by using the Affymetrix GeneChip 430 2.0 to obtain evidence about the within-locus mode of inheritance of genes. First, we studied all transcripts that are differentially expressed between the parental subspecies and assessed additivity vs. nonadditivity of expression of these transcripts in the F1 hybrids. Second, we investigated those transcripts which do not differ in expression between the parental lines, but which are expressed differently in the F1 hybrids relative to both of their parents.

Background corr dist: KL-Divergence = 0.0697, L1-Distance = 0.0890, L2-Distance = 0.0131, Normal std = 0.6057

0.712 Kernel fit Pairwise Correlations Normal fit

Density 0.356

0.000 CEM 1

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

Pre-normalization Quantiles

domesticusdomesticus malemusculus 1, malebiologicalmusculus 2,male biologicalF1 rep1,1, malehybridbiological brainF1 rep2,2, (musculushybridbiological (0.00836078) rep1,brainF1 (musculushybrid brain(0.00952009) rep2,motherF1 (domesticus(0.0139517)hybrid brain motherxcastaneus domesticus (domesticus(0.0134303) xcastaneus motherdomesticus male father)F1 mother x1, musculus hybrid malebiological 1,father) F1biological x2, (musculusmusculushybrid biological 2,father) rep1, F1biological (musculushybridrep1, brain 1, father) motherrep2, F1biological brain (castaneushybrid(0.00909141)rep2, brain2, motherx (0.0190529)domesticus biological castaneusbrain (castaneus(0.0112866)rep1, x mother(0.0182349)domesticus castaneusbrain rep2, father)male motherx(0.00894805)musculus musculusbrain 1, 1, father) malebiological biological x(0.0099339)musculus musculus 2,male 2,father biological biologicalF1 rep1,1, rep1, malehybridbiological) father1, liver biologicalF1brain rep2,2, rep2, (musculus hybrid biological)(0.0286269) 2, (0.0112119)rep1,liver biologicalF1brain rep1,(musculushybrid (0.0173521) liver (0.0126103)rep2,motherF1 brain (0.0172153) rep2,(domesticushybrid liver mother(0.0114194)xcastaneus braindomesticus (0.0205406) (domesticus (0.0149816)xcastaneus motherdomesticus male father)F1 mother x1, musculus hybrid malebiological 1,father) F1biological x2, (musculusmusculushybrid biological 2,father) rep1, F1biological (musculushybridrep1, liver 1, father) motherrep2, F1biological liver (0.0198418) (castaneushybridrep2, liver2, mother(0.0166259)x domesticus biological castaneusliver (0.0273266)(castaneus rep1, (0.0210249)xmotherdomesticus castaneusliver rep2, father)male (0.0162569) motherxmusculus musculusliver 1, 1, father) malebiological biological(0.0180505) xmusculus musculus 2,male 2,father biological biologicalF1 rep1,1, rep1, malehybridbiological) father1, testis biologicalF1liver rep2,2, rep2, (musculus hybridbiological) 2,(0.0362281)(0.0168214) rep1,testis biologicalF1liver rep1,(musculushybrid testis(0.0324716)(0.0210855) rep2,motherF1 liver rep2,(domesticus(0.0523755)hybrid testis (0.0199488) motherxcastaneus liverdomesticus (domesticus(0.0559701) (0.0205968) xcastaneus motherdomesticus male father)F1 mother x1, musculus hybrid malebiological 1,father) F1biological x2, (musculusmusculushybrid biological 2,father) rep1, F1biological (musculushybridrep1, testis 1, father) motherrep2, F1biological testis (castaneus hybridrep2,(0.0269939) testis2, motherx (0.0329134) biological castaneustestis (castaneus rep1,(0.0282302) xmother (0.0315263) castaneustestis rep2, father) mother x(0.0430481) musculustestis 1,father) biological x(0.0377258)[ musculus min 2,father biological rep1, ) father1,] biologicaltestis rep2, ) 2, (0.0507928) biologicaltestis rep1,[ medium(0.0366295) testis rep2, (0.0385215) testis (0.0432254) ] [ max ] CEM 1 Cep290 20.1 248.8 1257.7 P ( S | Z, I ) = 1.00 Ift88 210.1 418.3 2385.0 Mean Corr = 0.38912 Ift122 9.0 205.6 2212.3 Nphp1 48.2 348.2 10440.1 Wdr19 47.3 304.0 558.9 Arl3 1837.9 6452.0 9872.7 Ift57 84.5 1335.1 4379.5 Rp1 1.0 15.1 96.4 Tbcc 477.5 827.1 2988.4 Ttc8 157.0 755.6 1357.2 Ift140 246.5 546.6 7754.1 Iqcb1 120.7 359.2 2655.8 Cetn1 4.0 40.2 16484.3 Fam161a 47.3 146.5 220.7 Cetn3 714.5 1706.5 7180.6 Myo7a 123.4 291.6 1463.3 Kif3a 34.2 713.5 1876.9 Topors 95.6 281.8 1577.7 Ift52 490.5 866.3 1377.2 Gnat1 7.0 37.1 405.3 Cetn2 279.0 995.1 1336.4 Whrn 180.7 390.2 717.4 Rp1l1 2.0 12.0 57.4 Wdr34 125.7 593.9 2719.7 Tmem107 286.6 1461.7 6982.0 AK129341 4.0 341.1 2495.1 Ttc26 97.6 257.8 1230.0 Ift80 132.8 526.5 1315.9 CEM 1 + Katnal2 7.0 89.5 1936.2 Top 10 Genes Dync2li1 117.7 563.9 1370.1 Bbs2 15.1 396.2 1171.7 Dyx1c1 31.2 111.3 1151.3 Wdr31 42.2 191.6 5386.7

Null module GEO Series "GSE54056" 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=GSE54056 Status: Public on Mar 06 2014 Title: Expression data from adult mouse normal and damaged retina from B6 and 129 mouse strains Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 24747725 Summary & Design: Summary: Retinal damage causes proliferation of Muller glia, but the degree of proliferation depends on mouse strains. Muller glial proliferation was significantly promoted by the addition of GSK3 inhibitor in 129, but not in B6. We used retinal explant culture as a model for retinal damage which caused preferential photoreceptor death in a few days.

We used microarrays to detail the global programme of gene expression regulating the proliferative potential of Muller glia after retinal damage.

Overall design: Total RNA from intact whole retina, retinal tissue cultured for three days, and retinal tissue cultured with chir99021 for three days was used. Retinal tissues from 10 weeks old mice were used.

Background corr dist: KL-Divergence = 0.0576, L1-Distance = 0.0272, L2-Distance = 0.0009, Normal std = 0.5454

0.751 Kernel fit Pairwise Correlations Normal fit

Density 0.376

0.000 CEM 1

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

Pre-normalization Quantiles

intact retinaintact from retinaB6 B6retinal from mouse,B6 explantB6retinal mouse,biologicalB6 explantculturedretinal biologicalB6 rep1 explantculturedretinal for (0.160458)intact three rep2 explantcultured for retinadays, (0.109743)intact three cultured forbiologicalfrom retinadays,129 three 129 retinal forbiologicalfrom days mouse, 129rep1three 129 explantretinalwith (0.0340991) days mouse, 129biologicalrep2 chir99021, explantculturedretinalwith (0.0513313) 129biological chir99021, rep1 explantculturedretinal biologicalfor (0.162266) three rep2 explantcultured biologicalfor days, (0.128661)rep1 three cultured for(0.075372)biological days, rep2 three for(0.058089)biological days[ rep1three min with (0.0336731) days rep2 chir99021, ]with (0.0445646) chir99021, biological[ mediumbiological rep1 (0.0719324) rep2 (0.0698104) ] [ max ] CEM 1 Cep290 1028.5 1309.7 2072.1 P ( S | Z, I ) = 1.00 Ift88 432.2 457.8 654.0 Mean Corr = 0.23127 Ift122 182.8 348.5 537.2 Nphp1 522.2 677.9 820.8 Wdr19 231.6 362.7 564.0 Arl3 6705.0 7614.7 11436.8 Ift57 1116.2 1888.4 2277.2 Rp1 5516.8 9443.4 15049.8 Tbcc 690.2 899.7 1191.1 Ttc8 1765.9 2690.7 4728.1 Ift140 416.3 653.1 997.9 Iqcb1 416.7 467.6 557.2 Cetn1 20.5 26.2 28.7 Fam161a 462.8 740.6 2260.7 Cetn3 3163.0 4008.6 4501.8 Myo7a 58.9 288.3 381.7 Kif3a 995.9 1153.3 1383.1 Topors 388.2 521.8 546.7 Ift52 484.0 543.1 590.1 Gnat1 9028.6 16731.6 34034.4 Cetn2 1430.4 1565.0 1962.2 Whrn 267.2 364.7 556.6 Rp1l1 905.9 1734.8 4457.7 Wdr34 432.2 589.9 795.6 Tmem107 2425.3 3889.0 6509.1 AK129341 276.7 317.4 485.1 Ttc26 250.0 310.5 485.7 Ift80 714.3 807.4 1305.0 CEM 1 + Katnal2 85.8 128.1 331.4 Top 10 Genes Dync2li1 914.8 1070.4 1341.8 Bbs2 739.6 1667.8 2458.1 Dyx1c1 88.1 123.7 200.3 Wdr31 118.9 224.1 335.3

Null module GEO Series "GSE49346" 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=GSE49346 Status: Public on Mar 07 2014 Title: Expression data from adult ATII and E18 Bipotent progenitor cells in the mouse lung Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 24499815 Summary & Design: Summary: Alveoli are thin-walled sacs that serve as the gas exchange units of the lung. They are affected in devastating lung diseases including COPD, Idiopathic Pulmonary Fibrosis, and the major form (adenocarcinoma) of lung cancer, the leading cause of cancer deaths. The alveolar epithelium is composed of two morphologically distinct cell types: alveolar type (AT) 1 cells, exquisitely thin cells across which oxygen diffuses to reach the blood, and AT2 cells, specialized surfactant-secreting cells. Classical studies suggested that AT1 cells arise from AT2 cells during development and following injury, but more recent studies suggest other sources. Here we use histological and marker analysis, lineage tracing, and clonal analysis in mice to identify alveolar progenitor and stem cells and map their locations and potential in vivo. The results show that AT1 and AT2 cells arise independently during development from a bipotential progenitor. After birth, new AT1 cells derive from rare, long-lived, self-renewing AT2 cells, each producing a slowly expanding clonal focus of regenerated alveoli contiguous with the founder AT2 cell. This stem cell function of AT2 cells is broadly activated by diffuse AT1 cell injury, and AT2 self-renewal can be induced in vitro by EGF ligands and permanently activated in vivo by AT2 cell-specific targeting of the oncogenic KrasG12D allele, efficiently transforming AT2 cells into monoclonal adenomatous tumors that rapidly enlarge and prove fatal. Thus, there is a developmental switch in alveolar progenitor cells after birth, when mature AT2 cells function as facultative stem cells that contribute to local alveolar renewal, repair, and cancer. We propose that short-range signals from dying AT1 cells regulate AT2 stem cell activity: a signal transduced by EGFR-KRAS controls AT2 self-renewal and is hijacked during oncogenic transformation, and a separate signal controls reprogramming to AT1 cell fate.

Overall design: To compare expression between ATII and E18 BP populations, RNA was isolated from either population purified by FACS. Two populations are analyzed with 3 biological replicates per population.

Background corr dist: KL-Divergence = 0.0359, L1-Distance = 0.0425, L2-Distance = 0.0025, Normal std = 0.6765

0.609 Kernel fit Pairwise Correlations Normal fit

Density 0.304

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

Muc1+_Pdpn+_E18-1Muc1+_Pdpn+_E18-2Muc1+_Pdpn+_E18-3 (0.0675332)Lyz2+_EpCAM+_Adult-1 (0.0351589)Lyz2+_EpCAM+_Adult-2 (0.115135)Lyz2+_EpCAM+_Adult-3 (0.154153) (0.175242) (0.452778)[ min ] [ medium ] [ max ] CEM 1 Cep290 48.7 144.4 584.5 P ( S | Z, I ) = 1.00 Ift88 110.5 536.5 1765.9 Mean Corr = 0.31098 Ift122 2.6 96.2 279.1 Nphp1 16.9 250.3 867.5 Wdr19 45.1 223.5 1466.5 Arl3 2490.3 5202.8 9306.7 Ift57 512.7 783.2 2787.9 Rp1 3.6 10.4 25.1 Tbcc 275.8 337.0 414.6 Ttc8 56.6 347.1 947.3 Ift140 923.2 949.3 2394.0 Iqcb1 228.8 285.7 383.0 Cetn1 1.7 2.8 4.1 Fam161a 179.0 431.3 1721.6 Cetn3 1345.2 2240.8 2333.0 Myo7a 154.8 1009.2 1921.1 Kif3a 70.1 555.8 992.0 Topors 629.4 876.6 1577.2 Ift52 403.6 507.4 588.9 Gnat1 6.8 11.3 24.5 Cetn2 610.4 1551.6 2528.3 Whrn 69.7 182.6 237.7 Rp1l1 1.7 3.2 17.6 Wdr34 84.6 289.7 1473.1 Tmem107 1421.1 4156.0 10521.2 AK129341 39.8 113.7 932.9 Ttc26 35.8 127.8 553.9 Ift80 95.7 247.7 590.2 CEM 1 + Katnal2 28.1 97.6 294.2 Top 10 Genes Dync2li1 82.5 392.1 1845.6 Bbs2 52.6 155.9 533.7 Dyx1c1 55.1 106.0 779.5 Wdr31 51.5 128.3 318.8

Null module GEO Series "GSE39391" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 21 -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=GSE39391 Status: Public on Aug 30 2012 Title: Gene expression data from ahES cells, ES cells, MEF cells and round sperm Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 23023130 Summary & Design: Summary: Haploid stem cells offer an easy-to-manipulate genetic system and therefore have great values for studies of recessive phenotypes. Here, we show that mouse androgenetic haploid ES (ahES) cell lines can be established by transferring sperm into enucleated oocyte. The ahES cells maintain haploidy and stable growth over 30 passages, express pluripotent markers, possess the ability to differentiate into all three germ-layers in vitro and in vivo, and contribute to germline of chimeras when injected into blastocysts. Although epigenetically distinct from sperm cells, the ahES cells can produce viable and fertile progenies after intracytoplasmic injection into mature oocytes. The oocyte injection procedure can also produce viable transgenic mice from genetically engineered ahES cells.

We used microarrays to compare the global programme of gene expression among ahES cells, normal diploid ES cells, MEF cells and round sperm cells and found that gene expression pattern of ahES cells was highly similar with ES cells but was distinct from MEF cells and round sperms.

Overall design: Androgenetic haploid ES cells were FACS sorted to harvest the G0/G1 phase haploid cells. Total RNA were extracted from three ahES cell lines (AH129-5, AH129-N1, AH129-NC1, all 129Sv genetic background), two ES cell lines ( CS1-1, R1, 129Sv background), MEF cells and round sperm and hybridized with Affymetrix GeneChip 430 2.0 array. Data were collected and analyzed to compare their gene expression pattern.

Background corr dist: KL-Divergence = 0.0710, L1-Distance = 0.0949, L2-Distance = 0.0148, Normal std = 0.6873

0.712 Kernel fit Pairwise Correlations Normal fit

Density 0.356

0.000 CEM 1

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

Pre-normalization Quantiles

AH129-5,AH129-5, biologicalAH129-5, biological rep1AH129-N1,biological biological(0.0273753) rep2AH129-N1,biological (0.0162648) rep3AH129-N1,biological (0.0124773) rep1AH129-NC1, (0.020353) rep2AH129-NC1, (0.0300858) biological rep3AH129-NC1, (0.0302726) biologicalCS1-1, rep1 biological(0.0158409) biologicalCS1-1, rep2 (0.0224178) biologicalCS1-1, rep3 rep1 (0.020731) biologicalR1,(0.0181439) rep2 biological R1,(0.0287812) rep3 biological rep1 R1,(0.0207708) biological(0.0127499) rep2MEF, (0.0128374) biological rep3MEF, (0.0137644) biologicalMEF, rep1 biological(0.0466001)round rep2 (0.0552594)sperm,round rep3 (0.0459088)sperm,biologicalround sperm,biological rep1 biological(0.223741) rep2 (0.164192) rep3 (0.161433)[ min ] [ medium ] [ max ] CEM 1 Cep290 149.7 237.0 925.0 P ( S | Z, I ) = 0.99 Ift88 159.3 254.4 2139.4 Mean Corr = 0.16034 Ift122 43.6 70.4 3324.4 Nphp1 214.9 278.1 19415.0 Wdr19 60.7 128.8 402.4 Arl3 2145.1 3915.0 12330.0 Ift57 477.0 650.4 6023.8 Rp1 1.0 4.2 53.2 Tbcc 333.7 467.6 4339.5 Ttc8 127.5 185.9 538.5 Ift140 244.6 470.1 10236.3 Iqcb1 418.7 1108.1 1598.2 Cetn1 1.0 1.9 20123.0 Fam161a 14.6 54.3 150.5 Cetn3 2414.9 3911.7 8945.3 Myo7a 8.5 39.8 183.2 Kif3a 411.8 547.4 2785.9 Topors 430.4 2052.7 2716.8 Ift52 430.9 927.8 1294.5 Gnat1 1.4 13.1 51.3 Cetn2 255.3 1249.0 2770.0 Whrn 55.9 104.6 206.9 Rp1l1 1.0 6.5 37.0 Wdr34 142.1 315.3 1216.4 Tmem107 1267.8 2636.4 14123.2 AK129341 22.8 44.2 2311.9 Ttc26 253.8 403.2 989.0 Ift80 150.5 293.7 471.7 CEM 1 + Katnal2 4.2 30.9 4968.3 Top 10 Genes Dync2li1 222.3 527.3 2616.8 Bbs2 46.0 268.4 1169.9 Dyx1c1 20.2 58.4 1125.6 Wdr31 45.5 191.1 7969.6

Null module GEO Series "GSE24207" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 73 -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=GSE24207 Status: Public on Nov 18 2010 Title: mRNA analysis in different mouse tissues Organism: Mus musculus Experiment type: Third-party reanalysis Platform: GPL1261 Pubmed ID: 21088282 Summary & Design: Summary: The functioning of a specific tissue depends on the expression pattern of the different genes. We used microarrays to compare gene expression across different murine tissues, to get a better understanding in the expression pattern and functioning of the different tissues. With this analysis, we were not only able to identify genes that were specifically expressed in a spicific tissue but, as important, we also identified genes that were specifically repressed in a tissue, compared to al the other analysed tissues.

Overall design: For every tissue, at least 3 biological replicates were used.

Background corr dist: KL-Divergence = 0.3994, L1-Distance = 0.0931, L2-Distance = 0.0289, Normal std = 0.2840

1.542 Kernel fit Pairwise Correlations Normal fit

Density 0.771

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 diaphragm,Mouse diaphragm,Mouse biological diaphragm,Mouse biological spleen,replicateMouse biological spleen,replicateMousebiological 1 (0.0069512) spleen,replicateMousebiological 2 replicate(0.00605722) muscle,Mousebiological 3 replicate(0.00942959) 1 (0.00559432)muscle,Mouse biological replicate 2 (0.00543698)muscle,Mouse biological replicate 3 (0.00637881)muscle,Mouse biological replicate 1 liver,(0.00675443)Mouse biological replicate biological2 liver,(0.00544747)Mouse replicate biological3 liver,(0.00543576)Mouse replicate biological4 brain,(0.00588368)Mouse replicate 1 (0.00769807) biological brain,Mouse replicate 2 (0.00845017) biological brain,Mouse replicate 3 (0.00744873) biological lung,Mouse replicate 1 (0.0124753)biological lung,Mouse replicate 2 (0.0117875)biological lung,Mouse replicate 3 (0.0100995)biological kidney,Mouse replicate 1 (0.00503693) kidney,Mousebiological replicate 2 (0.00283078) kidney,Mousebiological 3replicate (0.00328647) adrenalMousebiological replicate 1 (0.00299184)adrenal Mousegland, replicate 2 (0.00498568)biologicaladrenal Mousegland, 3 (0.00471453)biologicalbone Mousegland, replicate marrow, biologicalboneMouse replicate 1 marrow, (0.0211206) biologicalboneMouse replicate 2 marrow, (0.0229811) biologicalboneMouse replicate 3 marrow, (0.0127605) biologicaladiposeMouse replicate 1 (0.00816358) biologicaladiposeMouse tissue, replicate 2 (0.0105217) adiposeMouse biologicaltissue, replicate 3 (0.0076863) pituitaryMouse biologicaltissue, replicate4 (0.00750114) pituitaryMouse biologicalgland, replicate 1 (0.00343722)pituitaryMouse biological gland, replicate 2 (0.00336354)pituitaryMouse biological gland, replicate 3 (0.00284314)pituitaryMouse biological gland, replicate 1 (0.0221873)salivaryMouse biological gland, replicate 2 (0.0162741)salivaryMouse biologicalgland, replicate 3 (0.0181159)salivaryMousebiological gland, replicate 4 (0.0134408)seminalMousebiological gland, replicate 5 (0.00781067)seminalMousebiological vesicle, replicate 1 (0.00455853) seminalMouse vesicle, biological replicate 2 (0.00623194) thymus,Mouse vesicle, biological replicate3 (0.00703955) thymus,Mouse biologicalbiological replicate 1 thymus,Mouse (0.00198304)biological replicatereplicate 2 testis,Mouse (0.00713484)biological replicate 13biological testis,Mouse (0.00365197)(0.00219837) replicate 2 biological testis,Mouse(0.00443547) replicate 3 biological heart,Mouse(0.00521924) replicate 1 (0.0738712)biological heart,Mouse replicate 2 (0.0804668)biological heart,Mouse replicate 3 (0.0942653)biological smallMouse replicate 1 (0.00825192)intestine, smallMouse replicate 2 (0.00551282)intestine, smallMouse biological 3 (0.00557887)intestine, eye,Mouse biological replicate biological eye,Mouse biological replicate biological 1 (0.00879522)eye,Mousereplicate replicate biological 2 (0.00931633)placenta,Mousereplicate 1 (0.0699519) 3 (0.0110567)placenta,Mousereplicate 2biological (0.0641984) placenta,Mouse 3biological (0.0593517) replicate ovary,Mouse biological replicate biological 1ovary,Mouse (0.00948658) replicate biological 2ovary,Mouse (0.00733099) replicate biological 3pancreaticMouse (0.00802635) replicate 1 (0.00286571) pancreaticMouse replicate acini,2 (0.00284101) pancreaticMouse biological acini,3 (0.00396302) pancreaticMouse biological acini, replicate pancreaticMouse biological islets, replicate 1pancreaticCell-line, (0.0129513) biological islets, replicate 2Cell-line, (0.00592976) MIN6, biological islets, replicate 3Cell-line, biological(0.00658323) MIN6, biological replicate 1 biological (0.0145753)MIN6, replicate replicate 2 biological (0.015546) replicate 1 (0.0142686)3 (0.0133631) replicate 2 (0.013065)[ min 3 (0.0127514) ] [ medium ] [ max ] CEM 1 Cep290 3.4 180.8 801.8 P ( S | Z, I ) = 0.02 Ift88 120.6 452.0 886.7 Mean Corr = 0.25676 Ift122 6.7 214.4 2785.1 Nphp1 10.1 270.8 7956.9 Wdr19 36.8 201.2 832.6 Arl3 589.2 3774.8 12352.9 Ift57 50.2 723.0 2916.8 Rp1 3.3 6.7 9166.5 Tbcc 311.5 676.0 2872.2 Ttc8 73.6 415.1 2412.4 Ift140 70.3 569.7 8308.2 Iqcb1 103.9 314.7 1100.0 Cetn1 3.3 13.4 16402.3 Fam161a 20.1 150.8 1209.0 Cetn3 1120.3 2524.1 6738.9 Myo7a 36.8 365.4 2035.8 Kif3a 90.4 428.3 2290.7 Topors 133.9 371.8 712.2 Ift52 414.7 796.0 1402.5 Gnat1 3.3 16.8 36752.6 Cetn2 224.3 1370.8 2815.3 Whrn 26.8 260.9 696.8 Rp1l1 3.3 30.1 2470.3 Wdr34 30.1 261.5 1948.2 Tmem107 374.6 1505.8 10515.3 AK129341 3.4 147.5 438.0 Ttc26 33.5 236.1 765.3 Ift80 20.1 404.4 1819.8 CEM 1 + Katnal2 3.3 70.2 2873.1 Top 10 Genes Dync2li1 90.5 541.7 2434.4 Bbs2 13.4 190.6 899.9 Dyx1c1 3.3 70.3 1244.7 Wdr31 6.7 153.9 5623.8

Null module GEO Series "GSE27630" 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=GSE27630 Status: Public on Feb 05 2013 Title: The transcription factor Otx2 regulates choroid plexus development and function Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 23364326 Summary & Design: Summary: The choroid plexuses (ChPs) are the main regulators of cerebrospinal fluid (CSF) composition and thereby also control the composition of a principal source of signaling molecules that is in direct contact with neural stem cells in the developing brain. The regulators of ChP development mediating the acquisition of a fate that differs from the neighboring neuroepithelial cells are poorly understood. Here, we demonstrate in mice a crucial role for the transcription factor Otx2 in the development and maintenance of ChP cells. Deletion of Otx2 by the Otx2-CreERT2 driver line at E9 resulted in a lack of all ChPs, whereas deletion by the Gdf7-Cre driver line affected predominately the hindbrain ChP, which was reduced in size, primarily owing to an increase in apoptosis upon Otx2 deletion. Strikingly, Otx2 was still required for the maintenance of hindbrain ChP cells at later stages when Otx2 deletion was induced at E15, demonstrating a central role of Otx2 in ChP development and maintenance. Moreover, the predominant defects in the hindbrain ChP mediated by Gdf7-Cre deletion of Otx2 revealed its key role in regulating early CSF composition, which was altered in protein content, including the levels of Wnt4 and the Wnt modulator Tgm2. Accordingly, proliferation and Wnt signaling levels were increased in the distant cerebral cortex, suggesting a role of the hindbrain ChP in regulating CSF composition, including key signaling molecules. Thus, Otx2 acts as a master regulator of ChP development, thereby influencing one of the principal sources of signaling in the developing brain, the CSF.

Overall design: We performed gene expression microarray analysis of fourth ventricular choroid plexus tissue from Otx2 k.o. mice compared to wildtype mice from the same litters.

Background corr dist: KL-Divergence = 0.0475, L1-Distance = 0.0207, L2-Distance = 0.0005, Normal std = 0.5785

0.695 Kernel fit Pairwise Correlations Normal fit

Density 0.348

0.000 CEM 1

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

Pre-normalization Quantiles

Fourth ventricularFourth ventricularFourth choroid ventricularFourth choroid plexus ventricularFourth choroid fromplexus ventricularFourth Otx2ko choroid fromplexus ventricularFourth Otx2komice choroid fromplexus ventricular Fourthat Otx2ko miceE13, choroid fromplexus ventricularbiologicalat Otx2ko miceE13, choroid fromplexus biologicalat wildtype mice E13, replicatechoroid fromplexus biologicalat wildtype E13, replicatemice from plexus1 (0.217269) [biological atwildtype min replicate miceE13,from 2 (0.123414) biologicalatwildtype replicate miceE13, ]3 (0.0859902) biologicalat mice E13, replicate4 (0.114081) biologicalat[ E13, replicatemedium 1 (0.0889525) biological replicate 2 (0.105586) replicate 3 (0.0986986)] 4 (0.166009)[ max ] CEM 1 Cep290 129.2 190.9 230.7 P ( S | Z, I ) = 0.00 Ift88 631.3 795.1 912.3 Mean Corr = 0.33528 Ift122 414.3 605.6 674.0 Nphp1 1459.9 2484.8 2721.1 Wdr19 649.9 885.0 1002.3 Arl3 6664.9 7488.6 7980.6 Ift57 1350.2 1844.5 1949.8 Rp1 9.9 11.6 12.9 Tbcc 720.7 750.8 814.5 Ttc8 815.3 1148.8 1204.1 Ift140 990.1 1226.8 1356.8 Iqcb1 283.9 366.1 398.9 Cetn1 21.6 25.7 29.4 Fam161a 389.9 627.0 823.2 Cetn3 3190.7 3439.1 3652.1 Myo7a 399.4 593.2 931.8 Kif3a 942.0 1217.0 1277.9 Topors 264.6 353.9 385.1 Ift52 870.4 994.4 1058.3 Gnat1 29.1 42.3 52.0 Cetn2 2755.6 4594.7 5214.7 Whrn 393.0 430.0 475.0 Rp1l1 19.9 23.5 29.5 Wdr34 773.3 1301.0 1446.1 Tmem107 4945.1 8498.7 10972.3 AK129341 327.8 570.8 724.8 Ttc26 472.6 696.2 796.0 Ift80 1147.5 1833.4 1995.0 CEM 1 + Katnal2 195.7 423.9 491.0 Top 10 Genes Dync2li1 2768.3 3799.3 4263.2 Bbs2 498.1 787.0 838.1 Dyx1c1 285.1 560.9 633.5 Wdr31 155.6 219.8 247.3

Null module GEO Series "GSE36833" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 49 -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=GSE36833 Status: Public on Mar 28 2012 Title: Gene Expression profiling in DBA/2J glaucoma Organism: Mus musculus Experiment type: Third-party reanalysis Platform: GPL1261 Pubmed ID: 22426214 Summary & Design: Summary: Glaucoma is a common ocular disorder that is a leading cause of blindness worldwide. It is characterized by the dysfunction and loss of retinal ganglion cells (RGCs). Although many studies have implicated various molecules in glaucoma, no mechanism has been shown to be responsible for the earliest detectable damage to RGCs and their axons in the optic nerve. Here, we show that the leukocyte transendothelial migration pathway is activated in the optic nerve head at the earliest stages of disease in an inherited mouse model of glaucoma. This resulted in proinflammatory monocytes entering the optic nerve prior to detectable neuronal damage. A 1-time x-ray treatment prevented monocyte entry and subsequent glaucomatous damage. A single x-ray treatment of an individual eye in young mice provided that eye with long-term protection from glaucoma but had no effect on the contralateral eye. Localized radiation treatment prevented detectable neuronal damage and dysfunction in treated eyes, despite the continued presence of other glaucomatous stresses and signaling pathways. Injection of endothelin-2, a damaging mediator produced by the monocytes, into irradiated eyes, combined with the other glaucomatous stresses, restored neural damage with a topography characteristic of glaucoma. Together, these data support a model of glaucomatous damage involving monocyte entry into the optic nerve. Genome-wide assessment of gene expression changes was performed in DBA/2J-Gpnmb+, DBA/2J mice and irradiated DBA/2J mice at 8.5 and 10.5 months of age.

Overall design: In this study (Howell et al, JCI, 2012), 50 samples (10 D2-Gpnmb+ control at 8.5 mos, 20 NOE DBA/2J at 8.5 mos, 10 radiation-treated DBA2J at 8.5 mos and 10 radiation-treated DBA/2J at 10.5 mos) were combined with 30 of ONH samples from the GSE26299 study (10 D2-Gpnmb+ and 20 NOE DBA/2J all at 10.5 mos). One D2-Gpnmb+ 8.5mo sample failed QC and was not included in the analysis. Quantile normalization was performed for all optic nerve head samples reported in the study. The complete dataset is linked below as a supplementary file.

Background corr dist: KL-Divergence = 0.4034, L1-Distance = 0.0737, L2-Distance = 0.0161, Normal std = 0.2470

1.615 Kernel fit Pairwise Correlations Normal fit

Density 0.808

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

Rad-D2 Rad-D2rep C4.7 Rad-D2rep (ONH) C3.6 D2-Gp2rep (0.0250242) (ONH) C4.3D2-Gp1 rep(0.00706353) (ONH) B1.5Rad-D2 rep(0.0137588) (ONH) B6 Rad-D2(ONH)rep (0.0111447) C5.5 (0.0136274) Stg1Arep (ONH) C5.10 repStg1A (0.0172869) B2.1(ONH) repStg1A (ONH) (0.0169102) B2.2 rep (0.0226614)Stg1B (ONH) B3.1 rep (0.0245986)Stg1B (ONH) B2.3 rep (0.0102526)Stg1B (ONH) B2.4 rep (0.0251906)Stg1C (ONH) B3.2 rep (0.0266282)Stg1B (ONH) B3.4 rep (0.00767082)Rad-D2 (ONH) B2.9 (0.0171011) Rad-D2rep(ONH) C3.10 (0.0147663) Stg1Brep (ONH) C4.9 repRad-D2 (ONH)(0.0118542) B2.10 D2-Gp2rep (0.01298) (ONH) C3.4D2-Gp2 rep(0.0257512) (ONH) B1.2D2-Gp2 rep(0.0142277) (ONH) B1.3D2-Gp2 rep (0.0208961) (ONH) B1.4D2-Gp1 rep (0.0455751) (ONH) B1.7Rad-D2 rep (0.0134885) (ONH) B10 Rad-D2rep (0.0284706)(ONH) C5.4 Stg1Brep(0.00789212) (ONH) C5.9 repStg1B (0.0207223) (ONH) B2.5 repStg1B (ONH)(0.0344403) B2.6 rep (0.00654997)Stg1C (ONH) B3.5 rep (0.0214931)Stg1C (ONH) B3.6 rep (0.0181264)Stg1A (ONH) B3.9 rep (0.00873517)No_cluster (ONH) B3.10 (0.0239995)No_cluster (ONH) repNo_cluster C4.5(0.0288517) rep (ONH)No_cluster C3.2 rep (0.0373169) (ONH)No_cluster B1.1 rep (0.0240737) (ONH)No_cluster C5.1 rep (0.00708063) (ONH)No_cluster C5.2 rep (0.0147693) (ONH)No_cluster C5.6 rep (0.0167654) (ONH)No_cluster C5.7 rep (0.0187037) (ONH)No_cluster B2.7 rep (0.059958) (ONH)No_cluster B3.7 rep (0.0303078) (ONH)No_cluster C3.8 rep (0.0104284) (ONH)No_cluster B1.8 rep (0.0208139) (ONH)No_cluster C5.3 rep (0.0112272) (ONH)No_cluster C5.8 rep (0.0336868) (ONH)No_cluster B3.3 rep (0.0293422) (ONH)No_cluster B2.8 rep (0.0105007) (ONH) B3.8 rep (0.0299744) (ONH) C4.1 (0.0128421) (ONH) (0.0344696)[ min ] [ medium ] [ max ] CEM 1 Cep290 265.7 437.5 808.8 P ( S | Z, I ) = 0.00 Ift88 97.7 132.6 168.4 Mean Corr = 0.17617 Ift122 31.7 55.6 90.2 Nphp1 157.2 226.3 332.6 Wdr19 537.2 717.0 984.5 Arl3 3465.0 4730.6 6458.9 Ift57 650.6 856.0 1241.4 Rp1 638.5 2973.6 5386.6 Tbcc 154.8 237.7 364.5 Ttc8 341.8 601.0 1081.2 Ift140 1743.1 2145.3 3053.7 Iqcb1 124.2 168.1 222.4 Cetn1 42.6 55.5 68.1 Fam161a 331.5 1484.9 2690.8 Cetn3 1694.9 2027.9 2428.9 Myo7a 118.8 186.7 296.8 Kif3a 201.2 339.1 443.5 Topors 93.8 196.8 285.9 Ift52 158.3 224.3 286.9 Gnat1 2753.9 10220.4 15272.6 Cetn2 1582.4 1847.3 2342.4 Whrn 145.2 502.9 1129.1 Rp1l1 495.6 1899.4 4100.9 Wdr34 143.5 215.7 328.1 Tmem107 204.7 323.9 458.8 AK129341 35.6 63.6 115.2 Ttc26 64.0 116.7 203.7 Ift80 2070.0 2644.8 3486.5 CEM 1 + Katnal2 24.4 36.8 77.6 Top 10 Genes Dync2li1 429.4 530.2 744.7 Bbs2 689.5 1063.7 1657.3 Dyx1c1 25.1 40.1 57.5 Wdr31 23.2 36.7 60.3

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

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

Background corr dist: KL-Divergence = 0.0440, L1-Distance = 0.0244, L2-Distance = 0.0009, Normal std = 0.5775 GEO Series "GSE23200" 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=GSE23200 Status: Public on Jun 23 2011 Title: Immunoprotective properties of sertoli cells: potential genes and pathways that confer immune privilege for sertoli cell transplantation and in the testis Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21900683 Summary & Design: Summary: Immune privileged Sertoli cells (SC) survive when transplanted across immunological barriers and prolong the survival of co-transplanted allogeneic and xenogeneic cells in rodent models. However, the mechanism for this survival and protection remains unresolved. We have recently identified a mouse Sertoli cell line (MSC-1) that lacks some of the immunoprotective abilities associated with primary SC. The objective of this study was to compare the survival and gene expression profiles of primary SC and MSC-1 cells to identify factors or immune-related pathways potentially important for SC immune privilege. Primary SC or MSC-1 cells were transplanted as allografts to the renal subcapsular area of naÃ¯ve BALB/c mice and cell survival was analyzed by immunohistochemistry. Additionally, transcriptome differences were investigated by microarray and pathway analyses. While primary SC were detected within the grafts with 100% graft survival throughout the 20-day study, MSC-1 cells w ere rejected between 11 and 14 days with 0% graft survival at 20 days post-transplantation. Microarray analysis identified 3198 genes that were differentially expressed with a Â± 4-fold or higher level in primary SC. Cluster and pathway analyses indicate that the mechanism of SC immune privilege is likely complex with multiple immune modulators being involved such as immunosuppressive cytokines and complement inhibitors, lipid mediators for controlling inflammation, and junctional molecules that control leukocyte movement in and out of the immune privileged space. Further study of these immune modulators will increase our understanding of SC immune privilege and in the long-term lead to improvements in transplantation success.

Overall design: Aggregated 19 to 20-day mice primary Sertoli cells and MSC-1 cell line were used to determine the global transcriptome differences important for the survival and protection of transplanted cells.

Background corr dist: KL-Divergence = 0.0095, L1-Distance = 0.0345, L2-Distance = 0.0013, Normal std = 0.9520

0.445 Kernel fit Pairwise Correlations Normal fit

Density 0.222

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

apSC_Rep1apSC_Rep2 (0.0883327)apSC_Rep3 (0.22531)aMSC_1_Rep1 (0.204182)aMSC_1_Rep2 aMSC_1_Rep3(0.133305) (0.155362) (0.193508) [ min ] [ medium ] [ max ] CEM 1 Cep290 254.9 453.8 639.2 P ( S | Z, I ) = 0.00 Ift88 268.2 1014.3 1206.0 Mean Corr = 0.29238 Ift122 329.5 1521.9 2522.0 Nphp1 368.7 7987.1 10922.6 Wdr19 384.2 501.0 540.2 Arl3 4667.9 6643.6 8608.1 Ift57 884.8 1245.6 1709.1 Rp1 4.0 4.7 18.0 Tbcc 574.0 953.4 997.8 Ttc8 451.6 559.9 657.4 Ift140 860.4 6064.9 7640.8 Iqcb1 334.9 3155.6 3878.7 Cetn1 4.0 8442.9 11168.2 Fam161a 18.9 99.0 116.6 Cetn3 2078.4 4240.7 5929.1 Myo7a 327.2 697.7 1509.6 Kif3a 1235.4 1371.4 1594.4 Topors 484.9 1073.0 1222.7 Ift52 1062.3 1292.4 1371.3 Gnat1 4.0 6.1 18.6 Cetn2 573.1 2274.3 2485.2 Whrn 136.6 197.4 273.3 Rp1l1 4.0 4.8 22.9 Wdr34 503.1 803.9 1110.2 Tmem107 3356.7 4485.3 5772.0 AK129341 4.0 1227.9 1865.8 Ttc26 446.3 683.9 794.3 Ift80 831.2 1392.9 1683.2 CEM 1 + Katnal2 254.1 1119.6 1426.5 Top 10 Genes Dync2li1 722.7 1113.2 1271.7 Bbs2 292.4 625.3 732.7 Dyx1c1 30.9 696.4 1417.7 Wdr31 133.7 1107.7 1281.9

Null module GEO Series "GSE24512" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 29 -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=GSE24512 Status: Public on Mar 15 2012 Title: Expression variation in the mouse retina Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21779340 Summary & Design: Summary: Expression analysis of multiple mouse strains across two developmental timepoints to determine both strain specific and temporal expression of genes in the mouse retina

Overall design: A total of 29 retinas were collected from 15 mice of each strain at similar time points during the day. Equimolar amounts of RNA isolated from ten retinas were pooled into three separate pools from each strain and time point, then hybridized to Affymetrix Mouse 420A 2.0 GeneChip arrays.

Background corr dist: KL-Divergence = 0.1455, L1-Distance = 0.0524, L2-Distance = 0.0048, Normal std = 0.3969

1.073 Kernel fit Pairwise Correlations Normal fit

Density 0.536

0.000 CEM 1

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

Pre-normalization Quantiles

C57BL6/JC57BL6/J P30.5C57BL6/J 5-3-07 P30.5C57BL6/J (0.0207119) 4-12-07 P30.5C57BL6/J 4-19-07(0.0372632) E18.5C57BL6/J 5-3-07(0.0284345) E18.5RD7 (0.0315532) 4-19-07 E18.5 P30.5RD7 4-20-07(0.03714) 5-3-07 P30.5RD7 (0.03557) (0.0416083) 4-12-07 P30.5RD7 4-19-07(0.0317398) E18.5RD7 5-3-07(0.029279) E18.5RD7 (0.0407513) 4-12-07 E18.5AKR/J 4-19-07(0.0347359) P30.5AKR/J (0.0374026) 5-3-07 P30.5AKR/J (0.0277401) 14 P30.5AKR/J 4-19-07 15 E18.5AKR/J 4-19-07(0.0160634) 5-3-07 E18.5NOD.NON-H2-NB1 (0.0284066) (0.0300242) 4-19-07NOD.NON-H2-NB1 (0.0500082)NOD.NON-H2-NB1 P30.5NOD.NON-H2-NB1 5-3-07 P30.5NOD.NON-H2-NB1 (0.0431812) 4-12-07 P30.5NOD.NON-H2-NB1 4-19-07(0.0586151) E18.5CAST/EiJ 5-3-07(0.0546418) E18.5CAST/EiJ (0.0356172) 4-12-07P30.5 E18.5CAST/EiJ 5-3-07 4-19-07P30.5(0.0304899) CAST/EiJ(0.0306628) 4-12-07 P30.5(0.0281533)CAST/EiJ 4-19-07(0.0435978) E18.5CAST/EiJ 5-3-07(0.0227772) E18.5 (0.0333013) 4-12-07 E18.5 4-19-07(0.0338353) (0.0266948)[ min ] [ medium ] [ max ] CEM 1 Cep290 318.0 1705.0 3849.3 P ( S | Z, I ) = 0.00 Ift88 530.0 705.7 1012.6 Mean Corr = 0.06017 Ift122 188.6 322.3 443.2 Nphp1 327.1 433.0 576.1 Wdr19 342.7 609.0 898.6 Arl3 6489.2 12690.9 20832.5 Ift57 833.0 1430.1 1999.2 Rp1 75.1 9196.5 15349.8 Tbcc 349.0 790.8 1406.8 Ttc8 847.3 3577.3 5682.8 Ift140 788.0 1243.7 1675.3 Iqcb1 388.6 527.3 798.8 Cetn1 1.1 4.1 32.3 Fam161a 126.4 2113.9 4450.3 Cetn3 1820.9 2932.1 4222.4 Myo7a 87.8 276.3 618.5 Kif3a 421.8 965.7 2323.8 Topors 95.0 182.2 672.2 Ift52 448.6 635.9 830.9 Gnat1 1.5 20792.4 43309.2 Cetn2 1513.2 2232.2 3933.8 Whrn 88.0 295.2 1117.8 Rp1l1 3.6 329.2 8623.9 Wdr34 469.0 646.0 880.9 Tmem107 4223.3 5412.3 7972.4 AK129341 195.1 383.8 622.9 Ttc26 161.1 313.4 411.5 Ift80 687.7 1257.7 1643.4 CEM 1 + Katnal2 56.2 391.6 581.1 Top 10 Genes Dync2li1 801.7 1111.6 1353.5 Bbs2 238.2 1100.5 1945.2 Dyx1c1 87.8 165.5 412.4 Wdr31 113.9 297.7 1724.4

Null module GEO Series "GSE39458" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 6 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

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

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

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

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

0.495 Kernel fit Pairwise Correlations Normal fit

Density 0.247

0.000 CEM 1

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

Pre-normalization Quantiles

KSL cells_B6xG7_sortedKSL cells_KRN_sortedKSL cells_KRNxG7_sortedLin+_B6xG7_sorted (0.16212)Lin+_KRN_sorted (0.137015)Lin+_KRNxG7_sorted (0.188962)(0.155892) (0.168536) (0.187474)[ min ] [ medium ] [ max ] CEM 1 Cep290 94.5 319.6 386.3 P ( S | Z, I ) = 0.00 Ift88 94.6 252.9 277.1 Mean Corr = 0.28123 Ift122 33.2 94.3 115.2 Nphp1 32.2 295.2 324.6 Wdr19 33.0 88.2 99.5 Arl3 2280.2 3617.9 3987.0 Ift57 399.0 949.4 1145.8 Rp1 5.5 14.6 22.5 Tbcc 181.3 238.4 264.7 Ttc8 22.6 218.3 356.9 Ift140 496.7 956.1 1083.0 Iqcb1 167.6 220.2 256.0 Cetn1 8.1 12.8 17.4 Fam161a 36.2 81.9 106.3 Cetn3 2468.4 3088.5 3720.0 Myo7a 152.1 238.9 383.3 Kif3a 84.9 216.7 268.7 Topors 427.0 1000.3 1112.8 Ift52 620.5 958.1 1110.5 Gnat1 1.6 3.6 9.9 Cetn2 584.2 1112.1 1187.0 Whrn 102.1 134.4 151.6 Rp1l1 1.1 8.0 15.8 Wdr34 61.7 341.0 397.3 Tmem107 669.2 2148.0 2667.0 AK129341 33.9 41.6 56.4 Ttc26 23.3 79.1 103.2 Ift80 471.5 561.9 601.9 CEM 1 + Katnal2 7.0 23.0 30.1 Top 10 Genes Dync2li1 83.7 166.2 218.7 Bbs2 37.2 81.5 121.0 Dyx1c1 20.9 44.3 64.9 Wdr31 19.6 35.1 52.3

Null module GEO Series "GSE48338" 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=GSE48338 Status: Public on Jun 03 2014 Title: Tpl2 promotes chemokine/chemokine receptor expression and macrophage migration during acute inflammation Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 24713702 Summary & Design: Summary: In autoimmune diseases, accumulation of activated leukocytes correlates with inflammation and disease progression, and therefore, disruption of leukocyte trafficking is an active area of research. The protein kinase Tpl2 (MAP3K8) regulates leukocyte inflammatory responses and is also being investigated for therapeutic inhibition during autoimmunity. Herein, we addressed the contribution of Tpl2 to the regulation of macrophage chemokine and chemokine receptor expression and subsequent migration in vivo using a mouse model of Tpl2 ablation. We found that gene expression of the chemokine ligands CCL2, CCL7, CXCL2, and CXCL3 as well as the chemokine receptors CCR1 and CCR5 were reduced in macrophages from the bone marrow and peritoneal cavities of tpl2-/- mice following stimulation with LPS. LPS stimulation repressed chemokine receptor expression of CCR1, CCR2 and CCR5. Notably, LPS-induced repression of CCR1 and CCR5 was significantly enhanced in Tpl2-deficient macrophages and was observed to be dependent upon Erk activation and independent of PI3K and mTOR signaling. Consistent with alterations in chemokine and chemokine receptor expression, tpl2-/- macrophages were defective in trafficking to the peritoneal cavity following thioglycollate-induced inflammation. Overall, this study demonstrates a Tpl2-dependent mechanism for macrophage expression of both chemokine receptors and their ligands and provides further insight into how Tpl2 inhibition may disrupt inflammatory networks in vivo.

Overall design: microarray was used to profile the genome-wide expression patterns in Tpl2 wild-type and deficient macrophage.

Background corr dist: KL-Divergence = 0.0154, L1-Distance = 0.0201, L2-Distance = 0.0004, Normal std = 0.8097

0.493 Kernel fit Pairwise Correlations Normal fit

Density 0.246

0.000 CEM 1

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

Pre-normalization Quantiles

BMDM, BMDM,Tpl2 WT, BMDM,Tpl2 unstimulated, WT, BMDM,Tpl2 unstimulated, KO, BMDM,Tpl2 biologicalunstimulated, KO, BMDM,Tpl2 biologicalunstimulated, replicate WT, BMDM,Tpl2 biological LPS replicate WT, 1treated, BMDM, Tpl2(0.139661) biological LPS replicate KO, 2treated, biologicalTpl2(0.157368) LPS replicate KO, 1treated, biological(0.0849653) LPS replicate 2treated, biological(0.128537) replicate 1 (0.14862) biological[ minreplicate 2 (0.119107) replicate ]1 (0.146095) 2 (0.0756469)[ medium ] [ max ] CEM 1 Cep290 27.7 45.7 49.7 P ( S | Z, I ) = 0.00 Ift88 113.5 187.1 228.7 Mean Corr = 0.27065 Ift122 37.2 65.8 84.8 Nphp1 152.1 258.4 285.9 Wdr19 134.8 236.2 276.9 Arl3 1205.6 1462.6 1809.4 Ift57 380.7 1086.5 1716.5 Rp1 11.5 12.3 13.4 Tbcc 349.4 612.0 887.5 Ttc8 71.5 196.1 284.0 Ift140 219.0 765.6 842.9 Iqcb1 91.5 111.5 129.3 Cetn1 21.5 25.2 31.3 Fam161a 154.0 179.8 206.7 Cetn3 1423.3 2004.7 2180.0 Myo7a 69.3 597.1 804.7 Kif3a 260.4 1582.3 1654.2 Topors 203.3 267.3 331.5 Ift52 456.1 779.8 860.5 Gnat1 48.9 63.6 83.5 Cetn2 774.6 1150.2 1247.3 Whrn 229.9 298.4 357.9 Rp1l1 19.2 23.5 28.5 Wdr34 100.6 187.1 221.2 Tmem107 99.8 621.4 819.7 AK129341 11.1 13.6 15.6 Ttc26 40.9 56.5 64.3 Ift80 73.9 136.6 193.2 CEM 1 + Katnal2 31.7 35.4 39.0 Top 10 Genes Dync2li1 213.5 252.4 324.3 Bbs2 44.3 159.3 180.6 Dyx1c1 27.4 35.8 46.0 Wdr31 47.2 64.8 74.0

Null module GEO Series "GSE10246" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 182 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

Details of this dataset are not shown due to large number of samples and the page size limit. Find details in http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10246

Background corr dist: KL-Divergence = 0.5414, L1-Distance = 0.1198, L2-Distance = 0.0520, Normal std = 0.2635 GEO Series "GSE31797" 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=GSE31797 Status: Public on Mar 01 2012 Title: Activation of SREBP in Alveolar Type II Cells Enhances Lipogenesis Causing Pulmonary Lipotoxicity Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 22267724 Summary & Design: Summary: Background: Lung function is dependent upon the precise regulation of the synthesis, storage, and catabolism of tissue and alveolar lipids.

Results: Activation of SREBP (Sterol Response Element Binding Protein) induced lipogenesis in alveolar epithelial cells, causing neutral lipid accumulation, lung inflammation, and tissue remodeling.

Conclusions: The accumulation of neutral lipids in type II epithelial cells and alveolar macrophages caused lung inflammation, consistent with findings in lipid storage disorders.

Significance: Pulmonary lipotoxicity may contribute to the pathogenesis of lung dysfunction associated with diabetes, obesity, and other metabolic disorders.

Overall design: Genome-wide transcription profiling comparison between doxycycline-exposed SFTPC-rtTAWT/Tg/(tetO)7CMV-CreWT/Tg/Insig1flox/flox/Insig2-/- mice (i.e., Insig1/2/ ) and Insig1flox/flox/Insig2-/- . Three independent pooled RNA from isolated lung type 2 cells of each genotype were used.

Background corr dist: KL-Divergence = 0.0437, L1-Distance = 0.0184, L2-Distance = 0.0004, Normal std = 0.5976

0.674 Kernel fit Pairwise Correlations Normal fit

Density 0.337

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

Insig1 flox/floxInsig1 flox/flox Insig1/Insig2 flox/flox Insig1-/-/Insig2 InsigKO_C1 / Insig1-/-/Insig2 InsigKO_C2 /Insig2 / Insig1-/-(0.228097) InsigKO_C3 -/-/Insig2 InsigKO_E1/ (0.155846) -/-/Insig2 InsigKO_E2 (0.280305) -/-(0.0855966) InsigKO_E3 (0.114955)[ min (0.135201) ] [ medium ] [ max ] CEM 1 Cep290 174.3 263.7 474.4 P ( S | Z, I ) = 0.00 Ift88 637.0 827.4 1444.2 Mean Corr = 0.29530 Ift122 215.1 247.8 348.2 Nphp1 230.6 343.0 619.5 Wdr19 397.0 599.5 804.0 Arl3 3002.3 5205.5 5972.1 Ift57 1239.4 1524.8 2297.4 Rp1 14.0 26.8 48.8 Tbcc 356.1 472.3 602.9 Ttc8 467.9 573.2 1014.9 Ift140 1068.6 1164.4 1462.2 Iqcb1 678.6 838.9 1005.6 Cetn1 8.8 29.7 61.4 Fam161a 183.7 365.0 553.1 Cetn3 1524.7 2032.6 2303.6 Myo7a 74.4 151.3 213.3 Kif3a 407.2 461.8 749.5 Topors 284.7 377.1 450.0 Ift52 512.2 545.2 665.0 Gnat1 6.5 13.1 18.2 Cetn2 1377.5 1915.9 2254.8 Whrn 408.1 505.3 565.3 Rp1l1 5.1 37.2 56.0 Wdr34 415.2 643.4 824.5 Tmem107 5561.7 6677.4 9385.4 AK129341 486.9 756.4 1630.8 Ttc26 282.4 387.2 597.6 Ift80 595.3 756.9 871.7 CEM 1 + Katnal2 100.0 131.9 238.1 Top 10 Genes Dync2li1 1828.2 2201.7 2660.2 Bbs2 334.5 386.4 528.4 Dyx1c1 230.6 360.1 458.6 Wdr31 176.5 285.6 381.8

Null module GEO Series "GSE42601" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 6 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

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

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

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

0.430 Kernel fit Pairwise Correlations Normal fit

Density 0.215

0.000 CEM 1

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

Pre-normalization Quantiles

Wild-typeMutant testes Wild-typetestes at P21, atMutant P21,biological testes biological Wild-typetestes at P21,rep1 atMutant P21,biological rep1(0.115029)testes biological(0.151155)testes at P21,rep2 at P21,biologicalrep2(0.183498) biological(0.135) rep3[ rep3(0.175128)min (0.240191) ] [ medium ] [ max ] CEM 1 Cep290 812.7 1021.2 1181.0 P ( S | Z, I ) = 0.00 Ift88 1037.2 1502.8 1735.5 Mean Corr = 0.22921 Ift122 867.7 2491.4 3511.8 Nphp1 2768.3 9040.4 10157.0 Wdr19 385.5 670.1 763.1 Arl3 3731.8 8577.9 9564.7 Ift57 696.5 1690.3 1827.0 Rp1 1.6 17.1 37.7 Tbcc 781.2 1330.3 1559.9 Ttc8 665.1 1015.5 1116.0 Ift140 1717.2 7573.4 9247.5 Iqcb1 2077.3 2423.0 2576.4 Cetn1 386.6 9376.9 11469.9 Fam161a 47.7 82.7 111.2 Cetn3 3359.7 5797.5 6412.0 Myo7a 1006.3 2042.8 2845.1 Kif3a 781.3 1219.4 1357.9 Topors 757.6 1251.5 1563.8 Ift52 1401.8 1701.3 1831.0 Gnat1 7.7 21.7 38.6 Cetn2 385.2 958.4 1033.3 Whrn 68.1 106.7 131.4 Rp1l1 1.7 12.7 33.4 Wdr34 926.7 1478.9 1959.8 Tmem107 5437.2 6348.9 6599.5 AK129341 361.4 1595.9 1973.1 Ttc26 710.9 1177.3 1257.8 Ift80 917.8 2198.9 2507.9 CEM 1 + Katnal2 300.3 1745.3 1924.8 Top 10 Genes Dync2li1 1453.1 1981.1 2110.1 Bbs2 492.7 601.3 789.0 Dyx1c1 372.5 1626.2 1716.7 Wdr31 736.4 2267.1 2590.1

Null module GEO Series "GSE1986" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 17 -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=GSE1986 Status: Public on Feb 23 2007 Title: Global gene expression across a range of tissues Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: The aim of this study is to survey global gene expression across a range of mouse tissues. Biotinylated cRNA was synthesized from total RNA, then fragmented and hybridized to Affymetrix Mouse Genome 430 2.0 GeneChip arrays at the Siteman Cancer Center Gene Chip Core Facility (Washington University, St Louis, Missouri) according to manufacturer's protocols. Image files were generated using MicroArray Suite 5.0 (Affymetrix).

Keywords: other

Overall design:

Background corr dist: KL-Divergence = 0.2441, L1-Distance = 0.0808, L2-Distance = 0.0181, Normal std = 0.3425

1.239 Kernel fit Pairwise Correlations Normal fit

Density 0.620

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

brain (0.031192)CD4+ naiveembryo_d7 (0.0626077)eye (0.190307)(0.0165431)heart (0.0415577)kidney (0.031415)liver (0.0223888)lung (0.0130891)lymph nodeovary (0.0188858) (0.0376021)placentaskeletal (0.0558245)spleen muscle (0.0250057)stomach (0.0636927)submax (0.0400971)testis gland (0.29982) (0.0137926)thymus (0.0361794) [ min ] [ medium ] [ max ] CEM 1 Cep290 11.3 105.2 669.8 P ( S | Z, I ) = 0.00 Ift88 332.4 410.6 947.4 Mean Corr = 0.22688 Ift122 32.5 242.1 1971.6 Nphp1 73.8 369.8 9933.4 Wdr19 328.0 527.4 705.8 Arl3 1347.4 2653.8 8066.1 Ift57 176.7 457.4 1598.0 Rp1 3.2 45.0 3116.3 Tbcc 589.0 1004.2 2755.8 Ttc8 14.0 167.0 1747.3 Ift140 176.4 528.8 5603.8 Iqcb1 415.8 691.1 1173.8 Cetn1 51.5 74.1 4716.2 Fam161a 179.3 257.7 828.9 Cetn3 209.8 1829.5 3881.2 Myo7a 135.8 232.9 671.2 Kif3a 3.2 367.7 506.6 Topors 8.4 172.4 590.5 Ift52 365.9 539.8 742.7 Gnat1 2.8 19.2 14347.4 Cetn2 150.3 725.8 1135.8 Whrn 268.7 468.3 963.6 Rp1l1 299.4 619.8 2727.1 Wdr34 142.6 372.8 986.9 Tmem107 119.5 766.2 2566.0 AK129341 94.8 254.2 870.5 Ttc26 139.0 235.4 597.0 Ift80 115.5 490.5 750.2 CEM 1 + Katnal2 47.2 83.6 1043.7 Top 10 Genes Dync2li1 529.1 845.1 1310.3 Bbs2 64.0 211.2 1026.5 Dyx1c1 9.5 53.8 511.7 Wdr31 35.6 120.2 1644.4

Null module GEO Series "GSE27261" 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=GSE27261 Status: Public on Jul 29 2011 Title: Dmrt1 (doublesex and mab-3 related transcription factor 1) conditional knockout expression analysis of P28 testes Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21775990 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. This study examines the result of conditional removal of Dmrt1 from Sertoli cells in P28 testis tissue.

Overall design: Testes from P28 Dmrt1 flox/flox mice were compared to testes from P28 Dmrt1 flox/flox mice with the Sertoli cell-specific Sf1 (Nr5a1; MGI:1346833) or Dhh (MGI:94891) promoters driving Cre expression.

Background corr dist: KL-Divergence = 0.0110, L1-Distance = 0.0306, L2-Distance = 0.0011, Normal std = 0.9264

0.431 Kernel fit Pairwise Correlations Normal fit

Density 0.215

0.000 CEM 1

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

Pre-normalization Quantiles

Clint-Cont-1-011411Clint-Cont-2-011411Clint-Dhh-1-011411 (0.251225)Clint-Dhh-2-011411 (0.28086)Clint-Sf1-1-011411 (0.122346)Clint-Sf1-2-011411 (0.0768357)Clint-Sf1-3-011411 (0.0525641)Clint-Sf1-4-011411 (0.0707826) (0.0870049) (0.0583806)[ min ] [ medium ] [ max ] CEM 1 Cep290 1479.8 2427.3 4783.4 P ( S | Z, I ) = 0.00 Ift88 322.7 408.7 924.2 Mean Corr = 0.26944 Ift122 205.8 288.4 1120.1 Nphp1 2008.0 3908.0 9126.0 Wdr19 103.8 147.8 200.1 Arl3 5764.7 8270.7 11621.8 Ift57 293.5 914.8 5026.4 Rp1 5.9 7.8 11.6 Tbcc 434.6 593.4 960.1 Ttc8 16.7 34.1 53.7 Ift140 4005.7 7117.5 10362.0 Iqcb1 351.7 541.2 785.9 Cetn1 382.0 4527.0 9974.7 Fam161a 79.6 572.1 942.0 Cetn3 1392.8 2059.6 3061.5 Myo7a 642.7 1599.6 3920.4 Kif3a 58.7 92.0 243.9 Topors 84.5 131.3 307.6 Ift52 268.3 374.5 473.5 Gnat1 8.8 10.6 13.4 Cetn2 598.1 709.6 1283.1 Whrn 18.1 41.7 49.8 Rp1l1 8.7 9.2 10.8 Wdr34 1722.1 2388.2 3269.8 Tmem107 842.9 1260.3 3053.5 AK129341 21.8 75.1 395.6 Ttc26 160.8 444.2 869.6 Ift80 699.4 1558.7 2554.5 CEM 1 + Katnal2 69.4 269.3 1202.6 Top 10 Genes Dync2li1 290.9 451.5 602.3 Bbs2 324.2 533.1 639.1 Dyx1c1 344.7 1185.5 2603.2 Wdr31 287.4 1296.2 4738.8

Null module GEO Series "GSE12769" 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=GSE12769 Status: Public on Sep 18 2008 Title: Murine postpartum testis developmental time course (0 to 35 day) Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: Murine testis developmental time course created from tissue samples collected from birth through adulthood and hybridized to M430_2 chips in duplicate.

Keywords: time-course

Overall design: Time course of gene expression in the murine postpartum testis development (duplicates in day 0, 3, 6, 8, 10, 14, 18, 20, 30, 35). Total 20 samples.

Background corr dist: KL-Divergence = 0.0289, L1-Distance = 0.0313, L2-Distance = 0.0017, Normal std = 0.6762

0.590 Kernel fit Pairwise Correlations Normal fit

Density 0.295

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

mtestis_D0pp_rep1mtestis_D0pp_rep2mtestis_D3pp_rep1 (0.0355175)mtestis_D3pp_rep2 (0.0368091)mtestis_D6pp_rep1 (0.037659)mtestis_D6pp_rep2 (0.043814)mtestis_D8pp_rep1 (0.0360891)mtestis_D8pp_rep2 (0.0273694)mtestis_D10pp_rep1 (0.0347335)mtestis_D10pp_rep2 (0.0334981)mtestis_D14pp_rep1 (0.0301124)mtestis_D14pp_rep2 (0.0310033)mtestis_D18pp_rep1 (0.0349837)mtestis_D18pp_rep2 (0.026416)mtestis_D20pp_rep1 (0.050181)mtestis_D20pp_rep2 (0.0587916)mtestis_D30pp_rep1 (0.0842302)mtestis_D30pp_rep2 (0.0603701)mtestis_D35pp_rep1 (0.104522)mtestis_D35pp_rep2 (0.0918447) (0.069266) (0.0727892)[ min ] [ medium ] [ max ] CEM 1 Cep290 152.4 371.9 972.1 P ( S | Z, I ) = 0.00 Ift88 406.3 1011.6 1717.8 Mean Corr = 0.25324 Ift122 261.9 1148.6 2220.4 Nphp1 663.1 2513.1 11006.5 Wdr19 210.8 470.8 853.6 Arl3 2075.0 4583.1 11991.3 Ift57 531.8 788.3 2539.0 Rp1 4.0 12.6 78.7 Tbcc 652.8 797.4 2577.7 Ttc8 245.1 746.9 1016.5 Ift140 949.6 1664.2 7935.6 Iqcb1 801.7 1253.1 3223.1 Cetn1 5.3 1207.6 17489.7 Fam161a 13.8 103.0 324.5 Cetn3 4067.8 5405.6 9971.7 Myo7a 795.3 2418.3 3223.5 Kif3a 869.8 1164.8 1529.6 Topors 233.7 452.3 638.9 Ift52 797.2 1053.4 1531.5 Gnat1 4.9 21.1 77.6 Cetn2 150.6 1160.6 1679.3 Whrn 170.0 319.3 542.2 Rp1l1 4.0 20.3 175.0 Wdr34 396.1 774.7 1952.4 Tmem107 2058.8 4938.1 8182.6 AK129341 52.6 479.5 1392.6 Ttc26 156.1 651.9 1190.3 Ift80 365.9 786.3 2131.9 CEM 1 + Katnal2 29.6 306.6 2004.4 Top 10 Genes Dync2li1 552.8 1138.2 1904.3 Bbs2 196.6 462.3 811.2 Dyx1c1 63.1 421.9 1793.4 Wdr31 189.4 496.5 4890.2

Null module GEO Series "GSE16585" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 31 -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=GSE16585 Status: Public on Oct 19 2009 Title: Expression profiling of P14 and P28 mouse retina from 4 genotypes: +/+, Rorb-/- , +/+;CrxpNrl and Rorb-/-;CrxpNrl Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 19805139 Summary & Design: Summary: Rorb is essential for rod photoreceptor development in the mouse retina. Using Affymetrix mouse GeneChips, we have generated expression profiles of the +/+, Rorb-/- , +/+;CrxpNrl and Rorb-/-;CrxpNrl retina at P14 and P28.

In this dataset, we include the expression data obtained from retina of wt and mutants. These data are used to obtain 1189 genes that are differentially expressed in Rorb-/- vs wt.

Overall design: 31 total samples were analyzed

Background corr dist: KL-Divergence = 0.1975, L1-Distance = 0.0336, L2-Distance = 0.0018, Normal std = 0.3390

1.177 Kernel fit Pairwise Correlations Normal fit

Density 0.588

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

P14 +/+ P14retina, +/+ biologicalP14retina, +/+ biologicalP14retina, rep1 +/+ biologicalP14retina,(0.0313174) rep2 Rorb-/- biologicalP14(0.0366868) rep3 Rorb-/-retina, P14(0.0269556) rep4 biologicalRorb-/- retina, P14(0.0227755) Rorb-/- biologicalretina, rep1P14 +/+;CrxpNrl (0.0322661)biologicalretina, rep2P14 +/+;CrxpNrl biological(0.0333005) rep3P14 retina, +/+;CrxpNrl (0.0324004) rep4P14 biologicalretina, +/+;CrxpNrl (0.0185497)P14 biologicalretina, rep1Rorb-/-;CrxpNrlP14 biologicalretina,(0.0216422) rep2Rorb-/-;CrxpNrlP14 biological(0.022307) rep3Rorb-/-;CrxpNrl retina,P14 (0.0494582) rep4 Rorb-/-;CrxpNrl biologicalretina,P28 (0.0338084) +/+ biologicalretina, P28rep1retina, +/+ biologicalretina,(0.0098023) biologicalP28rep2retina, +/+ biological(0.0298726) biologicalP28rep3retina, rep1 +/+ (0.0198083) biologicalP28rep4retina,(0.0210789) rep2 Rorb-/- (0.0167891) biologicalP28(0.0259011) rep3 Rorb-/-retina, P28(0.0203403) rep4 biologicalRorb-/- retina, P28(0.0314932) Rorb-/- biologicalretina, rep1P28 +/+;CrxpNrl (0.0266849)biologicalretina, rep2P28 +/+;CrxpNrl biological(0.0415682) rep3P28 retina, +/+;CrxpNrl (0.0360641) rep4P28 biologicalretina, Rorb-/-;CrxpNrl (0.0199098)P28 biologicalretina, rep1Rorb-/-;CrxpNrlP28 biological(0.0318144) rep2Rorb-/-;CrxpNrl retina,P28 (0.0277309) rep3 Rorb-/-;CrxpNrl biologicalretina, (0.0268342) biologicalretina, rep1 biologicalretina,(0.0175387) rep2 biological(0.0659587) [rep3 min (0.0878184) rep4 ] (0.081524) [ medium ] [ max ] CEM 1 Cep290 619.2 1473.3 1945.6 P ( S | Z, I ) = 0.00 Ift88 401.2 539.8 662.8 Mean Corr = 0.21895 Ift122 275.1 479.9 672.7 Nphp1 323.1 525.4 725.0 Wdr19 391.8 545.5 656.3 Arl3 4456.8 6962.0 10276.1 Ift57 870.2 994.9 1227.7 Rp1 922.7 8122.5 15561.9 Tbcc 804.8 1091.4 1797.8 Ttc8 2174.7 4616.7 6169.4 Ift140 615.4 796.6 988.7 Iqcb1 446.0 582.4 702.3 Cetn1 21.1 25.2 31.2 Fam161a 421.5 1486.5 2572.4 Cetn3 1915.5 2291.5 2923.8 Myo7a 28.1 368.3 956.9 Kif3a 1267.5 1578.3 2255.9 Topors 180.4 310.6 384.4 Ift52 643.0 762.5 962.8 Gnat1 733.4 34653.7 45439.2 Cetn2 1037.4 1608.9 1954.7 Whrn 282.4 498.4 656.3 Rp1l1 245.5 2817.0 4246.4 Wdr34 357.0 589.6 697.7 Tmem107 1200.5 2627.7 3913.9 AK129341 194.4 306.8 390.8 Ttc26 162.8 299.3 376.4 Ift80 1033.4 1272.0 1443.2 CEM 1 + Katnal2 138.8 262.1 451.9 Top 10 Genes Dync2li1 644.6 893.3 1229.2 Bbs2 878.3 1452.8 2139.5 Dyx1c1 72.2 153.2 286.9 Wdr31 147.2 1128.2 1701.0

Null module GEO Series "GSE31972" 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=GSE31972 Status: Public on Dec 07 2011 Title: Transcriptional profiling of ICAM-positive and -negative cells from the mouse olfactory epithelium Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: We used trasncriptional profiling of fluorescent activated cell sorting (FACS) purified ICAM1-positive and negative cells from the olfactory epithelium (OE) of three-week old mice to identify genes enriched in the horizontal basal cells.

Overall design: The olfactory epithelia from P21-P25 CD1 mice (Charles River Laboratories, Wilmington, MA), were isolated, dissociated, and then purified by FACS using a FITC-conjugated antibody for ICAM1 (CD54). ICAM1-positive and negative cell populations were collected and compared. RNA was purified with TRIzol reagent (Invitrogen, Carlsbad, CA), subjected to two rounds of amplification, labeled, and hybridized to Affymetrix Mouse Genome 430.2 GeneChip microarrays (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix reagents and protocols (http://www.affymetrix.com). There were three experimental replicates, each consisting of the ICAM1 (+) and ICAM1 (-) FACS purified cell populations from individual litters of mice that were dissected/dissociated/FACS-purified using an ICAM1-FITC conjugated antibody; one microarray was used for each ICAM1 (+) and ICAM1 (-) sample for a total of six microarrays. Microarray data were normalized using GCRMA.

Background corr dist: KL-Divergence = 0.0145, L1-Distance = 0.0398, L2-Distance = 0.0017, Normal std = 0.8821

0.490 Kernel fit Pairwise Correlations Normal fit

Density 0.245

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

Mm OE MmICAM1-negative-1 OE MmICAM1-positive-1 OE MmICAM1-negative-2 (0.133087)OE MmICAM1-positive-2 (0.205733) OE MmICAM1-negative-3 (0.15664)OE ICAM1-positive-3 (0.193498) (0.183136) (0.127906)[ min ] [ medium ] [ max ] CEM 1 Cep290 260.1 415.1 975.8 P ( S | Z, I ) = 0.00 Ift88 603.6 2041.3 2178.4 Mean Corr = 0.17962 Ift122 204.1 495.2 715.6 Nphp1 416.9 799.9 946.3 Wdr19 453.7 1726.9 2077.6 Arl3 6562.5 11733.4 13616.1 Ift57 997.0 2270.3 3309.4 Rp1 1.9 6.4 27.1 Tbcc 267.9 535.2 758.6 Ttc8 605.9 2544.7 3537.1 Ift140 1557.3 2804.6 3509.3 Iqcb1 198.1 343.9 355.9 Cetn1 1.1 3.1 5.8 Fam161a 118.5 595.4 641.0 Cetn3 2516.6 3845.6 6034.0 Myo7a 12.0 91.7 164.5 Kif3a 294.2 1587.3 1678.0 Topors 348.9 444.7 652.0 Ift52 725.9 1077.7 1119.5 Gnat1 2.2 5.8 44.9 Cetn2 2180.9 3589.3 3928.8 Whrn 91.5 206.6 227.9 Rp1l1 1.9 15.3 19.9 Wdr34 465.6 1348.5 1653.1 Tmem107 2422.0 9119.1 11899.8 AK129341 74.2 401.7 662.7 Ttc26 240.7 823.9 1062.5 Ift80 806.5 3155.2 3379.5 CEM 1 + Katnal2 103.9 347.5 466.9 Top 10 Genes Dync2li1 1212.8 1989.3 2755.2 Bbs2 520.5 808.0 916.2 Dyx1c1 90.2 261.0 311.0 Wdr31 130.4 338.7 474.6

Null module GEO Series "GSE34423" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 40 -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=GSE34423 Status: Public on Dec 14 2011 Title: Phenobarbital mediates an epigenetic switch at the constitutive androstane receptor (CAR) target gene Cyp2b10 in the liver of B6C3F1 mice [Expression array]. Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21455306 Summary & Design: Summary: Evidence suggests that epigenetic perturbations are involved in the adverse effects associated with some drugs and toxicants, including certain classes of non-genotoxic carcinogens. Such epigenetic changes (altered DNA methylation and covalent histone modifications) may take place at the earliest stages of carcinogenesis and their identification holds great promise for biomedical research. Here, we evaluate the sensitivity and specificity of genome-wide epigenomic and transcriptomic profiling in phenobarbital (PB)-treated B6C3F1 mice, a well-characterized rodent model of non-genotoxic liver carcinogenesis. Methylated DNA Immunoprecipitation (MeDIP)-coupled microarray profiling of 17,967 promoter regions and 4,566 intergenic CpG islands was combined with genome-wide mRNA expression profiling to identify liver tissue-specific PB-mediated DNA methylation and transcriptional alterations. Only a limited number of significant anti-correlations were observed between PB-induced transcriptional and promoter-based DNA methylation perturbations. However, the constitutive androstane receptor (CAR) target gene Cyp2b10 was found to be concomitantly hypomethylated and transcriptionally activated in a liver tissue-specific manner following PB treatment. Furthermore, analysis of active and repressive histone modifications using chromatin immunoprecipitation revealed a strong PB-mediated epigenetic switch at the Cyp2b10 promoter. Our data reveal that PB-induced transcriptional perturbations are not generally associated with broad changes in the DNA methylation status at proximal promoters and suggest that the drug-inducible CAR pathway regulates an epigenetic switch from repressive to active chromatin at the target gene Cyp2b10. This study demonstrates the utility of integrated epigenomic and transcriptomic profiling for elucidating early mechanisms and biomarkers of non-genotoxic carcinogenesis.

Overall design: 2932 days old male B6C3F1/Crl (C57BL/6 x C3H/He ) mice were obtained from Charles River Laboratories (Germany). Animals were allowed to acclimatise for 5 days prior to being randomly divided into two treatment groups (n = 10) and phenobarbital (Sigma 04710, 0.05% (w/v) in drinking water) was administered to one group through ad libitum access to drinking water for 28 days. Mice were checked daily for activity and behavior and sacrificed on the last day of dosing (day 28). Blood was withdrawn for PK analysis and target (liver) and non-target (kidney) tissues removed, split into several sections, frozen in liquid nitrogen and stored at 80´C for subsequent analyses. Total RNA from liver and kidney was purified and processed for Affymetrix gene expression profiling while genomic DNA was prepared for promoter array based methylome analysis using the Methylated DNA immunoprecipitation (MeDIP) procedure. Remaining tissue material was used for chromatin immunoprecipitation (ChIP) to analyze histone modifications at individual promoters. Plasma samples were also collected to evaluate phenobarbital exposure in individual animals by LC-MS.

Background corr dist: KL-Divergence = 0.0734, L1-Distance = 0.0729, L2-Distance = 0.0087, Normal std = 0.5583

0.829 Kernel fit Pairwise Correlations Normal fit

Density 0.415

0.000 CEM 1

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

Pre-normalization Quantiles

PB_Kidney_Control_5PB_Kidney_Control_1PB_Kidney_Control_9 PB_Kidney_Control_4(0.0294746) PB_Kidney_Control_10(0.0136295) PB_Kidney_Control_8(0.0152682) PB_Kidney_Control_3(0.0256408)PB_Kidney_Control_7 (0.0255086) PB_Kidney_Control_2(0.021595) PB_Kidney_Control_6(0.0168006) PB_Liver_Control_10(0.0237041) PB_Liver_Control_9(0.0242689) PB_Liver_Control_2(0.0217891) (0.0287018)PB_Liver_Control_3 (0.0291006)PB_Liver_Control_6 (0.0338776)PB_Liver_Control_5 (0.0257816)PB_Liver_Control_4 (0.0313411)PB_Liver_Control_8 (0.0201109)PB_Liver_Control_1 (0.024897)PB_Liver_Control_7 (0.0382991)PB_Kidney_treated_20 (0.0252981)PB_Kidney_treated_18 (0.0272991)PB_Kidney_treated_12PB_Kidney_treated_11 (0.0287927)PB_Kidney_treated_17 (0.0184982)PB_Kidney_treated_16 (0.0283488)PB_Kidney_treated_14 (0.0214503)PB_Kidney_treated_15 (0.0142666)PB_Kidney_treated_13 (0.0200975)PB_Kidney_treated_19 (0.0268594)PB_Liver_treated_12 (0.0193555)PB_Liver_treated_13 (0.0159462)PB_Liver_treated_14 (0.0229605) (0.0279329)PB_Liver_treated_15 (0.0278379)PB_Liver_treated_11 (0.02372)PB_Liver_treated_16 (0.021872)PB_Liver_treated_18 (0.0469349)PB_Liver_treated_19 (0.0286824)PB_Liver_treated_20 (0.020787)PB_Liver_treated_17 (0.0329618) (0.0196741) (0.0306352)[ min ] [ medium ] [ max ] CEM 1 Cep290 15.1 125.6 320.9 P ( S | Z, I ) = 0.00 Ift88 161.1 466.5 599.0 Mean Corr = 0.15279 Ift122 4.7 356.4 513.9 Nphp1 14.1 235.2 510.9 Wdr19 114.8 195.3 284.4 Arl3 1510.5 3652.7 4470.4 Ift57 14.8 877.7 1243.5 Rp1 3.3 10.1 59.4 Tbcc 367.1 513.3 748.4 Ttc8 126.1 637.2 957.7 Ift140 274.0 418.0 495.9 Iqcb1 101.0 188.6 265.6 Cetn1 3.3 10.1 52.7 Fam161a 18.8 79.4 283.5 Cetn3 1015.3 1385.1 1710.7 Myo7a 188.2 416.7 540.0 Kif3a 135.1 270.3 484.7 Topors 144.2 284.1 512.5 Ift52 517.4 837.8 1041.6 Gnat1 3.3 48.6 402.8 Cetn2 687.7 1297.7 1679.6 Whrn 86.1 191.9 296.5 Rp1l1 3.3 25.8 87.6 Wdr34 103.7 247.6 377.2 Tmem107 457.1 1430.2 1985.6 AK129341 21.8 133.0 304.2 Ttc26 22.1 277.9 374.6 Ift80 110.7 325.3 514.1 CEM 1 + Katnal2 3.4 22.4 104.3 Top 10 Genes Dync2li1 106.3 785.2 1058.3 Bbs2 9.4 231.1 407.5 Dyx1c1 12.1 72.7 129.0 Wdr31 61.7 176.4 278.2

Null module GEO Series "GSE9954" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 70 -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=GSE9954 Status: Public on Dec 20 2007 Title: Large-scale analysis of the mouse transcriptome Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 18365009 Summary & Design: Summary: We used microarrays to compare gene expression across different murine tissues.

Keywords: Other

Overall design: Different tissues were dissected from 10-12 week old C57Bl6 mice for RNA extraction and hybridization on Affymetrix microarrays.

Background corr dist: KL-Divergence = 0.3484, L1-Distance = 0.0923, L2-Distance = 0.0272, Normal std = 0.2989

1.449 Kernel fit Pairwise Correlations Normal fit

Density 0.724

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 diaphragm,Mouse diaphragm,Mouse biological diaphragm,Mouse biological spleen,replicateMouse biological spleen,replicateMousebiological 1 (0.00791989) spleen,replicateMousebiological 2 replicate(0.00710608) muscle,Mousebiological 3 replicate(0.0074796) 1 (0.00434127)muscle,Mouse biological replicate 2 (0.00392555)muscle,Mouse biological replicate 3 (0.00588767)muscle,Mouse biological replicate 1 liver,(0.00516294)Mouse biological replicate biological2 liver,(0.00369655)Mouse replicate biological3 liver,(0.0040334)Mouse replicate biological4 brain,(0.00407313)Mouse replicate 1 (0.00776519) biological brain,Mouse replicate 2 (0.00959909) biological brain,Mouse replicate 3 (0.00763745) biological lung,Mouse replicate 1 (0.0106682)biological lung,Mouse replicate 2 (0.016415)biological lung,Mouse replicate 3 (0.009684)biological kidney,Mouse replicate 1 (0.00343183) kidney,Mousebiological replicate 2 (0.00277065) kidney,Mousebiological 3replicate (0.00257387) adrenalMousebiological replicate 1 (0.00451891)adrenal Mousegland, replicate 2 (0.00546506)biologicaladrenal Mousegland, 3 (0.00526885)biologicalbone Mousegland, replicate marrow, biologicalboneMouse replicate 1 marrow, (0.0185522) biologicalboneMouse replicate 2 marrow, (0.0209724) biologicalboneMouse replicate 3 marrow, (0.0163337) biologicaladiposeMouse replicate 1 (0.00823846) biologicaladiposeMouse tissue, replicate 2 (0.0113902) adiposeMouse biologicaltissue, replicate 3 (0.00759504) pituitaryMouse biologicaltissue, replicate4 (0.00589786) pituitaryMouse biologicalgland, replicate 1 (0.00259111)pituitaryMouse biological gland, replicate 2 (0.00313326)pituitaryMouse biological gland, replicate 3 (0.00275927)pituitaryMouse biological gland, replicate 1 (0.0266324)salivaryMouse biological gland, replicate 2 (0.0216618)salivaryMouse biologicalgland, replicate 3 (0.0253513)salivaryMousebiological gland, replicate 4 (0.0163145)seminalMousebiological gland, replicate 5 (0.012633)seminalMousebiological vesicle, replicate 1 (0.00535605) seminalMouse vesicle, biological replicate 2 (0.00526239) thymus,Mouse vesicle, biological replicate3 (0.0056102) thymus,Mouse biologicalbiological replicate 1 thymus,Mouse (0.0073448)biological replicatereplicate 2 testis,Mouse (0.00701464)biological replicate 13biological testis,Mouse (0.00428311)(0.00825158) replicate 2 biological testis,Mouse(0.00473427) replicate 3 biological heart,Mouse(0.00393161) replicate 1 (0.0694549)biological heart,Mouse replicate 2 (0.073687)biological heart,Mouse replicate 3 (0.101299)biological smallMouse replicate 1 (0.00768527)intestine, smallMouse replicate 2 (0.00824365)intestine, smallMouse biological 3 (0.0106547)intestine, eye,Mouse biological replicate biological eye,Mouse biological replicate biological 1 (0.00820856)eye,Mousereplicate replicate biological 2 (0.00994517)ESMousereplicate 1 cells,(0.083434) 3 (0.00861058)ESMousereplicate biological2 cells,(0.0641698) ESMouse biological3 cells,(0.0587827) replicate placenta,Mouse biological replicate 1 placenta,Mouse (0.0181366) biological replicate 2 placenta,Mouse (0.01981) biological replicate 3 ovary,Mouse (0.0159238) biological replicate biological 1ovary,Mouse (0.00691602) replicate biological 2ovary,Mouse (0.00676409) replicate biological 3fetus,Mouse (0.00601143) replicate 1 (0.0043966)biological fetus,Mouse replicate 2 (0.00363285)biological fetus, replicate 3 (0.00471404)biological replicate 1 (0.00608321) replicate 2 (0.00603381)[ min3 (0.006133) ] [ medium ] [ max ] CEM 1 Cep290 138.9 237.9 572.7 P ( S | Z, I ) = 0.00 Ift88 300.8 444.8 764.4 Mean Corr = 0.24653 Ift122 208.2 324.4 1686.6 Nphp1 298.8 527.7 6092.7 Wdr19 188.9 278.5 871.4 Arl3 411.0 2165.8 6934.0 Ift57 261.1 589.8 1172.5 Rp1 109.9 141.9 6053.9 Tbcc 385.0 585.4 1944.2 Ttc8 209.8 418.6 1605.3 Ift140 333.5 552.7 4758.6 Iqcb1 206.7 307.6 803.4 Cetn1 134.8 177.5 9245.0 Fam161a 253.6 366.3 1006.9 Cetn3 805.7 1591.2 3728.3 Myo7a 254.4 441.6 1410.7 Kif3a 270.9 497.2 1942.7 Topors 246.3 402.7 1053.7 Ift52 492.7 708.6 1204.5 Gnat1 153.5 206.8 32063.0 Cetn2 298.7 983.8 1985.3 Whrn 281.5 424.1 804.5 Rp1l1 150.1 190.6 1858.2 Wdr34 206.3 340.1 1347.0 Tmem107 376.8 1119.4 4600.3 AK129341 153.4 214.6 480.4 Ttc26 170.0 284.2 657.8 Ift80 233.3 454.1 1170.2 CEM 1 + Katnal2 165.5 224.0 1897.1 Top 10 Genes Dync2li1 250.3 526.0 1775.9 Bbs2 215.6 323.0 925.2 Dyx1c1 148.0 199.7 948.1 Wdr31 194.0 289.4 3431.1

Null module GEO Series "GSE24813" 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=GSE24813 Status: Public on Aug 24 2011 Title: Gene expression data of BCR-ABL1 transformed myeloid cells from BCL6 wild-type and BCL6 knockout mice treated with and without Imatinib and RI-BPI Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21911423 Summary & Design: Summary: To identify differences in the gene regulation between BCL6+/+ and BCL6-/- CML cells a gene expression analysis has been performed. We investigated the gene expression pattern in BCL6+/+ cells in the presence or absence of Imatinib and a combination of Imatinib and RI-BPI (a novel retro-inverso BCL6 peptide inhibitor). In BCL6-/- CML cells, we investigated the gene expression pattern in the presence or absence of Imatinib.

Overall design: BCR-ABL1 transformed myeloid cells from BCL6+/+ mice were cultured in the presence or absence of 10´M Imatinib or 10´M Imatinib and 20´M RI-BPI for 16 hours. BCR-ABL1 transformed myeloid cells from BCL6-/- mice were cultured in the presence or absence of 10´M Imatinib. Two samples for each condition were processed.

Background corr dist: KL-Divergence = 0.0654, L1-Distance = 0.0414, L2-Distance = 0.0023, Normal std = 0.5423

0.785 Kernel fit Pairwise Correlations Normal fit

Density 0.393

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

BCL6 WTBCL6 chip WT 1BCL6 untreated chip WT 2BCL6 untreated chip (0.0852481) WT 1BCL6 Imatinib chip (0.128164) WT 2BCL6 Imatinib chiptreated WT 1BCL6 Imatinib/RI-BPI chiptreated(0.0819616) KO 2BCL6 Imatinib/RI-BPI chip (0.0951533) KO 1BCL6 untreated chiptreated KO 2BCL6 untreated chiptreated(0.0835885) (0.119362) KO 1 Imatinib chip(0.0858878) (0.130808) 2 Imatinib treated treated(0.0920692)[ min(0.0977571) ] [ medium ] [ max ] CEM 1 Cep290 172.6 332.9 435.7 P ( S | Z, I ) = 0.00 Ift88 205.3 352.3 493.7 Mean Corr = 0.28317 Ift122 99.5 240.9 318.1 Nphp1 146.6 283.6 345.1 Wdr19 94.8 263.0 394.5 Arl3 1536.0 2312.0 3030.4 Ift57 1078.4 1295.5 1535.6 Rp1 12.5 14.3 16.9 Tbcc 595.9 657.6 717.6 Ttc8 24.1 238.8 501.6 Ift140 792.0 1231.3 1557.7 Iqcb1 118.1 186.7 210.3 Cetn1 15.7 18.2 20.4 Fam161a 114.9 177.4 197.7 Cetn3 2175.8 2654.8 3422.6 Myo7a 22.5 77.0 139.0 Kif3a 528.8 674.6 823.5 Topors 543.1 795.9 1056.6 Ift52 1273.1 1767.5 2008.0 Gnat1 31.8 36.0 40.8 Cetn2 3392.9 3712.7 4369.6 Whrn 190.6 232.8 270.9 Rp1l1 20.5 25.7 27.8 Wdr34 180.1 212.7 221.1 Tmem107 1228.6 1841.0 2256.0 AK129341 17.2 47.1 70.3 Ttc26 41.7 86.0 104.1 Ift80 276.2 541.5 680.9 CEM 1 + Katnal2 25.2 32.7 46.2 Top 10 Genes Dync2li1 50.0 65.9 130.5 Bbs2 138.7 563.3 742.1 Dyx1c1 17.6 23.8 33.8 Wdr31 62.7 74.4 99.9

Null module GEO Series "GSE49128" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 17 -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=GSE49128 Status: Public on Jul 23 2013 Title: Otitis Media Impact on Middle Ear Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 24124478 Summary & Design: Summary: Objective: Otitis media is known to alter expression of cytokine and other genes in the mouse middle ear and inner ear. However, whole mouse genome studies of gene expression in otitis media have not previously been undertaken. Ninety-nine percent of mouse genes are shared in the human, so these studies are relevant to the human condition.

Methods: To assess inflammation-driven processes in the mouse ear, gene chip analyses were conducted on mice treated with trans-tympanic heat-killed Hemophilus influenza using untreated mice as controls. Middle and inner ear tissues were separately harvested at 6 hours, RNA extracted, and samples for each treatment processed on the Affymetrix 430 2.0 Gene Chip for expression of its 34,000 genes.

Results: Statistical analysis of gene expression compared to control mice showed significant alteration of gene expression in 2,355 genes, 11% of the genes tested and 8% of the mouse genome. Significant middle and inner ear upregulation (fold change >1.5, p<0.05) was seen in 1,081 and 599 genes respectively. Significant middle and inner ear downregulation (fold change <0.67, p<0.05) was seen in 978 and 287 genes respectively. While otitis media is widely believed to be an exclusively middle ear process with little impact on the inner ear, the inner ear changes noted in this study were numerous and discrete from the middle ear responses. This suggests that the inner ear does indeed respond to otitis media and that its response is a distinctive process. Numerous new genes, previously not studied, are found to be affected by inflammation in the ear.

Conclusion: Whole genome analysis via gene chip allows simultaneous examination of expression of hundreds of gene families influenced by inflammation in the middle ear. Discovery of new gene families affected by inflammation may lead to new approaches to the study and treatment of otitis media.

Overall design: There are 8 control samples and 9 samples trans-tympanically injected with H flu 10e9 for 6 hours. Each sample is from a single animal.

Background corr dist: KL-Divergence = 0.1073, L1-Distance = 0.0314, L2-Distance = 0.0014, Normal std = 0.4348

0.937 Kernel fit Pairwise Correlations Normal fit

Density 0.469

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

ME controlME controlrep ME1 (0.105042) TTrep Hflu ME2 (0.0669281) controlrep ME1 (0.101276) controlrep ME3 (0.0402937) TTrep Hflu ME4 (0.0282737) controlrep ME2 (0.031143) controlrep ME5 (0.0558788) controlrep ME6 (0.0488016) TTrep Hflu ME7 (0.0780376) TTrep Hflu ME3 (0.0321696) TTrep Hflu ME4 (0.0557044) controlrep ME5 (0.0387755) TTrep Hflu ME8 (0.071523) TTrep Hflu ME6 (0.0594673) TTrep Hflu ME7 (0.0547398) TTrep Hflu 8 (0.0477267) rep 9 (0.0842192) [ min ] [ medium ] [ max ] CEM 1 Cep290 114.3 131.3 152.9 P ( S | Z, I ) = 0.00 Ift88 124.2 151.6 232.3 Mean Corr = 0.23942 Ift122 85.5 113.9 186.7 Nphp1 283.7 348.0 433.4 Wdr19 206.0 263.9 351.6 Arl3 3006.3 3838.4 5447.2 Ift57 714.7 908.1 992.1 Rp1 3.7 4.5 6.0 Tbcc 572.1 670.2 820.5 Ttc8 62.8 81.8 116.2 Ift140 1838.8 2113.5 2763.5 Iqcb1 124.6 155.8 189.6 Cetn1 13.2 18.4 24.5 Fam161a 211.4 426.9 1185.4 Cetn3 1689.1 1868.3 2111.9 Myo7a 285.2 337.9 383.2 Kif3a 166.2 229.5 292.1 Topors 274.4 311.5 387.2 Ift52 339.8 409.6 529.0 Gnat1 15.5 22.1 34.7 Cetn2 959.1 1212.7 1564.5 Whrn 25.8 31.4 50.2 Rp1l1 7.9 9.3 14.8 Wdr34 404.8 618.5 925.3 Tmem107 703.0 973.1 1516.0 AK129341 18.6 38.6 57.9 Ttc26 70.5 104.2 149.3 Ift80 802.9 984.6 1237.7 CEM 1 + Katnal2 40.7 61.4 92.5 Top 10 Genes Dync2li1 391.6 517.6 823.6 Bbs2 360.0 460.7 599.2 Dyx1c1 42.4 95.3 170.2 Wdr31 109.8 147.9 179.8

Null module GEO Series "GSE37431" 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=GSE37431 Status: Public on Apr 23 2012 Title: Endothelial cell-enriched genes expression in mouse embryo Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 22535667 Summary & Design: Summary: The early blood vessels of the embryo and yolk sac in mammals develop by aggregation of de novo forming angioblasts into a primitive vascular plexus, which then undergoes a complex remodeling process. Angiogenesis is also important for disease progression in the adult. However, the precise molecular mechanism of vascular development remains unclear.

It is therefore of great interest to determine which genes are specifically expressed in developing endothelial cells.Here, we utilized Flk1-deficient mouse embryos, which lack endothelial cells, to perform a genome-wide survey for genes related to vascular development.

Overall design: Wild type (WT), Flk1+/GFP and Flk1 KO embryos proper (fetuses) were dissected out at 8.5 dpc. Total RNAs from these embryos were prepared using RNeasy kit. Gene expression analysis was performed by GeneSpring software.

Background corr dist: KL-Divergence = 0.0198, L1-Distance = 0.0371, L2-Distance = 0.0015, Normal std = 0.8138

0.523 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

Mouse_EC1Mouse_EC2 (0.233439)Mouse_KO1 (0.207723)Mouse_KO2 (0.21519)Mouse_WT1 (0.114459)Mouse_WT2 (0.0553534) (0.173836) [ min ] [ medium ] [ max ] CEM 1 Cep290 185.3 331.1 391.7 P ( S | Z, I ) = 0.00 Ift88 270.8 413.3 447.0 Mean Corr = 0.30186 Ift122 238.8 384.3 408.7 Nphp1 227.1 391.7 412.5 Wdr19 139.4 216.5 273.7 Arl3 2190.9 3877.9 4701.3 Ift57 353.0 549.6 614.4 Rp1 1.2 5.8 7.7 Tbcc 648.0 704.7 748.4 Ttc8 389.6 741.6 843.0 Ift140 462.4 880.1 1198.5 Iqcb1 626.8 810.0 981.1 Cetn1 1.0 3.5 17.5 Fam161a 14.6 42.9 69.6 Cetn3 4582.5 4926.9 5045.7 Myo7a 101.1 152.2 1671.1 Kif3a 293.3 408.8 450.8 Topors 766.9 947.7 1017.3 Ift52 577.5 846.7 953.1 Gnat1 5.8 26.6 31.0 Cetn2 1207.6 1613.1 1774.3 Whrn 129.2 179.5 221.1 Rp1l1 1.0 19.6 37.1 Wdr34 212.3 266.1 324.7 Tmem107 1010.3 2016.4 2078.4 AK129341 102.6 168.9 201.6 Ttc26 221.1 448.8 522.3 Ift80 256.8 689.3 736.5 CEM 1 + Katnal2 34.5 105.1 133.9 Top 10 Genes Dync2li1 364.1 726.4 793.0 Bbs2 31.4 103.6 165.7 Dyx1c1 32.8 73.2 82.9 Wdr31 73.5 243.4 304.2

Null module GEO Series "GSE32095" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 24 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32095 Status: Public on Feb 22 2012 Title: GPR120 mediates high-fat diet induced obesity Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 22343897 Summary & Design: Summary: Analysis of GPR120 which play roles for the fatty acid sensor in adipose tissue. Results provide insight into the transcriptional effects caused by the loss of the GPR120 proteins and provide further insight into their functions.

Overall design: GPR120 KO mice and the corresponding wild-type with normal diet(ND) or high fat diet(HFD), were subjected to Affymetrix Mus musculus microarrays. Epididymal adipose tissue and liver were analyzed in triplicates.

Background corr dist: KL-Divergence = 0.1001, L1-Distance = 0.0645, L2-Distance = 0.0080, Normal std = 0.4859

0.914 Kernel fit Pairwise Correlations Normal fit

Density 0.457

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

EpididymalLiver adipose GPR120KOEpididymal GPR120KOLiver HFD adipose GPR120KO Epididymal#427 HFD (0.0203816)GPR120KO #427Liver HFD adipose (0.0216757)GPR120KO Epididymal#428 HFD (0.0228311)GPR120KO #428Liver HFD adipose (0.0272248)WT Epididymal#429 HFDHFD (0.027028)WT #546#429Liver HFD adipose (0.0268972) (0.0448271)WT #546Epididymal HFD (0.0258677) WT #547Liver HFD adipose(0.0236435) WT #547Liver HFD (0.0174647) WT #560Epididymal HFDND (0.0176025) #686 #560Liver (0.0379099) adipose(0.0305531) WTEpididymal ND WT#687Liver ND (0.046062) adipose #687WTEpididymal ND (0.0364544) WT#690Liver ND (0.0527382) adipose #690GPR120KOEpididymal (0.0680694) GPR120KOLiver ND adipose GPR120KO#718Epididymal ND (0.0346082) GPR120KO#718Liver ND (0.0410995)adipose GPR120KO#719Epididymal ND (0.0372273) GPR120KO#719 ND (0.042655)adipose #720 ND (0.0362446) WT#720 ND (0.0404065) #686[ min(0.220528) ] [ medium ] [ max ] CEM 1 Cep290 16.1 89.9 473.9 P ( S | Z, I ) = 0.00 Ift88 124.4 262.8 536.2 Mean Corr = 0.31927 Ift122 5.0 62.3 655.6 Nphp1 19.6 216.8 2433.9 Wdr19 38.5 150.5 313.9 Arl3 1234.6 3246.7 5769.6 Ift57 60.1 479.5 1448.3 Rp1 5.0 5.0 51.2 Tbcc 497.3 634.4 996.4 Ttc8 83.3 327.1 650.3 Ift140 207.6 453.1 1622.6 Iqcb1 68.3 164.6 648.1 Cetn1 5.0 19.1 4028.7 Fam161a 8.4 67.4 157.6 Cetn3 1042.3 2575.1 3514.5 Myo7a 231.7 358.0 753.4 Kif3a 69.6 263.0 570.4 Topors 142.5 424.7 853.3 Ift52 534.1 753.8 1097.4 Gnat1 5.0 32.8 316.6 Cetn2 382.1 1031.1 1433.7 Whrn 14.9 124.7 233.6 Rp1l1 5.0 16.4 40.1 Wdr34 103.4 183.1 545.1 Tmem107 275.2 680.4 2045.3 AK129341 5.0 42.4 384.6 Ttc26 42.6 102.7 339.9 Ift80 56.8 147.7 532.8 CEM 1 + Katnal2 5.0 77.3 498.0 Top 10 Genes Dync2li1 59.4 298.9 680.6 Bbs2 16.4 159.5 637.0 Dyx1c1 7.3 56.5 404.4 Wdr31 5.2 67.2 1089.4

Null module GEO Series "GSE1871" 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=GSE1871 Status: Public on Oct 26 2004 Title: SCCOR_MouseLung_Simva_LPS Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 15665042 Summary & Design: Summary: This series contain mouse lung samples treated with Simvastatin and LPS and corresponded controls.

Keywords: other

Overall design:

Background corr dist: KL-Divergence = 0.0617, L1-Distance = 0.0228, L2-Distance = 0.0006, Normal std = 0.5246

0.764 Kernel fit Pairwise Correlations Normal fit

Density 0.382

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

VehVeh1VehVeh2 (0.30471)VehVeh3 (0.0655921)VehLPS1 (0.0444723)VehLPS2 (0.0439678)VehLPS (0.0567818)SimvaVeh1 (0.0747503)SimvaVeh2 (0.0601583)SimvaVeh3 (0.0457704)SimvaLPS1 (0.0364372)SimvaLPS2 (0.0676451)SimvaLPS3 (0.136392) (0.0633226) [ min ] [ medium ] [ max ] CEM 1 Cep290 146.3 281.9 367.0 P ( S | Z, I ) = 0.00 Ift88 349.2 636.8 1240.0 Mean Corr = 0.19918 Ift122 150.7 243.9 369.6 Nphp1 131.0 344.6 735.0 Wdr19 368.3 591.3 1168.8 Arl3 1475.7 3040.9 5506.8 Ift57 556.4 870.3 1174.1 Rp1 3.3 7.4 37.1 Tbcc 469.4 673.6 1093.4 Ttc8 189.5 605.1 1130.7 Ift140 392.3 873.3 1619.5 Iqcb1 232.1 340.4 418.0 Cetn1 3.3 5.3 8.3 Fam161a 211.4 393.4 1108.7 Cetn3 1345.7 1751.9 2317.1 Myo7a 196.5 313.6 368.1 Kif3a 352.6 598.0 948.9 Topors 131.3 223.9 302.6 Ift52 565.9 745.5 948.0 Gnat1 3.3 38.8 52.1 Cetn2 574.1 1182.1 1691.4 Whrn 240.2 302.9 410.3 Rp1l1 7.0 23.0 50.1 Wdr34 220.1 276.9 573.7 Tmem107 1638.4 2712.3 4604.7 AK129341 190.8 556.2 1293.4 Ttc26 384.4 498.9 934.2 Ift80 228.6 518.9 832.3 CEM 1 + Katnal2 52.4 75.5 154.0 Top 10 Genes Dync2li1 391.0 892.2 1781.9 Bbs2 96.9 290.3 421.4 Dyx1c1 95.6 232.4 501.2 Wdr31 217.5 260.9 409.3

Null module GEO Series "GSE11443" 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=GSE11443 Status: Public on May 17 2008 Title: Choroid plexus function in B10.pl WT mice versus B10.PL RAG-/- mice (carri-affy-mouse-302760) Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: Previous work has led us to examine the differences in the choroid plexus function in B10.pl WT mice versus B10.PL RAG-/- mice. We believe that there is a difference between those that are normal functioning and those that are lymphocyte deficient.

To determine the gene expression profile of the choroid plexus in wild type mice as compared to those that are lymphocyte deficient.

We hypothesize that there is altered expression in the genes that mediate cellular adhesion in choroid plexus from wild type mice as compared to those that are lymphocyte deficient.

8-10 week old animals (age and sex matched) were injected with Evan's blue post anesthetization. After waiting an hour the animals were euthanized and their brains were extracted and placed in RNALater for 24 hours. The brains were then sliced sagitally

Keywords: RAG mutant, choroid plexus

Overall design:

Background corr dist: KL-Divergence = 0.0359, L1-Distance = 0.0301, L2-Distance = 0.0012, Normal std = 0.6517

0.627 Kernel fit Pairwise Correlations Normal fit

Density 0.313

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

ChoroidChoroid plexusChoroid epithelium,plexusChoroid epithelium,plexus WholeChoroid epithelium,plexus brain:WholeChoroid epithelium,plexus B10_102406_le1 brain:Whole epithelium,plexus RAG_102406_le1 brain:Whole epithelium, B10_122205_le1 brain:Whole(0.120761) RAG_122205_le1 brain:Whole (0.0736287)[ min B10_011907_le1 brain: (0.0970564) RAG_011907_le1] (0.30218) (0.214081)[ medium (0.192293) ] [ max ] CEM 1 Cep290 141.5 359.3 659.3 P ( S | Z, I ) = 0.00 Ift88 564.6 740.3 1159.9 Mean Corr = 0.17906 Ift122 213.2 321.3 462.1 Nphp1 963.8 1863.0 2356.1 Wdr19 630.3 988.4 1393.2 Arl3 10038.7 13502.2 17693.8 Ift57 2058.9 4335.9 5413.9 Rp1 1.0 11.6 27.2 Tbcc 256.2 398.6 510.3 Ttc8 1269.6 1593.4 2364.5 Ift140 832.2 1130.1 1188.9 Iqcb1 207.4 251.9 282.0 Cetn1 1.7 13.3 29.6 Fam161a 499.6 1367.0 2197.3 Cetn3 1940.0 2349.1 2404.2 Myo7a 964.2 1695.8 2474.2 Kif3a 280.0 729.2 926.5 Topors 94.5 313.6 411.9 Ift52 723.1 980.9 1061.6 Gnat1 2.6 20.2 50.3 Cetn2 2733.3 4980.9 6408.0 Whrn 86.4 127.3 306.5 Rp1l1 1.7 9.6 18.6 Wdr34 797.8 1252.1 2174.3 Tmem107 4421.4 7912.0 9616.9 AK129341 455.9 545.5 687.7 Ttc26 292.1 379.3 493.2 Ift80 872.6 1612.4 2101.2 CEM 1 + Katnal2 273.8 536.2 674.7 Top 10 Genes Dync2li1 1516.0 2033.0 2890.1 Bbs2 334.0 487.3 523.7 Dyx1c1 169.6 272.1 372.3 Wdr31 158.6 199.9 294.8

Null module GEO Series "GSE23895" 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=GSE23895 Status: Public on Jan 19 2011 Title: Selenium toxicity but not deficient or super-nutritional selenium status vastly alters the transcriptome in rodents Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21226930 Summary & Design: Summary: Protein and mRNA levels for several selenoproteins, such as glutathione peroxidase-1 (Gpx1), are down-regulated dramatically by selenium (Se) deficiency.

Selenoprotein levels in rats increase sigmoidally with increasing dietary Se and reach defined plateaus at the Se requirement, making them sensitive biomarkers for Se deficiency, but not high for Se status. Biomarkers for high Se status are needed as super-nutritional Se intakes are associated with beneficial and adverse health outcomes, but conventional biomarkers are not especially useful above the Se requirement. To characterize Se regulation of the transcriptome, we conducted 3 microarray experiments in weanling mice and rats fed Se-deficient diets supplemented with levels of Se up to 5 ´g Se/g diet.

Overall design: Rats or mice were fed Se-deficient diets supplemented with sodium selenite up to 5 ug Se/g diet for 28 or 35 days. Affymetrix Rat 230 2.0 and Mouse 430 2.0 Genome Arrays were used to analyze gene expression in liver in all studies plus kidney in the mouse study.

Background corr dist: KL-Divergence = 0.0133, L1-Distance = 0.0509, L2-Distance = 0.0031, Normal std = 0.9121

0.437 Kernel fit Pairwise Correlations Normal fit

Density 0.219

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

MouseLiver_SeDef_rep1MouseLiver_SeDef_rep2MouseLiver_SeDef_rep3MouseLiver_0.05ugSe_rep1 (0.0672042)MouseLiver_0.05ugSe_rep2 (0.0582444)MouseLiver_0.05ugSe_rep3 (0.0486627)MouseLiver_0.2ugSe_rep1 (0.0668622)MouseLiver_0.2ugSe_rep2 (0.0530256)MouseLiver_0.2ugSe_rep3 (0.0668485)MouseKidney_SeDef_rep1 (0.0411856)MouseKidney_SeDef_rep2 (0.0358722)MouseKidney_SeDef_rep3 (0.051781)MouseKidney_0.05ugSe_rep1 (0.0684672)MouseKidney_0.05ugSe_rep2 (0.0411158)MouseKidney_0.05ugSe_rep3 (0.0527541)MouseKidney_0.2ugSe_rep1 MouseKidney_0.2ugSe_rep2(0.0618768) MouseKidney_0.2ugSe_rep3(0.0434105) (0.0549502) (0.0615508) (0.0657455) (0.0604428)[ min ] [ medium ] [ max ] CEM 1 Cep290 21.7 37.2 49.1 P ( S | Z, I ) = 0.00 Ift88 348.6 644.5 758.7 Mean Corr = 0.20201 Ift122 62.3 324.0 567.3 Nphp1 332.9 1508.7 1754.4 Wdr19 126.5 281.5 335.0 Arl3 1387.5 2461.2 3048.0 Ift57 74.7 750.9 925.3 Rp1 18.0 20.3 25.6 Tbcc 499.4 625.0 676.2 Ttc8 121.1 554.4 1168.8 Ift140 509.3 567.7 631.7 Iqcb1 120.6 151.1 189.2 Cetn1 34.8 48.8 91.6 Fam161a 164.3 223.9 259.9 Cetn3 623.2 828.1 962.9 Myo7a 487.7 556.9 653.2 Kif3a 158.1 383.9 608.8 Topors 142.1 252.5 306.0 Ift52 887.1 1085.3 1199.7 Gnat1 86.1 107.4 135.4 Cetn2 624.8 1410.1 1765.5 Whrn 553.2 840.7 1073.0 Rp1l1 48.2 56.3 75.4 Wdr34 136.4 195.4 287.1 Tmem107 301.6 954.5 1236.4 AK129341 29.5 115.4 188.6 Ttc26 88.8 282.3 343.6 Ift80 292.8 383.3 425.8 CEM 1 + Katnal2 47.3 81.7 115.9 Top 10 Genes Dync2li1 173.7 846.0 1208.3 Bbs2 73.9 219.7 324.4 Dyx1c1 33.7 60.9 82.5 Wdr31 208.1 280.9 350.3

Null module GEO Series "GSE27568" 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=GSE27568 Status: Public on Feb 28 2011 Title: Ubb Knockout Mouse Testis Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21542049 Summary & Design: Summary: Analysis of Ubb knockout mouse testes at 7, 4, 21, and 28 dpp. Ubiquitin (Ub) is an essential protein found in all eukaryotic cells and plays important roles in a variety of cellular functions including germ cell development. Targeted disruption of the polyubiquitin gene Ubb results in male and female infertility in mice with germ cells arrested at meiotic prophase I.

Overall design: Whole testes from wild-type (WT) and Ubb/ (KO) mice were harvested at 7, 14, 21, and 28 days postpartum. Total RNA was extracted and hybridized to Affymetrix Mouse Genome 430 2.0 arrays.

Background corr dist: KL-Divergence = 0.0537, L1-Distance = 0.0652, L2-Distance = 0.0066, Normal std = 0.6280

0.679 Kernel fit Pairwise Correlations Normal fit

Density 0.340

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

ubb_d7_ko_1ubb_d7_ko_2 (0.0365046)ubb_d7_wt_1 (0.0322509)ubb_d7_wt_2 (0.0330949)ubb_d14_ko_1 (0.0398407)ubb_d14_ko_2 ubb_d14_wt_1(0.0306596) ubb_d14_wt_2(0.0400546) ubb_d21_ko_1(0.042569) ubb_d21_ko_2(0.0283992) ubb_d21_wt_1(0.152475) ubb_d21_wt_2(0.0346846) ubb_d28_ko_1(0.108872) ubb_d28_ko_2(0.105077) ubb_d28_wt_1(0.0275287) ubb_d28_wt_2(0.0334926) (0.15972) (0.0947756) [ min ] [ medium ] [ max ] CEM 1 Cep290 218.0 830.9 2081.7 P ( S | Z, I ) = 0.00 Ift88 438.4 1000.2 2426.6 Mean Corr = 0.22826 Ift122 229.6 387.4 3102.7 Nphp1 515.1 2176.8 10753.4 Wdr19 264.3 495.5 739.6 Arl3 2022.7 4579.4 9834.3 Ift57 596.1 920.7 2774.3 Rp1 4.0 14.4 50.1 Tbcc 549.8 730.1 2668.4 Ttc8 574.9 804.8 1131.3 Ift140 937.7 1463.2 8249.0 Iqcb1 887.4 2164.7 4773.8 Cetn1 4.0 356.2 12576.1 Fam161a 29.3 79.4 144.0 Cetn3 1603.0 4885.7 7532.4 Myo7a 848.2 2102.7 3256.9 Kif3a 472.5 1133.3 1499.0 Topors 120.2 542.3 1224.3 Ift52 955.8 1293.3 2057.9 Gnat1 5.6 19.3 73.2 Cetn2 342.5 1396.9 1807.8 Whrn 107.5 153.2 630.6 Rp1l1 4.0 10.8 30.9 Wdr34 308.5 687.5 1270.2 Tmem107 2402.2 4629.5 6961.1 AK129341 53.4 319.7 2023.6 Ttc26 180.9 683.5 2382.8 Ift80 310.6 1180.0 2887.7 CEM 1 + Katnal2 65.8 221.8 3020.1 Top 10 Genes Dync2li1 662.5 1728.3 2937.1 Bbs2 265.6 570.4 841.8 Dyx1c1 108.3 335.3 2233.6 Wdr31 263.2 538.7 3894.3

Null module GEO Series "GSE21193" 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=GSE21193 Status: Public on Jul 22 2010 Title: The effects of subchronic arsenate exposure on gene expression in the mouse lung Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 20667999 Summary & Design: Summary: Eight week old female C57BL/6 mice were exposed to arsenate in drinking water (50 ppm) for a period of twelve weeks (n = 5). Control animals received distilled deionized water (n = 5). Lung tissue was dissected and used for RNA isolation and gene expression microarray analysis.

Overall design: Eight week old female C57BL/6 mice were exposed to arsenate in drinking water (50 ppm) for a period of twelve weeks (n = 5). Control animals received distilled deionized water (n = 5). Lung tissue was dissected and used for RNA isolation and gene expression microarray analysis.

Background corr dist: KL-Divergence = 0.0535, L1-Distance = 0.0371, L2-Distance = 0.0023, Normal std = 0.5581

0.715 Kernel fit Pairwise Correlations Normal fit

Density 0.357

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

FB_50_12wk_20-5_AsDW_MusLung_Mouse430_2_HJCENV601_2FB_0_12wk_4-3_AsDW_MusLung_Mouse430_2_HJCENV601_2FB_0_12wk_4-4_AsDW_MusLung_Mouse430_2_HJCENV601_2FB_50_12wk_20-4_AsDW_MusLung_Mouse430_2_HJCENV601_2FB_50_12wk_20-3_AsDW_MusLung_Mouse430_2_HJCENV601_2FB_50_12wk_20-2_AsDW_MusLung_Mouse430_2_HJCENV601_2FB_50_12wk_20-1_AsDW_MusLung_Mouse430_2_HJCENV601_2FB_0_12wk_4-5_AsDW_MusLung_Mouse430_2_HJCENV601_2FB_0_12wk_4-1_AsDW_MusLung_Mouse430_2_HJCENV601_2 (0.226894)FB_0_12wk_4-2_AsDW_MusLung_Mouse430_2_HJCENV601_2 (0.0752236) (0.187414) (0.0287862) (0.0934696)[ min (0.0959624) ] (0.0200217) (0.143768)[ (0.0586807) medium (0.0697801) ] [ max ] CEM 1 Cep290 16.8 20.1 33.4 P ( S | Z, I ) = 0.00 Ift88 76.3 151.1 234.4 Mean Corr = 0.31584 Ift122 104.3 151.2 200.5 Nphp1 102.3 158.5 253.7 Wdr19 305.7 667.7 845.0 Arl3 2660.0 3101.6 3513.0 Ift57 407.7 536.4 760.6 Rp1 10.7 11.6 12.2 Tbcc 269.4 382.4 490.3 Ttc8 484.2 747.0 986.2 Ift140 632.8 818.5 1149.8 Iqcb1 132.4 179.1 202.9 Cetn1 5.8 6.0 6.2 Fam161a 35.1 59.5 105.0 Cetn3 1922.4 2530.6 2979.7 Myo7a 571.4 642.3 891.3 Kif3a 122.4 158.5 171.9 Topors 59.1 100.6 150.1 Ift52 426.5 507.7 622.3 Gnat1 7.8 8.1 8.3 Cetn2 1125.0 1612.1 2125.3 Whrn 18.1 18.8 19.5 Rp1l1 7.6 8.1 8.4 Wdr34 142.1 213.1 325.3 Tmem107 4066.6 7294.9 10031.8 AK129341 11.7 21.4 41.8 Ttc26 135.2 244.8 349.3 Ift80 146.9 268.6 451.6 CEM 1 + Katnal2 10.1 17.4 32.8 Top 10 Genes Dync2li1 1402.5 1776.8 2121.0 Bbs2 134.0 195.4 251.9 Dyx1c1 34.0 101.0 172.0 Wdr31 63.8 98.9 167.5

Null module GEO Series "GSE15315" 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=GSE15315 Status: Public on Mar 20 2009 Title: ERK1/2 in Ovarian Granulosa Cells are Essential for Female Fertility Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 19443782 Summary & Design: Summary: A surge of luteinizing hormone (LH) from the pituitary gland triggers ovulation, oocyte maturation, and luteinization for successful reproduction in mammals. Since the signaling molecules RAS and ERK1/2 are activated by a LH surge in granulosa cells of preovulatory follicles, we disrupted Erk1/2 in mouse granulosa cells and provide in vivo evidence that these kinases are necessary for LH-induced oocyte resumption of meiosis, ovulation, and luteinization. In addition, biochemical analyses and selected disruption of the Cebpb gene in granulosa cells demonstrate that C/EBP is a critical downstream mediator of ERK1/2 activation. These mouse models provide in vivo systems in which to define the context specific and molecular mechanisms by which granulosa cells respond to LH and these mechanisms are relevant to the regulation of human fertility and infertility.

Overall design: Immature wild type or ERK1/2 conditonal knock-out mice were injected with 5IU equine chorionic gonadotropin (eCG)-48h followed by 5 IU hCG injection. The ovarian granulosa cells were collected at hCG 0h, 2.5h, or 4h and the gene expression pforiles were compared by microarray method.

Background corr dist: KL-Divergence = 0.0268, L1-Distance = 0.0170, L2-Distance = 0.0004, Normal std = 0.6851

0.582 Kernel fit Pairwise Correlations Normal fit

Density 0.291

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

GranulosaGranulosa cellsGranulosa from cells wildGranulosa from cellstype wildGranulosa ovary,from cellstype wildGranulosa eCG-treated ovary,from cellstype ERK1/2 eCG-treated ovary,from cells 48h, ERK1/2conditional eCG-treated from no 48h,hCG ERK1/2conditional hCG (0.149008)KO 48h, conditional [ ovary,2.5h minhCG KO (0.0702357) eCG-treated ovary,4h (0.378569)KO] eCG-treated ovary, 48h, eCG-treated no[ 48h,hCGmedium hCG (0.204244) 48h, 2.5h hCG (0.0953625) 4h ] (0.102582) [ max ] CEM 1 Cep290 62.1 106.7 123.3 P ( S | Z, I ) = 0.00 Ift88 264.4 536.8 595.6 Mean Corr = 0.11849 Ift122 60.3 98.9 126.9 Nphp1 493.3 869.7 964.5 Wdr19 110.0 195.8 290.5 Arl3 2695.4 4412.7 4782.4 Ift57 516.4 612.8 696.0 Rp1 18.1 20.3 21.3 Tbcc 309.1 357.8 386.6 Ttc8 113.6 206.2 397.0 Ift140 479.1 1050.0 1363.7 Iqcb1 411.1 473.0 533.4 Cetn1 21.4 23.6 26.6 Fam161a 257.2 410.6 592.7 Cetn3 1625.4 2032.5 2435.8 Myo7a 237.8 332.8 701.9 Kif3a 651.2 933.3 1082.8 Topors 309.1 348.5 366.3 Ift52 429.4 732.6 885.1 Gnat1 32.1 42.3 43.4 Cetn2 683.2 922.6 1026.4 Whrn 204.5 234.6 269.7 Rp1l1 28.4 28.9 31.3 Wdr34 175.7 334.2 479.7 Tmem107 2065.5 3609.2 4499.0 AK129341 50.6 56.8 64.3 Ttc26 121.5 194.3 225.9 Ift80 296.3 665.1 743.3 CEM 1 + Katnal2 63.9 106.6 162.2 Top 10 Genes Dync2li1 637.0 1163.1 1341.7 Bbs2 170.3 334.2 574.3 Dyx1c1 24.7 30.8 35.5 Wdr31 92.3 110.0 139.3

Null module GEO Series "GSE21900" 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=GSE21900 Status: Public on May 18 2011 Title: Expression profiling of the Otx2 CKO retina Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21602925 Summary & Design: Summary: In the vertebrate retina, the Otx2 transcription factor plays a crucial role in the cell fate determination of both rod and cone photoreceptors. Otx2 conditional knockout (CKO) mice exhibited a total absence of rods and cones in the retina due to their cell fate conversion to amacrine-like cells. In order to investigate the entire transcriptome regulated by Otx2 in the developing retina, we performed microarray analysis on the Otx2 CKO retina.

Overall design: In order to clarify the molecular role of Otx2 in transcriptional regulation during development, we investigated the expression profile of the Otx2 CKO retina compared with that of the control retina with the genotype Otx2flox/flox;Crx-cre- using microarrays at two time points, P1 and P12.

Background corr dist: KL-Divergence = 0.0680, L1-Distance = 0.0265, L2-Distance = 0.0012, Normal std = 0.5091

0.784 Kernel fit Pairwise Correlations Normal fit

Density 0.392

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

P1-control-ex1P1-control-ex2 P1-control-ex3(0.0315709) P1-Otx2-CKO-ex1(0.0598374) P1-Otx2-CKO-ex2(0.031237)P1-Otx2-CKO-ex3 (0.0530424)P12-control-ex1 (0.0472542)P12-control-ex2 (0.0286921)P12-control-ex3 (0.212802)P12-Otx2-CKO-ex1 (0.187462)P12-Otx2-CKO-ex2 (0.160943)P12-Otx2-CKO-ex3 (0.070147) (0.0696455) (0.0473657)[ min ] [ medium ] [ max ] CEM 1 Cep290 44.1 185.0 1637.3 P ( S | Z, I ) = 0.00 Ift88 177.6 399.7 837.1 Mean Corr = 0.15757 Ift122 237.7 430.2 933.1 Nphp1 57.8 386.8 499.2 Wdr19 305.4 433.4 815.8 Arl3 2910.6 6242.2 12059.5 Ift57 694.3 828.2 1049.1 Rp1 25.0 216.4 12154.5 Tbcc 531.4 976.8 1979.4 Ttc8 700.5 1270.9 5100.8 Ift140 981.5 1151.6 1554.5 Iqcb1 163.4 511.1 809.9 Cetn1 5.2 17.5 32.0 Fam161a 52.4 151.8 1070.4 Cetn3 897.0 2563.4 4730.1 Myo7a 17.5 47.7 564.8 Kif3a 476.6 1379.5 1581.3 Topors 131.9 234.5 355.5 Ift52 555.8 856.0 1112.9 Gnat1 17.5 487.3 34718.4 Cetn2 752.8 1775.7 2221.9 Whrn 133.7 301.9 922.1 Rp1l1 22.8 183.5 6183.4 Wdr34 257.2 601.8 922.0 Tmem107 677.6 4386.5 6773.0 AK129341 36.9 264.1 388.5 Ttc26 118.5 285.8 342.1 Ift80 173.0 621.1 916.4 CEM 1 + Katnal2 12.3 152.5 208.4 Top 10 Genes Dync2li1 402.0 969.8 1904.7 Bbs2 301.3 387.0 937.9 Dyx1c1 45.5 112.5 257.3 Wdr31 121.7 214.9 1845.6

Null module GEO Series "GSE4193" 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=GSE4193 Status: Public on Feb 09 2006 Title: Gene expression in murine germ cells Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 16581510 Summary & Design: Summary: In mammals, the X and Y chromosomes are subject to meiotic sex chromosome inactivation (MSCI) during prophase I in the male germline, but their status thereafter is currently unclear. An abundance of X-linked spermatogenesis genes has spawned the view that the X must be active [1-8]. On the other hand, the idea that the imprinted paternal X of the early embryo may be pre-inactivated by MSCI suggests that silencing may persist longer [9-12]. To clarify this issue, we establish a comprehensive X-expression profile during mouse spermatogenesis. Here, we discover that the X and Y occupy a novel compartment in the post-meiotic spermatid and adopt a non-Rabl configuration. We demonstrate that this post-meiotic sex chromatin (PMSC) persists throughout spermiogenesis into mature sperm and exhibits epigenetic similarity to the XY body. In the spermatid, 87% of X-linked genes remain suppressed post-meiotically, while autosomes are largely active. We conclude that chromosome-wide X-silencing continues from meiosis to the end of spermiogenesis and discuss implications for proposed mechanisms of imprinted X-inactivation.

Keywords: Specific germ cells from murine testis

Overall design: Independent germ cell preps were used for array analysis. Duplicates were provided for each sample.

Background corr dist: KL-Divergence = 0.0209, L1-Distance = 0.0329, L2-Distance = 0.0015, Normal std = 0.7625

0.523 Kernel fit Pairwise Correlations Normal fit

Density 0.262

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

Type A Typespermatogonia A Typespermatogonia B Typespermatogonia replicate B Pachytenespermatogonia replicate 1 (0.145742)Pachytene replicate 2 spermatocytes (0.0915944)Round replicate 1 spermatocytes (0.113591) spermatidsRound 2 replicate(0.0636498) spermatids replicate 1 (0.17178) replicate 12 (0.116088)(0.163648) 2 [(0.133907) min ] [ medium ] [ max ] CEM 1 Cep290 288.6 757.6 1381.8 P ( S | Z, I ) = 0.00 Ift88 690.7 1438.3 2572.0 Mean Corr = 0.23044 Ift122 406.3 2268.9 4431.1 Nphp1 480.6 9793.9 11096.9 Wdr19 155.3 294.8 758.1 Arl3 1710.0 6351.4 9475.7 Ift57 476.9 2079.8 4211.9 Rp1 4.0 47.7 85.0 Tbcc 646.9 1560.6 3405.1 Ttc8 229.4 482.6 1227.9 Ift140 1239.8 7407.9 11636.7 Iqcb1 1064.1 1632.1 2217.7 Cetn1 6.4 8591.2 11696.2 Fam161a 85.4 152.3 233.8 Cetn3 1589.0 4165.1 5191.2 Myo7a 174.5 763.9 2478.2 Kif3a 1004.9 1341.6 1690.8 Topors 540.7 1679.1 3172.6 Ift52 810.2 1166.4 2020.7 Gnat1 14.0 64.6 80.2 Cetn2 11.2 711.5 775.8 Whrn 278.7 405.1 505.8 Rp1l1 8.4 32.1 94.3 Wdr34 339.8 864.5 3305.1 Tmem107 1842.0 3710.9 6598.1 AK129341 162.5 1170.3 3562.2 Ttc26 356.2 505.8 2337.9 Ift80 397.9 603.2 2994.2 CEM 1 + Katnal2 177.7 2309.5 2725.6 Top 10 Genes Dync2li1 563.1 1296.6 1536.6 Bbs2 192.6 565.1 883.9 Dyx1c1 49.7 359.8 2762.1 Wdr31 293.6 2243.7 4503.7

Null module GEO Series "GSE2197" 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=GSE2197 Status: Public on Mar 01 2005 Title: DC response to ISD vs CpG Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 16413926 Summary & Design: Summary: Bone marrow-derived dendritic cells were left untreated or stimulated with lipid-transfected double-stranded DNA or CpG oligonucleotides for four hours before harvesting.

Keywords: other

Overall design:

Background corr dist: KL-Divergence = 0.0357, L1-Distance = 0.0292, L2-Distance = 0.0011, Normal std = 0.6498

0.625 Kernel fit Pairwise Correlations Normal fit

Density 0.312

0.000 CEM 1

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

Pre-normalization Quantiles

ISD Exp.1CpG (0.119748) Exp.1Untreated (0.138161)CpG Exp1 Exp2ISD (0.339787) (0.187356) Exp2Untreated (0.104969) Exp2 (0.10998) [ min ] [ medium ] [ max ] CEM 1 Cep290 1.7 33.6 41.7 P ( S | Z, I ) = 0.00 Ift88 15.6 68.1 149.5 Mean Corr = 0.31907 Ift122 11.7 84.4 159.1 Nphp1 9.4 16.2 69.9 Wdr19 53.3 87.9 152.9 Arl3 1379.6 1724.9 2006.3 Ift57 574.5 744.6 1520.5 Rp1 1.1 3.4 21.4 Tbcc 452.2 556.7 715.1 Ttc8 70.0 89.5 187.8 Ift140 266.0 623.4 907.3 Iqcb1 55.7 115.4 154.0 Cetn1 2.6 4.6 30.1 Fam161a 25.1 107.4 139.6 Cetn3 1910.8 2334.6 2464.9 Myo7a 420.4 851.4 1168.6 Kif3a 156.8 228.2 361.8 Topors 267.8 476.6 563.8 Ift52 562.4 820.7 1069.0 Gnat1 7.2 35.5 52.6 Cetn2 736.1 938.9 1175.2 Whrn 91.2 122.6 130.5 Rp1l1 6.1 19.6 56.5 Wdr34 25.5 63.3 112.2 Tmem107 357.6 432.1 869.0 AK129341 8.5 44.3 58.2 Ttc26 24.6 41.5 59.6 Ift80 108.2 128.9 133.9 CEM 1 + Katnal2 2.5 7.4 48.3 Top 10 Genes Dync2li1 80.1 116.6 138.4 Bbs2 5.2 64.7 143.2 Dyx1c1 5.3 27.6 43.0 Wdr31 33.6 68.8 129.6

Null module GEO Series "GSE32529" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 224 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

Details of this dataset are not shown due to large number of samples and the page size limit. Find details in http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE32529

Background corr dist: KL-Divergence = 0.0225, L1-Distance = 0.0447, L2-Distance = 0.0023, Normal std = 0.7763 GEO Series "GSE17263" 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=GSE17263 Status: Public on Apr 13 2010 Title: Gene expression profiling of constitutive activation of Smoothened in the mouse uterus Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 20130264 Summary & Design: Summary: In order to gain a better understanding of Ihh action during embryo implantation, we constitutively activated Smo in the murine uterus using the PRcre mouse model (PRcre/+SmoM2+; SmoM2). Female SmoM2 mice were infertile. They exhibited normal serum progesterone levels and normal ovulation, but ova failed to be fertilized in vivo and the uterus failed to undergo the artificially induced decidual response. SmoM2 mice exhibited uterine hypertrophy. The endometrium had a reduced number of uterine glands and the endometrial stroma lost its normal morphologic characteristics. Microarray analysis of 3 month old SmoM2 uteri demonstrated a chondrocytic signature and confirmed that constitutive activation of SmoM2 increased extracellular matrix production. Thus, constitutive activation of Smo in the mouse uterus alters the extracellular matrix which interferes with early pregnancy.

Keywords: two group comparison

Overall design: We constitutively activated Hh signaling in the uterus by the expression of a mutant SmoM2 allele. We crossed these mice to the PRcre mouse model to constitutively activate Smo in the murine uterus (PRcre/+SmoM2+; SmoM2). High density DNA microarray analysis was performed on 3 month old control and SmoM2 uteri.

Background corr dist: KL-Divergence = 0.0278, L1-Distance = 0.0182, L2-Distance = 0.0003, Normal std = 0.6861

0.590 Kernel fit Pairwise Correlations Normal fit

Density 0.295

0.000 CEM 1

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

Pre-normalization Quantiles

Control,Control, replicateControl, replicate 1 (0.191981)SmoM2, replicate 2 (0.125689)SmoM2, replicate 3 (0.178362)SmoM2, replicate 1 (0.179336) replicate 2 (0.161729) 3 (0.162903)[ min ] [ medium ] [ max ] CEM 1 Cep290 91.1 96.2 100.1 P ( S | Z, I ) = 0.00 Ift88 312.7 401.4 462.4 Mean Corr = 0.23662 Ift122 459.9 580.2 704.5 Nphp1 400.0 480.0 590.6 Wdr19 236.2 313.0 385.6 Arl3 1502.9 2336.8 2515.8 Ift57 446.7 688.5 886.2 Rp1 15.0 23.5 42.2 Tbcc 886.9 1054.4 1163.0 Ttc8 415.5 616.1 695.4 Ift140 309.4 383.7 436.1 Iqcb1 182.8 319.2 369.9 Cetn1 3.7 17.9 29.2 Fam161a 65.9 81.5 107.7 Cetn3 2585.1 3234.1 3930.8 Myo7a 230.1 321.4 359.1 Kif3a 307.1 485.9 683.3 Topors 224.9 355.3 373.1 Ift52 561.7 735.9 801.7 Gnat1 7.6 16.6 25.5 Cetn2 861.2 1010.1 1393.1 Whrn 54.5 90.0 94.0 Rp1l1 10.5 23.0 30.4 Wdr34 273.5 324.4 375.5 Tmem107 502.3 841.2 1343.5 AK129341 78.8 163.0 224.8 Ttc26 126.9 180.6 271.0 Ift80 176.0 337.9 445.0 CEM 1 + Katnal2 15.7 39.6 54.7 Top 10 Genes Dync2li1 615.0 1135.3 1235.1 Bbs2 264.2 315.7 343.2 Dyx1c1 24.3 43.7 73.2 Wdr31 36.7 65.8 82.2

Null module 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(0.175895) rep. CTL, 2 transduced(0.0949355) rep. biological CTL, 3 (0.309321) biological CTL, rep. 1biological (0.10172)[ rep. min 2 (0.160615) rep. ] 3 (0.157513)[ medium ] [ max ] CEM 1 Cep290 25.0 46.0 56.4 P ( S | Z, I ) = 0.00 Ift88 147.3 170.6 195.2 Mean Corr = 0.23446 Ift122 42.9 44.5 47.6 Nphp1 171.9 221.2 248.0 Wdr19 35.0 42.7 51.7 Arl3 1394.7 1496.3 1628.5 Ift57 541.4 708.6 918.5 Rp1 11.6 12.6 13.7 Tbcc 662.9 722.8 753.8 Ttc8 41.3 93.7 130.1 Ift140 390.5 484.3 572.7 Iqcb1 70.3 146.4 157.7 Cetn1 13.6 16.6 17.7 Fam161a 105.1 127.8 134.8 Cetn3 3207.9 4013.5 4366.6 Myo7a 69.6 92.7 121.8 Kif3a 274.6 432.4 733.6 Topors 454.6 622.1 626.8 Ift52 875.2 967.6 1010.6 Gnat1 27.9 32.9 37.4 Cetn2 1324.9 1433.7 1484.6 Whrn 111.3 121.0 137.5 Rp1l1 23.1 24.6 26.4 Wdr34 113.6 156.8 172.7 Tmem107 1976.9 2287.1 2391.4 AK129341 13.7 16.3 17.2 Ttc26 27.0 32.2 33.5 Ift80 430.4 521.9 566.4 CEM 1 + Katnal2 30.3 31.3 37.0 Top 10 Genes Dync2li1 31.0 41.7 46.6 Bbs2 54.9 71.7 79.7 Dyx1c1 220.1 280.4 356.2 Wdr31 63.4 79.8 93.6

Null module GEO Series "GSE27713" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 7 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27713 Status: Public on Aug 07 2012 Title: Genome-wide analysis of gene expression patterns in mir-122 knockout mice livers Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 22820290 Summary & Design: Summary: To invesigate the physiology roles of mir-122 in liver, we performed expression profiling of mir-122 knockout mice and the control B6/129 mice.

Overall design: Total RNA was extracted from four mir-122 knockout mice and three control mice of 2 months of age. Gene expression was quantified by robust multi-array analysis (RMA) using the Genomic Suite software from Partek.

Background corr dist: KL-Divergence = 0.0468, L1-Distance = 0.0155, L2-Distance = 0.0003, Normal std = 0.5728

0.696 Kernel fit Pairwise Correlations Normal fit

Density 0.348

0.000 CEM 1

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

Pre-normalization Quantiles

miR122-WT-27miR122-WT-103 miR122-WT-104(0.185891)miR122-KO-03 (0.110883)miR122-KO-90 (0.0947844) miR122-KO-91(0.123709) miR122-KO-94(0.081469) (0.13314) (0.270124) [ min ] [ medium ] [ max ] CEM 1 Cep290 24.1 29.6 38.2 P ( S | Z, I ) = 0.00 Ift88 172.2 197.0 261.7 Mean Corr = 0.27126 Ift122 59.2 120.7 219.3 Nphp1 228.3 353.5 453.4 Wdr19 75.6 93.9 140.4 Arl3 860.2 1200.8 1429.1 Ift57 136.2 278.0 719.1 Rp1 23.5 27.3 37.0 Tbcc 431.7 594.1 729.6 Ttc8 182.4 262.1 371.9 Ift140 338.8 392.2 512.7 Iqcb1 43.5 56.4 61.9 Cetn1 30.9 39.9 52.5 Fam161a 127.5 137.4 154.1 Cetn3 621.6 1131.2 1416.5 Myo7a 330.1 441.8 480.3 Kif3a 139.6 172.1 222.3 Topors 309.4 387.3 443.7 Ift52 992.6 1090.4 1185.3 Gnat1 56.4 123.4 289.4 Cetn2 675.9 860.6 956.4 Whrn 171.2 189.7 237.7 Rp1l1 43.0 46.8 49.6 Wdr34 101.6 146.6 197.1 Tmem107 372.5 524.0 600.5 AK129341 34.7 36.8 46.6 Ttc26 65.2 85.4 250.9 Ift80 110.9 135.9 187.9 CEM 1 + Katnal2 34.5 40.8 49.5 Top 10 Genes Dync2li1 96.4 138.2 226.8 Bbs2 105.8 170.9 285.3 Dyx1c1 33.2 38.2 47.5 Wdr31 56.8 82.4 124.7

Null module GEO Series "GSE15872" 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=GSE15872 Status: Public on Oct 01 2009 Title: Dynamic patterning at the pylorus: formation of an epithelial intestine-stomach boundary in late fetal life Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 19877272 Summary & Design: Summary: In the adult mouse, distinct morphological and transcriptional differences separate stomach from intestinal epithelium. Remarkably, the epithelial boundary between these two organs is literally one cell thick. This discrete junction is established suddenly and precisely at embryonic day (E) 16.5, by sharpening a previously diffuse intermediate zone. In the present study, we define the dynamic transcriptome of stomach, pylorus and intestinal tissues between E14.5 and E16.5. We show that establishment of this boundary is concomitant with the induction of over a thousand genes in intestinal epithelium, and these gene products provide intestinal character. Hence, we call this process intestinalization. We identify specific transcription factors (Hnf4g, Creb3l3 and Tcfec) and examine signaling pathways (Hedgehog and Wnt) that may play a role in this process. Finally, we define a unique expression domain at the pylorus itself and detect novel pylorus-specific patterns for the transcription factor Gata3 and the secreted protein nephrocan.

Overall design: Stomach, pylorus and duodenum tissue from E14.5 and E16.5 mouse embryos were collected for RNA extraction and hybridization on Affymetrix microarrays. We sought to study the gene expression profiles and identify genes and pathways enriched in these three tissues at two important developmental times.

Background corr dist: KL-Divergence = 0.0387, L1-Distance = 0.0489, L2-Distance = 0.0046, Normal std = 0.6254

0.638 Kernel fit Pairwise Correlations Normal fit

Density 0.319

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

stomachstomach at E14.5,stomach at biological E14.5,pylorus at biological E14.5, rep1pylorus at E14.5, biological(0.0447826) rep2pylorus at biological E14.5, (0.0428109) rep3duodenum at biological E14.5, (0.0347755) rep1duodenum biological(0.00968591) at rep2 E14.5,duodenum (0.0709105) at rep3biological E14.5,stomach (0.0714979) at biological E14.5,stomach rep1 at E16.5, biological(0.040088)stomach rep2 at biological E16.5, (0.0307702)pylorus rep3 at biological E16.5, (0.052867)rep1pylorus at E16.5, biological(0.0601858) rep2pylorus at biological E16.5, (0.0417554) rep3duodenum at biological E16.5, (0.0309589) rep1duodenum biological(0.027298) at rep2 E16.5,duodenum (0.0353055) at rep3biological E16.5, (0.0427339) at biological E16.5, rep1 biological(0.143029) rep2 (0.0974775)[ rep3 min (0.123067) ] [ medium ] [ max ] CEM 1 Cep290 57.3 109.3 136.6 P ( S | Z, I ) = 0.00 Ift88 195.0 272.0 316.4 Mean Corr = 0.11791 Ift122 63.7 253.1 387.3 Nphp1 257.0 533.7 580.9 Wdr19 75.0 111.9 141.0 Arl3 1379.7 2499.2 3761.9 Ift57 134.4 357.9 483.5 Rp1 14.6 15.7 18.9 Tbcc 354.6 489.6 575.3 Ttc8 156.5 533.7 960.2 Ift140 602.0 869.5 1141.9 Iqcb1 138.5 286.0 463.8 Cetn1 17.5 19.6 27.0 Fam161a 53.6 76.1 99.7 Cetn3 2487.0 4269.3 5214.3 Myo7a 95.9 476.6 2732.0 Kif3a 231.3 739.2 1086.5 Topors 243.5 460.0 621.7 Ift52 694.7 923.9 1022.1 Gnat1 22.0 27.3 39.1 Cetn2 652.7 1302.6 1720.1 Whrn 126.6 179.0 254.5 Rp1l1 19.8 22.1 25.1 Wdr34 111.1 276.7 374.1 Tmem107 692.5 1486.0 1812.8 AK129341 43.8 56.3 78.6 Ttc26 68.1 191.3 289.9 Ift80 171.7 464.0 658.1 CEM 1 + Katnal2 19.9 30.2 45.1 Top 10 Genes Dync2li1 326.3 660.4 960.2 Bbs2 145.4 287.7 335.9 Dyx1c1 19.3 27.2 35.5 Wdr31 57.8 87.6 116.8

Null module GEO Series "GSE25737" 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=GSE25737 Status: Public on Mar 18 2011 Title: Geminin-regulated genes during neural fate acquisition of mouse embryonic stem cells Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21300881 Summary & Design: Summary: Formation of the complex vertebrate nervous system begins when pluripotent cells of the early embryo are directed to acquire a neural fate. Although cell intrinsic controls play an important role in this process, the molecular nature of this regulation is not well defined. Here we assessed the role for Geminin, a nuclear protein expressed in embryonic cells, in neural fate acquisition from mouse embryonic stem (ES) cells. While Geminin knockdown does not affect the ability of ES cells to maintain or exit pluripotency, we found that it significantly impairs their ability to acquire a neural fate. Conversely, Geminin overexpression promotes neural gene expression, even in the presence of growth factor signaling that antagonizes neural transcriptional responses. These data demonstrate that Geminins activity contributes to mammalian neural cell fate acquisition. We investigated the mechanistic basis of this phenomenon and found that Geminin maintains a hyperacetylated and open chromatin conformation at neural genes. Interestingly, recombinant Geminin protein also rapidly alters chromatin acetylation and accessibility even when Geminin is combined with nuclear extract and chromatin in vitro. These findings define a novel activity for Geminin in regulation of chromatin structure. Together, these data support a role for Geminin as a cell intrinsic regulator of neural fate acquisition that promotes expression of neural genes by regulating chromatin accessibility and histone acetylation. #!#

Overall design: Mouse embryonic stem cells were differentiated for two days in N2B27 medium, with or without Doxycycline-inducible shRNAmir knockdown of Geminin and compared by microarray. Three independent experiments were conducted, using two different mouse embryonic stem cell lines for Doxycycline-inducible knockdown of Geminin. The two ES lines express unique shRNAmir sequences targeting Geminin (shRNAmir #9 and #11) to control for off-target effects.

Background corr dist: KL-Divergence = 0.0255, L1-Distance = 0.0238, L2-Distance = 0.0006, Normal std = 0.7114

0.581 Kernel fit Pairwise Correlations Normal fit

Density 0.290

0.000 CEM 1

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

Pre-normalization Quantiles

E1-GemKDE1-uninduced (0.0830352)E2-GemKD (noE2-uninduced Dox) (0.0897587)E3-GemKD control (noE3-uninduced (0.0986304) Dox) (0.242501) control (no (0.196234) Dox) control[ (0.28984) min ] [ medium ] [ max ] CEM 1 Cep290 127.1 180.5 193.2 P ( S | Z, I ) = 0.00 Ift88 336.1 389.4 403.8 Mean Corr = 0.11427 Ift122 220.0 273.9 284.8 Nphp1 233.1 301.5 314.6 Wdr19 45.5 83.0 108.8 Arl3 2019.9 2332.4 2564.9 Ift57 742.7 919.2 959.1 Rp1 9.9 14.2 14.9 Tbcc 1521.0 1768.1 1892.3 Ttc8 395.9 450.2 474.7 Ift140 289.5 336.0 354.2 Iqcb1 738.0 860.2 893.3 Cetn1 3.7 11.6 14.6 Fam161a 9.8 41.2 46.3 Cetn3 4497.1 4680.2 5763.7 Myo7a 27.4 42.3 51.4 Kif3a 357.1 554.3 566.3 Topors 1585.0 1903.2 1960.8 Ift52 651.8 834.2 846.1 Gnat1 1.4 7.1 24.5 Cetn2 1223.3 1380.6 1542.7 Whrn 195.5 265.7 318.2 Rp1l1 10.8 22.2 28.7 Wdr34 761.2 985.1 1106.1 Tmem107 2098.5 2498.6 2584.9 AK129341 216.5 361.8 405.6 Ttc26 205.1 240.0 273.2 Ift80 426.0 468.3 493.0 CEM 1 + Katnal2 89.7 122.9 132.7 Top 10 Genes Dync2li1 496.0 692.6 727.5 Bbs2 217.2 239.2 271.0 Dyx1c1 27.8 53.8 69.4 Wdr31 299.8 330.9 393.7

Null module GEO Series "GSE46942" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 7 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE46942 Status: Public on May 16 2013 Title: Transcription Factor Foxo1 Controls Memory CD8+ T Cell Responses To Infection [Affymetrix] Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 23932570 Summary & Design: Summary: Memory T cells provide immunity against pathogen reinvasion, but mechanisms of their long-term maintenance is unclear. Here we show that mice with the deletion of the transcription factor Foxo1 in activated CD8+ T cells had defective secondary but not primary responses to Listeria monocytogenes infection. Compared to short-lived effector T cells, memory precursor effector T cells expressed higher amounts of Foxo1 that promoted their generation and maintenance. Gene expression profiling and chromatin immunoprecipitation sequencing experiments revealed the chemokine receptor CCR7 and the transcription factor TCF1 as novel Foxo1-bound target genes with critical functions in memory T cell trafficking and transcriptional regulation. These findings demonstrate that Foxo1 is selectively incorporated into the genetic program that regulates memory but not effector CD8+ T cell responses to infection.

Overall design: Wild-type and GzmB-cre Foxo1fl/fl CD27hiKLRG1lo OT-I T cells were isolated by FACS sorting at 7 days post LM-OVA infection. RNA was prepared with the miRNeasy kit according to the manufacturers instructions (Qiagen). RNA amplification, labeling and hybridization to Mouse 430 2.0 Array chips (Affymetrix) were carried out at the Genomics Core Facility of Memorial Sloan-Kettering Cancer Center.

Background corr dist: KL-Divergence = 0.0127, L1-Distance = 0.0277, L2-Distance = 0.0010, Normal std = 0.8280

0.482 Kernel fit Pairwise Correlations Normal fit

Density 0.241

0.000 CEM 1

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

Pre-normalization Quantiles

CD8+ wild-typeCD8+ Foxo1fl/flMPEC (0.245812) wild-typeMPEC (0.247282) wild-typeMPEC rep1 (0.137131)Foxo1fl/flMPEC rep2 (0.0644773)Foxo1fl/flSLEC rep1 wild-type(0.0749464) rep2 (0.0968477) (0.133503) [ min ] [ medium ] [ max ] CEM 1 Cep290 17.8 23.2 95.7 P ( S | Z, I ) = 0.00 Ift88 92.0 129.4 363.3 Mean Corr = 0.19803 Ift122 18.0 23.8 28.4 Nphp1 99.2 114.1 124.7 Wdr19 105.5 123.1 209.3 Arl3 1282.8 1558.8 2381.6 Ift57 229.6 323.3 510.5 Rp1 12.4 13.0 15.1 Tbcc 339.4 756.3 958.6 Ttc8 17.9 33.7 69.4 Ift140 396.2 450.3 1250.9 Iqcb1 67.6 79.6 149.5 Cetn1 17.9 19.7 23.3 Fam161a 124.7 158.3 220.0 Cetn3 2609.7 3047.5 3289.8 Myo7a 61.1 149.3 217.0 Kif3a 76.7 116.3 164.7 Topors 282.2 442.5 605.9 Ift52 939.7 1213.5 1321.5 Gnat1 22.8 31.0 72.9 Cetn2 1669.5 2237.6 2967.0 Whrn 164.7 190.7 366.8 Rp1l1 22.2 23.7 56.6 Wdr34 38.1 84.4 125.4 Tmem107 396.6 605.8 1106.0 AK129341 13.5 17.4 20.9 Ttc26 32.6 38.2 55.7 Ift80 275.8 378.2 2331.5 CEM 1 + Katnal2 33.2 33.6 39.7 Top 10 Genes Dync2li1 47.6 65.8 171.5 Bbs2 68.0 123.8 235.7 Dyx1c1 241.6 306.2 344.5 Wdr31 75.2 131.5 138.7

Null module GEO Series "GSE20696" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 8 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20696 Status: Public on Sep 30 2010 Title: Expression profiling of 3T3-L1 adipogenesis Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 20887899 Summary & Design: Summary: 3T3-L1 pre-adipocyte cells were grown to confluence and induced to differentiate in adipogeneic media.

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

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

0.651 Kernel fit Pairwise Correlations Normal fit

Density 0.325

0.000 CEM 1

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

Pre-normalization Quantiles

3T3-L1_t1_rep13T3-L1_t1_rep23T3-L1_t2_rep1 (0.0959779)3T3-L1_t2_rep2 (0.0913285)3T3-L1_t3_rep1 (0.14332)3T3-L1_t3_rep2 (0.129793)3T3-L1_t4_rep1 (0.161695)3T3-L1_t4_rep2 (0.0883497) (0.117438) (0.172098) [ min ] [ medium ] [ max ] CEM 1 Cep290 129.5 185.4 228.6 P ( S | Z, I ) = 0.00 Ift88 361.9 417.4 517.7 Mean Corr = 0.28974 Ift122 371.5 521.7 787.3 Nphp1 272.0 476.3 554.0 Wdr19 108.2 291.0 488.1 Arl3 4018.2 5563.6 6347.2 Ift57 607.5 1294.9 1590.9 Rp1 15.0 16.4 17.2 Tbcc 402.5 644.4 696.6 Ttc8 612.7 1308.0 1508.9 Ift140 517.4 648.1 722.2 Iqcb1 378.5 492.9 579.5 Cetn1 19.6 22.9 25.8 Fam161a 54.0 58.6 67.0 Cetn3 2138.1 2382.8 3072.6 Myo7a 37.1 153.0 211.1 Kif3a 642.1 895.3 1054.9 Topors 535.1 996.0 1105.9 Ift52 1029.4 1325.1 1461.7 Gnat1 24.6 27.5 33.4 Cetn2 1296.1 2021.5 2212.1 Whrn 118.4 147.6 163.1 Rp1l1 23.9 28.4 34.0 Wdr34 261.9 332.7 474.9 Tmem107 453.8 1407.9 2094.8 AK129341 34.8 37.9 42.9 Ttc26 91.8 388.2 591.4 Ift80 353.4 1193.5 1382.2 CEM 1 + Katnal2 27.1 52.2 144.3 Top 10 Genes Dync2li1 502.1 1006.8 1718.3 Bbs2 212.1 363.0 478.5 Dyx1c1 21.1 24.0 29.6 Wdr31 37.7 52.3 64.5

Null module GEO Series "GSE42061" 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=GSE42061 Status: Public on Nov 07 2012 Title: hyperlipidemia impaired innate response Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: To explore the effect of hyperlipidemia on macrophages' innate immune response to Porphyromonas gingivalis invasion

Overall design: 12 samples, 3 replicates in 4 groups, with cells from hyperlipidemic ApoE deficient mice and nonhyperlipidemic C57BL/6 mice stimulate with or without P.gingivalis(Pg)

Background corr dist: KL-Divergence = 0.0969, L1-Distance = 0.0429, L2-Distance = 0.0028, Normal std = 0.4676

0.895 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

Macrophages_hyperlipid_blank_rep1Macrophages_hyperlipid_blank_rep2Macrophages_hyperlipid_blank_rep3Macrophages_hyperlipid_Pg_rep1Macrophages_hyperlipid_Pg_rep2 Macrophages_hyperlipid_Pg_rep3(0.0867758) Macrophages_normallipid_blank_rep1(0.128133) Macrophages_normallipid_blank_rep2(0.102667) (0.0981376)Macrophages_normallipid_blank_rep3 (0.0668408)Macrophages_normallipid_Pg_rep1 (0.0818065)Macrophages_normallipid_Pg_rep2Macrophages_normallipid_Pg_rep3 (0.0578358) (0.0843707) (0.0626771) (0.0868926) (0.0683135)[ min (0.0755494) ] [ medium ] [ max ] CEM 1 Cep290 43.6 87.7 141.2 P ( S | Z, I ) = 0.00 Ift88 95.0 157.4 231.1 Mean Corr = 0.22733 Ift122 34.3 66.1 105.3 Nphp1 12.2 84.9 138.6 Wdr19 95.3 166.4 259.1 Arl3 1922.8 2479.2 3176.6 Ift57 804.8 1682.9 2047.2 Rp1 1.0 6.8 30.7 Tbcc 490.8 678.5 838.0 Ttc8 64.6 191.5 266.9 Ift140 169.4 254.6 324.2 Iqcb1 92.7 135.4 161.4 Cetn1 1.5 3.4 27.5 Fam161a 17.8 37.1 92.5 Cetn3 2700.8 3386.5 3842.3 Myo7a 286.8 530.2 659.0 Kif3a 468.6 903.0 1153.1 Topors 250.3 332.5 504.9 Ift52 529.3 849.3 955.2 Gnat1 1.4 15.2 27.8 Cetn2 1001.0 1657.4 1823.2 Whrn 43.8 111.7 166.9 Rp1l1 1.4 5.5 31.4 Wdr34 66.2 153.0 183.5 Tmem107 285.1 395.5 531.3 AK129341 1.3 21.7 36.8 Ttc26 7.7 43.8 84.9 Ift80 64.9 90.0 174.3 CEM 1 + Katnal2 1.6 6.5 56.2 Top 10 Genes Dync2li1 61.8 143.3 208.9 Bbs2 3.5 56.1 114.3 Dyx1c1 1.4 6.9 38.4 Wdr31 10.1 46.3 75.1

Null module GEO Series "GSE9441" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 36 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9441 Status: Public on Dec 07 2007 Title: The effect of sleep deprivation on gene expression in the brain and the liver of three inbred mouse strains Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 18077435 Summary & Design: Summary: These studies adress differential changes in gene expression between 6h sleep deprived and control mice in the brain and the liver. We profiled gene expression in three different inbred strains to understand the influence of genetic background.

Keywords: brain, genetic background, sleep deprivation

Overall design: Experiments were performed on male mice (C57BL/6J (B6), AKR/J (AK), DBA/2J (D2)), 12-13 weeks of aged, purchased from Jackson Laboratory. Animals were housed in a light/dark cycle of 24 hrs with water and food available ad libitum. Mice of the 3 inbred strains were sleep deprived for 6h starting at light onset (ZT0) and sacrificed together with their home-cage controls at ZT6 (n=9 / strain =3 / condition =2 / tissues =2; total = 108 mice).

Background corr dist: KL-Divergence = 0.0092, L1-Distance = 0.0360, L2-Distance = 0.0014, Normal std = 0.9491

0.436 Kernel fit Pairwise Correlations Normal fit

Density 0.218

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

B_AK_Control_ZTB_AK_Control_ZTB_AK_Control_ZT 6_1 B_AK_SleepDep_ZT(0.0334018) 6_2 B_AK_SleepDep_ZT(0.0367344) 6_3 B_AK_SleepDep_ZT(0.0400105) 6_1B_B6_Control_ZT (0.0258231) 6_2B_B6_Control_ZT (0.023829) 6_3B_B6_Control_ZT (0.0327633) 6_1 B_B6_SleepDep_ZT(0.0258533) 6_2 B_B6_SleepDep_ZT(0.0319374) 6_3 B_B6_SleepDep_ZT(0.0197545) 6_1B_D2_Control_ZT (0.0410923) 6_2B_D2_Control_ZT (0.0202511) 6_3B_D2_Control_ZT (0.0248604) 6_1 B_D2_SleepDep_ZT(0.0230513) 6_2 B_D2_SleepDep_ZT(0.0328628) 6_3 B_D2_SleepDep_ZT(0.0332278) 6_1L_AK_Control_ZT (0.0278879) 6_2L_AK_Control_ZT (0.0215157) 6_3L_AK_Control_ZT (0.0213597) 6_1 L_AK_SleepDep_ZT(0.0214601) 6_2 L_AK_SleepDep_ZT(0.037764) 6_3 L_AK_SleepDep_ZT(0.0237578) 6_1L_B6_Control_ZT (0.0192164) 6_2L_B6_Control_ZT (0.0212682) 6_3L_B6_Control_ZT (0.0307111) 6_1 (0.0297943)L_B6_SleepDep_ZT 6_2 (0.0248907)L_B6_SleepDep_ZT 6_3 (0.0319332)L_B6_SleepDep_ZT 6_1L_D2_Control_ZT (0.0253111) 6_2L_D2_Control_ZT (0.0234253) 6_3L_D2_Control_ZT (0.0320525) 6_1 (0.0215666)L_D2_SleepDep_ZT 6_2 (0.0266805)L_D2_SleepDep_ZT 6_3 (0.025866)L_D2_SleepDep_ZT 6_1 (0.0279869) 6_2 (0.0313326) 6_3 (0.028767)[ min ] [ medium ] [ max ] CEM 1 Cep290 32.2 50.4 93.4 P ( S | Z, I ) = 0.00 Ift88 138.9 269.4 421.9 Mean Corr = 0.17347 Ift122 53.6 228.0 501.7 Nphp1 216.4 399.8 569.9 Wdr19 76.1 284.9 360.9 Arl3 890.9 4486.7 6286.6 Ift57 75.3 795.9 1050.2 Rp1 30.6 37.8 44.4 Tbcc 365.0 795.1 1054.1 Ttc8 138.7 439.8 732.4 Ift140 306.7 507.8 727.1 Iqcb1 57.4 155.7 251.8 Cetn1 41.7 51.8 74.3 Fam161a 145.1 173.5 215.0 Cetn3 776.4 1179.2 1886.3 Myo7a 75.5 200.8 337.8 Kif3a 140.8 1074.6 2096.5 Topors 131.2 433.2 623.2 Ift52 476.9 754.6 1069.2 Gnat1 51.5 115.5 435.7 Cetn2 497.4 668.7 850.2 Whrn 165.1 249.9 363.0 Rp1l1 40.8 51.3 67.7 Wdr34 135.7 488.2 721.2 Tmem107 381.9 699.3 1157.4 AK129341 40.6 230.8 357.1 Ttc26 38.9 100.5 176.3 Ift80 74.1 360.3 530.6 CEM 1 + Katnal2 42.0 57.1 100.3 Top 10 Genes Dync2li1 105.9 381.3 517.2 Bbs2 79.8 337.0 621.8 Dyx1c1 39.5 50.9 67.5 Wdr31 71.6 98.1 167.7

Null module GEO Series "GSE8660" 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=GSE8660 Status: Public on Aug 01 2008 Title: C-terminal diversity within the p53 family accounts for differences in DNA binding and transcriptional activity Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 18267967 Summary & Design: Summary: The p53 family is known as a family of transcription factors with functions in tumor suppression and development. Whereas the central DNA binding domain is highly conserved among the three family members p53, p63 and p73, the C-terminal domains (CTDs) are diverse and subject to alternative splicing and post-translational modification. Here we demonstrate that the CTDs strongly influence DNA binding and transcriptional activity. While p53 and the p73 isoform p73gamma have basic CTDs and form weak sequence-specific protein-DNA complexes, the major p73 isoforms alpha, beta and delta have neutral CTDs and bind DNA strongly. A basic CTD has been previously shown to enable sliding along the DNA backbone and to facilitate the search for binding sites in the complex genome. Our experiments, however, reveal that a basic CTD also reduces protein-DNA complex stability, intranuclear mobility, promoter occupancy in vivo, transgene activation and induction of cell cycle arrest or apoptosis. A basic CTD in p53 and p73gamma therefore provides both positive and negative regulatory functions presumably to enable rapid switching of protein activity in response to stress. In contrast, most p73 isoforms exhibit constitutive DNA binding activity consistent with a predominant role in developmental control.

Keywords: Adenoviros, p73 / p53

Overall design: Infection of H1299 cell with different p73/p53 constructs by adenoviral system

Background corr dist: KL-Divergence = 0.0374, L1-Distance = 0.0263, L2-Distance = 0.0008, Normal std = 0.6403

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

p53 familyp53 members familyp53 members family inp53 myogenic members family inp53 myogenic members differentiationfamily inp53 myogenic members differentiationfamily in myogenic membersmockdifferentiation in myogenic 0 DeltaNp73differentiationh (0.150492)in myogenic DeltaNp73differentiation 0[ h min (0.141059) mockdifferentiation 6h 24(0.124722) DeltaNp72] h (0.285841) mock 24h 6[ (0.16055)h medium(0.137337) ] [ max ] CEM 1 Cep290 178.1 292.8 300.7 P ( S | Z, I ) = 0.00 Ift88 219.9 277.8 413.5 Mean Corr = 0.26328 Ift122 314.0 400.7 508.1 Nphp1 357.3 513.6 625.8 Wdr19 154.2 177.3 282.8 Arl3 1525.0 2093.5 2620.3 Ift57 903.8 1108.2 1166.7 Rp1 1.0 11.6 15.9 Tbcc 714.0 775.3 876.9 Ttc8 631.4 763.0 913.5 Ift140 585.5 705.2 793.7 Iqcb1 211.7 232.8 324.0 Cetn1 1.5 5.4 7.9 Fam161a 17.1 61.4 83.5 Cetn3 2222.3 2483.2 2743.4 Myo7a 4.3 8.8 13.3 Kif3a 901.9 1394.8 1546.3 Topors 497.1 666.6 801.9 Ift52 695.4 802.7 889.7 Gnat1 2.5 22.2 44.4 Cetn2 912.3 1102.1 2106.3 Whrn 47.7 68.2 146.1 Rp1l1 1.7 6.1 34.6 Wdr34 276.3 356.1 450.9 Tmem107 1972.9 2643.4 2942.4 AK129341 17.0 57.2 69.9 Ttc26 270.1 391.8 437.7 Ift80 476.2 595.9 718.9 CEM 1 + Katnal2 20.7 36.7 60.2 Top 10 Genes Dync2li1 457.0 606.6 1130.5 Bbs2 106.8 206.9 352.3 Dyx1c1 3.1 7.2 29.2 Wdr31 58.3 98.3 123.4

Null module GEO Series "GSE40087" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 15 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40087 Status: Public on Nov 13 2012 Title: Expression data from Middle Ear Mucosal Metaplasia in Mice Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: Chronic Otitis Media (OM) develops after sustained inflammation and is characterized by secretory middle ear epithelial metaplasia and effusion, most frequently mucoid. Non-typeable Haemophilus influenzae (NTHi), the most common acute OM pathogen, is known to activate inflammation and mucin expression in vitro and in animal models of OM. The goals of this study were to: examine expression profiling epithelial effects of NTHi challenge in murine middle ears.

We used microarrays to detail examine the global programme of gene expression underlying epithelial effects of NTHi challenge in murine middle ears during this study.

Overall design: Weekly transtympanic inoculation of Balb/c mice with 300 ´g/ml of NTHi lysates vs saline was performed. Bacteria were grown on chocolate agar at 37ÂºC in 5% CO2 overnight and inoculated in brain heart infusion (BHI) broth supplemented with 3.5 mg of nicotinamide adenine dinucleotide per ml. After overnight incubation, bacteria were subcultured into 5 ml of fresh brain heart infusion (BHI) and upon reaching log phase growth, NTHi were washed and suspended in phosphate-buffered saline (PBS) followed by sonication for lysis. Three transtympanic inoculation of 6 Balb/c mice middle ears (3 animals, 6 ears) with 50 uL of 300 ug/ml of NTHi bacterial lysate and 6 Balb/c mice middle ears (3 animals, 6 ears) with 50 uL of 1X phosphate buffered saline (PBS) were carried out weekly over 4 weeks (injection on days 7, 14, and 21). On day 28, the mice were euthanized and their bullae harvested. Expression microarray analysis was performed at 1 and 7 days. Microarray findings were validated in independent animal samples and in a cultured murine middle ear epithelial cell (mMEEC) line.

Background corr dist: KL-Divergence = 0.0855, L1-Distance = 0.0361, L2-Distance = 0.0025, Normal std = 0.4640

0.860 Kernel fit Pairwise Correlations Normal fit

Density 0.430

0.000 CEM 1

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

Pre-normalization Quantiles

S1 - salineS2 -treated salineS3 -treatedmouse, salineN1 -treated mouse, day1,NTHiN2 treated bio - mouse, dayNTHi rep1N3 1, treated mouse,-bio (0.0506737)dayNTHi rep2N4 1, treated mouse,-daybio NTHi(0.03563) rep3N51, biotreated mouse,-day NTHi(0.0238062) rep1 N61, biotreated mouse, -day(0.0731419) NTHi rep2 WT11, biotreated mouse, day(0.0459167) - rep3untreated WT27, bio mouse, day(0.0422592) - rep1untreated WT37, mouse, bio day(0.0665746) - rep2untreated S47, mouse,bio -(0.0922937) saline reprep3S5 mouse,bio1 - treated(0.0431802) (0.028036)saline repS6 bio2 - treatedmouse, (0.0600408)saline rep 3 treatedmouse,(0.0908067)day7, bio mouse,day7, rep1 bio (0.147166)day7, rep2[ biomin (0.0915575) rep3 (0.108917)] [ medium ] [ max ] CEM 1 Cep290 230.1 687.8 1208.8 P ( S | Z, I ) = 0.00 Ift88 780.7 1874.5 3202.7 Mean Corr = 0.24791 Ift122 151.5 332.9 545.5 Nphp1 498.8 1010.9 1531.7 Wdr19 577.1 937.5 1941.0 Arl3 5674.8 7986.7 10456.1 Ift57 2033.6 3150.9 5553.3 Rp1 2.0 20.4 78.8 Tbcc 630.2 879.8 1091.9 Ttc8 553.2 941.3 1523.8 Ift140 987.1 1714.3 2623.6 Iqcb1 224.3 327.6 608.5 Cetn1 1.6 7.9 30.2 Fam161a 1154.7 3229.8 6340.1 Cetn3 3235.5 4142.1 5194.5 Myo7a 35.7 80.9 336.7 Kif3a 533.1 954.6 1273.1 Topors 238.8 393.9 615.0 Ift52 723.7 982.4 1332.6 Gnat1 20.4 41.5 96.0 Cetn2 2081.1 3639.5 6311.9 Whrn 127.0 209.2 490.5 Rp1l1 6.7 25.1 67.2 Wdr34 322.2 952.4 2231.8 Tmem107 4123.0 10506.6 15739.8 AK129341 390.2 829.0 1561.5 Ttc26 391.9 693.9 1271.9 Ift80 501.0 1135.0 1722.1 CEM 1 + Katnal2 111.4 271.1 558.1 Top 10 Genes Dync2li1 1287.1 3096.9 6268.0 Bbs2 165.1 351.6 454.7 Dyx1c1 448.4 974.3 1944.4 Wdr31 144.3 240.5 394.0

Null module GEO Series "GSE11898" 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=GSE11898 Status: Public on Jun 27 2008 Title: Expression data from primary mesangial cells stimulated with DNA and RNA ligands Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21949095 Summary & Design: Summary: Extrarenal viral infections commonly trigger glomerulonephritis mostly in association with immune complex disease. The immunoglobulin component of immune complexes can activate glomerular cell Fc receptors but whether complexed viral nucleic acids contribute to glomerular inflammation remains unknown. Glomerular mesangial cells express TLR3 but lack TLR7-9, hence, it is unclear whether mesangial cells can recognize and respond to viral ssRNA or DNA. Here we studied the immune responses activated by 3P-RNA (5'Triphosphate RNA) and Non-CpG DNA (Double stranded DNA) in primary mesangial cells (PMC).

We used microarrays to detail the global programme of gene expression that induced by 3P-RNA and Non-CpG DNA.

Keywords: diffrent ligands

Overall design: PMC were stimulated with 3P-RNA and Non-CpG DNA for 6 hours and then total RNA was isolated for hybridization to MOE430_2 arrays.

Background corr dist: KL-Divergence = 0.0613, L1-Distance = 0.0257, L2-Distance = 0.0008, Normal std = 0.5353

0.763 Kernel fit Pairwise Correlations Normal fit

Density 0.382

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

lipofectaminelipofectamine atlipofectamine 6h-1 (0.21376)atNon-CpG 6h-2 (0.091301)atNon-CpG 6h-3 DNA (0.114002) Non-CpGat DNA6h-1 3P-RNA(0.100134)at DNA6h-2 3P-RNA(0.173992)at at 6h-3 6h-1 3P-RNA(0.0962838) (0.0567526)at 6h-2 (0.119733)at 6h-3 (0.034042) [ min ] [ medium ] [ max ] CEM 1 Cep290 51.4 66.1 74.8 P ( S | Z, I ) = 0.00 Ift88 146.6 163.1 225.2 Mean Corr = 0.10410 Ift122 54.0 71.8 131.3 Nphp1 788.7 889.8 1106.4 Wdr19 131.1 201.7 347.6 Arl3 4705.4 5200.5 5633.6 Ift57 638.4 748.6 856.1 Rp1 17.8 19.3 22.9 Tbcc 808.6 854.2 970.1 Ttc8 382.9 567.9 872.7 Ift140 240.9 275.3 494.4 Iqcb1 126.0 159.5 165.2 Cetn1 21.3 23.4 25.0 Fam161a 60.0 76.2 90.6 Cetn3 1755.5 1933.4 2104.5 Myo7a 159.6 267.0 681.1 Kif3a 573.9 648.3 717.0 Topors 557.6 647.0 685.4 Ift52 572.0 722.1 973.2 Gnat1 31.9 37.2 40.7 Cetn2 1001.5 1099.5 1197.3 Whrn 93.0 107.7 124.7 Rp1l1 19.6 25.6 33.2 Wdr34 223.5 348.4 576.1 Tmem107 1547.3 1926.1 2422.9 AK129341 19.8 22.4 28.3 Ttc26 284.9 413.0 472.5 Ift80 382.7 451.4 641.3 CEM 1 + Katnal2 24.9 27.3 31.9 Top 10 Genes Dync2li1 700.7 862.9 1059.9 Bbs2 124.6 196.0 330.1 Dyx1c1 16.9 24.0 28.9 Wdr31 45.5 57.4 63.0

Null module