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

Dataset: Num of genes in input gene set: 11 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. Tmem216 Tmem231 Tmem67 Tmem17 Cc2d2a Cep290 Tctn2 Mks1 Num ofGenesinQueryGeneset:11.CEMs:1. Overview ofCo-ExpressionModules(CEMs)withDatasetWeighting B9d1 B9d2 Ahi1

Tmem231 B9d1 Tmem216 Tctn2 Cep290 Cc2d2a Mks1 Tmem17 B9d2 Ahi1 Tmem67 CEM 1(19datasets) 0.0 Scale ofaveragePearsoncorrelations 0.2 0.4 0.6 0.8 1.0 1110051M20Rik 1110004E09Rik Symbol Num ofCEMGenes:11.Predicted338.SelectedDatasets:19.Strength:0.3 CEM 1,Geneset"[G]TCTN-B9Dcomplex",Page1 Tmem107 Tmem216 Tmem231 Fam179b Fam229b Dync2h1 Ccdc104 Dync2li1 Ccdc173 Tmem67 Tmem17 Traf3ip1 Cc2d2a Cep290 Ccp110 Spata7 Spice1 Nphp1 Nup35 Wdr31 Wdr34 Enkd1 Morn2 Otub2 Crocc Dnal4 Rabl2 Lekr1 Tctn2 Ttc26 Ift122 Lztfl1 Mks1 Dpcd Gas8 Bbs5 Bbs1 Bbs2 B9d2 B9d1 Rpgr Ahi1 Ttc8 Ift88 Ift80 Ift74 Arl3 Arl6 0.0 1.0

GSE31972 [6] GSE27630 [8]

GSE9441 [36] Only showingfirst200datasets-Seetxtoutputforfulldetails. GSE26299 [108] GSE29318 [9] GSE27605 [8] GSE15872 [18] GSE47196 [6] GSE31561 [36] GSE31797 [6] GSE34206 [8] GSE6540 [12] GSE28593 [9] GSE32529 [224] GSE16585 [31] GSE13106 [10] GSE21606 [6] GSE56777 [8] GSE45820 [6] GSE21568 [12] GSE32095 [24] GSE49346 [6] GSE23895 [18] GSE24726 [8] GSE27546 [51] GSE23408 [39] GSE4734 [61] GSE1871 [12] GSE54056 [12] GSE40087 [15] GSE22824 [24] GSE40412 [14] GSE10902 [6] GSE19729 [14] GSE49128 [17] GSE34126 [19] GSE16496 [102] GSE15760 [6] GSE9760 [12] GSE31940 [8] GSE53951 [10] GSE5245 [16] GSE51365 [28] GSE11165 [6] GSE34423 [40] GSE24695 [9] GSE34279 [30] GSE21193 [10] GSE12948 [9] GSE26476 [6] GSE27713 [7] GSE5671 [18] GSE5127 [18] GSE18396 [6] GSE31849 [18] GSE28457 [24] GSE40156 [42] GSE3181 [6] GSE21309 [9] GSE27195 [6] GSE50122 [10] GSE56482 [8] GSE7069 [8] GSE5313 [6] GSE15741 [6] GSE23200 [6] GSE4260 [6] GSE7141 [6] GSE28408 [6] GSE28823 [12] GSE20177 [14] GSE8357 [6] GSE40716 [12] GSE37431 [6] GSE33770 [8] GSE24813 [10] GSE13873 [27] GSE16110 [16] GSE17263 [6] GSE40856 [8] GSE17709 [18] GSE14004 [9] GSE38693 [8] GSE6383 [6] GSE16675 [72] GSE57425 [6] GSE29081 [6] GSE27675 [14] GSE36814 [20] GSE20954 [14] GSE22448 [6] GSE38215 [11] GSE21900 [12] GSE17794 [44] GSE36384 [12] GSE9338 [42] GSE6846 [6] GSE31744 [8] GSE32963 [6] GSE18010 [29] GSE31570 [6] GSE46797 [6] GSE30488 [52] GSE27568 [16] GSE15772 [8] GSE13227 [6] GSE27811 [9] GSE42601 [6] GSE45968 [6] GSE58296 [9] GSE42260 [6] GSE48203 [9] GSE13611 [8] GSE18907 [12] GSE14843 [6] GSE21393 [6] GSE11990 [20] GSE43713 [16] GSE48790 [8] GSE4695 [6] GSE18326 [8] GSE51483 [45] GSE47425 [7] GSE22073 [6] GSE48935 [12] GSE17316 [12] GSE39621 [51] GSE55238 [28] GSE18358 [10] GSE40230 [15] GSE15871 [18] GSE2527 [6] GSE34765 [6] GSE13563 [6] GSE38672 [6] GSE13421 [8] GSE4040 [6] GSE21755 [25] GSE17266 [59] GSE45143 [6] GSE27717 [11] GSE5891 [6] GSE23781 [6] GSE27159 [8] GSE6116 [70] GSE6875 [8] GSE4193 [8] GSE26308 [12] GSE58214 [6] GSE29648 [10] GSE57543 [6] GSE14007 [8] GSE35435 [6] GSE30873 [6] CEM+ CEM GSE11291 [60] GSE31208 [8] GSE31792 [18] GSE11572 [12] GSE4323 [6] GSE34839 [6] 0.0 GSE30863 [20] GSE40443 [6]

GSE9044 [6] Scale ofaveragePearsoncorrelations GSE7381 [6] GSE46209 [21] GSE28559 [30] GSE19338 [24] GSE39273 [6] GSE6285 [24] 0.2 GSE8024 [8] GSE8726 [7] GSE17553 [16] GSE13526 [6] GSE24207 [73] GSE4535 [6] GSE20570 [6] GSE40282 [6] GSE47872 [6] 0.4 GSE51608 [6] GSE6526 [16] GSE23600 [10] GSE17097 [20] GSE39391 [21] GSE10556 [6] GSE17886 [16] GSE15267 [8] GSE11386 [15] 0.6 GSE27378 [8] GSE15724 [9] GSE17112 [8] GSE13229 [6] GSE10113 [12] GSE43635 [9] GSE27261 [8] GSE46150 [8] GSE51108 [6] 0.8 GSE31938 [8] GSE8503 [6] GSE16874 [12] GSE46500 [6] Score 9.68 9.98 10.01 10.06 10.10 10.17 10.50 10.59 10.65 10.65 10.86 10.91 10.98 11.22 11.27 11.42 11.44 11.48 11.49 11.71 12.15 12.15 12.46 13.14 13.59 13.69 13.74 13.92 14.21 14.23 14.56 14.73 14.79 14.82 14.94 15.00 16.35 17.01 17.06 1.0 Notes 1810043G02Rik 2610301B20Rik Symbol Num ofCEMGenes:11.Predicted338.SelectedDatasets:19.Strength:0.3 CEM 1,Geneset"[G]TCTN-B9Dcomplex",Page2 Fam216a Ankdd1b Abhd14a Ccdc157 Efcab12 Chchd6 Ccdc39 Ccdc57 Dyx1c1 Mettl10 Btbd10 Cluap1 Pih1d2 Efcab7 Trim23 Zbtb26 Zfp446 Med31 Wdr35 Wdr78 Wdr47 Wdr60 Cops3 Wdr90 Wdr19 Cep19 Alms1 Cep41 Mdm1 Micu3 Pacrg Cetn2 Nme7 Nme5 Emc8 Stk30 Stk36 Pias2 Ttc25 Map9 Dph6 Cby1 Bbs9 Nek4 Tchp Lca5 Ttc5 Ift57 0.0 1.0

GSE31972 [6] GSE27630 [8]

GSE9441 [36] Only showingfirst200datasets-Seetxtoutputforfulldetails. GSE26299 [108] GSE29318 [9] GSE27605 [8] GSE15872 [18] GSE47196 [6] GSE31561 [36] GSE31797 [6] GSE34206 [8] GSE6540 [12] GSE28593 [9] GSE32529 [224] GSE16585 [31] GSE13106 [10] GSE21606 [6] GSE56777 [8] GSE45820 [6] GSE21568 [12] GSE32095 [24] GSE49346 [6] GSE23895 [18] GSE24726 [8] GSE27546 [51] GSE23408 [39] GSE4734 [61] GSE1871 [12] GSE54056 [12] GSE40087 [15] GSE22824 [24] GSE40412 [14] GSE10902 [6] GSE19729 [14] GSE49128 [17] GSE34126 [19] GSE16496 [102] GSE15760 [6] GSE9760 [12] GSE31940 [8] GSE53951 [10] GSE5245 [16] GSE51365 [28] GSE11165 [6] GSE34423 [40] GSE24695 [9] GSE34279 [30] GSE21193 [10] GSE12948 [9] GSE26476 [6] GSE27713 [7] GSE5671 [18] GSE5127 [18] GSE18396 [6] GSE31849 [18] GSE28457 [24] GSE40156 [42] GSE3181 [6] GSE21309 [9] GSE27195 [6] GSE50122 [10] GSE56482 [8] GSE7069 [8] GSE5313 [6] GSE15741 [6] GSE23200 [6] GSE4260 [6] GSE7141 [6] GSE28408 [6] GSE28823 [12] GSE20177 [14] GSE8357 [6] GSE40716 [12] GSE37431 [6] GSE33770 [8] GSE24813 [10] GSE13873 [27] GSE16110 [16] GSE17263 [6] GSE40856 [8] GSE17709 [18] GSE14004 [9] GSE38693 [8] GSE6383 [6] GSE16675 [72] GSE57425 [6] GSE29081 [6] GSE27675 [14] GSE36814 [20] GSE20954 [14] GSE22448 [6] GSE38215 [11] GSE21900 [12] GSE17794 [44] GSE36384 [12] GSE9338 [42] GSE6846 [6] GSE31744 [8] GSE32963 [6] GSE18010 [29] GSE31570 [6] GSE46797 [6] GSE30488 [52] GSE27568 [16] GSE15772 [8] GSE13227 [6] GSE27811 [9] GSE42601 [6] GSE45968 [6] GSE58296 [9] GSE42260 [6] GSE48203 [9] GSE13611 [8] GSE18907 [12] GSE14843 [6] GSE21393 [6] GSE11990 [20] GSE43713 [16] GSE48790 [8] GSE4695 [6] GSE18326 [8] GSE51483 [45] GSE47425 [7] GSE22073 [6] GSE48935 [12] GSE17316 [12] GSE39621 [51] GSE55238 [28] GSE18358 [10] GSE40230 [15] GSE15871 [18] GSE2527 [6] GSE34765 [6] GSE13563 [6] GSE38672 [6] GSE13421 [8] GSE4040 [6] GSE21755 [25] GSE17266 [59] GSE45143 [6] GSE27717 [11] GSE5891 [6] GSE23781 [6] GSE27159 [8] GSE6116 [70] GSE6875 [8] GSE4193 [8] GSE26308 [12] GSE58214 [6] GSE29648 [10] GSE57543 [6] GSE14007 [8] GSE35435 [6] GSE30873 [6] CEM+ CEM GSE11291 [60] GSE31208 [8] GSE31792 [18] GSE11572 [12] GSE4323 [6] GSE34839 [6] 0.0 GSE30863 [20] GSE40443 [6]

GSE9044 [6] Scale ofaveragePearsoncorrelations GSE7381 [6] GSE46209 [21] GSE28559 [30] GSE19338 [24] GSE39273 [6] GSE6285 [24] 0.2 GSE8024 [8] GSE8726 [7] GSE17553 [16] GSE13526 [6] GSE24207 [73] GSE4535 [6] GSE20570 [6] GSE40282 [6] GSE47872 [6] 0.4 GSE51608 [6] GSE6526 [16] GSE23600 [10] GSE17097 [20] GSE39391 [21] GSE10556 [6] GSE17886 [16] GSE15267 [8] GSE11386 [15] 0.6 GSE27378 [8] GSE15724 [9] GSE17112 [8] GSE13229 [6] GSE10113 [12] GSE43635 [9] GSE27261 [8] GSE46150 [8] GSE51108 [6] 0.8 GSE31938 [8] GSE8503 [6] GSE16874 [12] GSE46500 [6] Score 5.98 5.98 5.98 6.04 6.06 6.10 6.11 6.13 6.25 6.27 6.35 6.41 6.41 6.48 6.49 6.61 6.62 6.65 6.77 6.80 6.83 6.86 7.01 7.16 7.25 7.30 7.50 7.51 7.66 7.71 7.71 7.94 8.00 8.04 8.07 8.26 8.47 8.57 8.58 8.73 8.78 8.83 9.07 9.13 9.15 9.25 9.30 9.34 9.43 9.62 1.0 Notes B230118H07Rik A330021E22Rik Symbol Num ofCEMGenes:11.Predicted338.SelectedDatasets:19.Strength:0.3 CEM 1,Geneset"[G]TCTN-B9Dcomplex",Page3 AK129341 Hsp90aa1 Ccpg1os Rps6ka6 Ccdc181 Ankrd42 Prpsap2 Pwwp2a Fam98b Zswim1 Gemin8 Abhd10 Dzank1 Skiv2l2 Tada2a Gm166 Nap1l1 Trim37 Zfp329 Zfp763 Slc7a6 Glt8d1 Dalrd3 Wdr73 Cspp1 P4htm Ube3c Lyrm4 Bbs12 Soga2 Cep76 Elovl4 Tpgs2 Tusc3 Ccar2 Prps1 Btf3l4 Cetn4 Pcgf1 Pcgf6 Ift140 Fbxl2 Mns1 Prepl Eml1 Ppil4 Phc1 Iqcg 0.0 1.0

GSE31972 [6] GSE27630 [8]

GSE9441 [36] Only showingfirst200datasets-Seetxtoutputforfulldetails. GSE26299 [108] GSE29318 [9] GSE27605 [8] GSE15872 [18] GSE47196 [6] GSE31561 [36] GSE31797 [6] GSE34206 [8] GSE6540 [12] GSE28593 [9] GSE32529 [224] GSE16585 [31] GSE13106 [10] GSE21606 [6] GSE56777 [8] GSE45820 [6] GSE21568 [12] GSE32095 [24] GSE49346 [6] GSE23895 [18] GSE24726 [8] GSE27546 [51] GSE23408 [39] GSE4734 [61] GSE1871 [12] GSE54056 [12] GSE40087 [15] GSE22824 [24] GSE40412 [14] GSE10902 [6] GSE19729 [14] GSE49128 [17] GSE34126 [19] GSE16496 [102] GSE15760 [6] GSE9760 [12] GSE31940 [8] GSE53951 [10] GSE5245 [16] GSE51365 [28] GSE11165 [6] GSE34423 [40] GSE24695 [9] GSE34279 [30] GSE21193 [10] GSE12948 [9] GSE26476 [6] GSE27713 [7] GSE5671 [18] GSE5127 [18] GSE18396 [6] GSE31849 [18] GSE28457 [24] GSE40156 [42] GSE3181 [6] GSE21309 [9] GSE27195 [6] GSE50122 [10] GSE56482 [8] GSE7069 [8] GSE5313 [6] GSE15741 [6] GSE23200 [6] GSE4260 [6] GSE7141 [6] GSE28408 [6] GSE28823 [12] GSE20177 [14] GSE8357 [6] GSE40716 [12] GSE37431 [6] GSE33770 [8] GSE24813 [10] GSE13873 [27] GSE16110 [16] GSE17263 [6] GSE40856 [8] GSE17709 [18] GSE14004 [9] GSE38693 [8] GSE6383 [6] GSE16675 [72] GSE57425 [6] GSE29081 [6] GSE27675 [14] GSE36814 [20] GSE20954 [14] GSE22448 [6] GSE38215 [11] GSE21900 [12] GSE17794 [44] GSE36384 [12] GSE9338 [42] GSE6846 [6] GSE31744 [8] GSE32963 [6] GSE18010 [29] GSE31570 [6] GSE46797 [6] GSE30488 [52] GSE27568 [16] GSE15772 [8] GSE13227 [6] GSE27811 [9] GSE42601 [6] GSE45968 [6] GSE58296 [9] GSE42260 [6] GSE48203 [9] GSE13611 [8] GSE18907 [12] GSE14843 [6] GSE21393 [6] GSE11990 [20] GSE43713 [16] GSE48790 [8] GSE4695 [6] GSE18326 [8] GSE51483 [45] GSE47425 [7] GSE22073 [6] GSE48935 [12] GSE17316 [12] GSE39621 [51] GSE55238 [28] GSE18358 [10] GSE40230 [15] GSE15871 [18] GSE2527 [6] GSE34765 [6] GSE13563 [6] GSE38672 [6] GSE13421 [8] GSE4040 [6] GSE21755 [25] GSE17266 [59] GSE45143 [6] GSE27717 [11] GSE5891 [6] GSE23781 [6] GSE27159 [8] GSE6116 [70] GSE6875 [8] GSE4193 [8] GSE26308 [12] GSE58214 [6] GSE29648 [10] GSE57543 [6] GSE14007 [8] GSE35435 [6] GSE30873 [6] CEM+ CEM GSE11291 [60] GSE31208 [8] GSE31792 [18] GSE11572 [12] GSE4323 [6] GSE34839 [6] 0.0 GSE30863 [20] GSE40443 [6]

GSE9044 [6] Scale ofaveragePearsoncorrelations GSE7381 [6] GSE46209 [21] GSE28559 [30] GSE19338 [24] GSE39273 [6] GSE6285 [24] 0.2 GSE8024 [8] GSE8726 [7] GSE17553 [16] GSE13526 [6] GSE24207 [73] GSE4535 [6] GSE20570 [6] GSE40282 [6] GSE47872 [6] 0.4 GSE51608 [6] GSE6526 [16] GSE23600 [10] GSE17097 [20] GSE39391 [21] GSE10556 [6] GSE17886 [16] GSE15267 [8] GSE11386 [15] 0.6 GSE27378 [8] GSE15724 [9] GSE17112 [8] GSE13229 [6] GSE10113 [12] GSE43635 [9] GSE27261 [8] GSE46150 [8] GSE51108 [6] 0.8 GSE31938 [8] GSE8503 [6] GSE16874 [12] GSE46500 [6] Score 3.75 3.75 3.87 4.00 4.01 4.02 4.10 4.12 4.15 4.20 4.35 4.43 4.43 4.45 4.46 4.47 4.51 4.51 4.57 4.61 4.64 4.68 4.69 4.76 4.80 4.82 4.91 4.94 4.99 5.02 5.03 5.03 5.04 5.07 5.09 5.11 5.13 5.16 5.17 5.18 5.43 5.48 5.55 5.58 5.60 5.60 5.65 5.69 5.77 5.89 1.0 Notes A830010M20Rik 9530077C05Rik 1700007K13Rik 2210016L21Rik 1700029J07Rik Symbol Num ofCEMGenes:11.Predicted338.SelectedDatasets:19.Strength:0.3 CEM 1,Geneset"[G]TCTN-B9Dcomplex",Page4 Mphosph8 BC022687 Tmem138 Atp6v1g2 Fam188b Slc25a14 Slc25a12 Ankrd32 Ttc30a1 Fgfr1op Ccdc34 Vps13a Sssca1 Aarsd1 Dhrs13 Trim39 Pcnxl4 Zfp770 Zfp420 Tspyl4 Wdr77 Glcci1 Riiad1 Rab28 Pcbp3 Znhit3 Dtwd1 Eif1ax Zc3h6 Atmin Rsrc1 Nupl2 Spef1 Trps1 Map2 Actr8 Eno2 Bbs4 Eno4 Rad1 Ddx1 Eid2 Scai Taf3 Gtl3 0.0 1.0

GSE31972 [6] GSE27630 [8]

GSE9441 [36] Only showingfirst200datasets-Seetxtoutputforfulldetails. GSE26299 [108] GSE29318 [9] GSE27605 [8] GSE15872 [18] GSE47196 [6] GSE31561 [36] GSE31797 [6] GSE34206 [8] GSE6540 [12] GSE28593 [9] GSE32529 [224] GSE16585 [31] GSE13106 [10] GSE21606 [6] GSE56777 [8] GSE45820 [6] GSE21568 [12] GSE32095 [24] GSE49346 [6] GSE23895 [18] GSE24726 [8] GSE27546 [51] GSE23408 [39] GSE4734 [61] GSE1871 [12] GSE54056 [12] GSE40087 [15] GSE22824 [24] GSE40412 [14] GSE10902 [6] GSE19729 [14] GSE49128 [17] GSE34126 [19] GSE16496 [102] GSE15760 [6] GSE9760 [12] GSE31940 [8] GSE53951 [10] GSE5245 [16] GSE51365 [28] GSE11165 [6] GSE34423 [40] GSE24695 [9] GSE34279 [30] GSE21193 [10] GSE12948 [9] GSE26476 [6] GSE27713 [7] GSE5671 [18] GSE5127 [18] GSE18396 [6] GSE31849 [18] GSE28457 [24] GSE40156 [42] GSE3181 [6] GSE21309 [9] GSE27195 [6] GSE50122 [10] GSE56482 [8] GSE7069 [8] GSE5313 [6] GSE15741 [6] GSE23200 [6] GSE4260 [6] GSE7141 [6] GSE28408 [6] GSE28823 [12] GSE20177 [14] GSE8357 [6] GSE40716 [12] GSE37431 [6] GSE33770 [8] GSE24813 [10] GSE13873 [27] GSE16110 [16] GSE17263 [6] GSE40856 [8] GSE17709 [18] GSE14004 [9] GSE38693 [8] GSE6383 [6] GSE16675 [72] GSE57425 [6] GSE29081 [6] GSE27675 [14] GSE36814 [20] GSE20954 [14] GSE22448 [6] GSE38215 [11] GSE21900 [12] GSE17794 [44] GSE36384 [12] GSE9338 [42] GSE6846 [6] GSE31744 [8] GSE32963 [6] GSE18010 [29] GSE31570 [6] GSE46797 [6] GSE30488 [52] GSE27568 [16] GSE15772 [8] GSE13227 [6] GSE27811 [9] GSE42601 [6] GSE45968 [6] GSE58296 [9] GSE42260 [6] GSE48203 [9] GSE13611 [8] GSE18907 [12] GSE14843 [6] GSE21393 [6] GSE11990 [20] GSE43713 [16] GSE48790 [8] GSE4695 [6] GSE18326 [8] GSE51483 [45] GSE47425 [7] GSE22073 [6] GSE48935 [12] GSE17316 [12] GSE39621 [51] GSE55238 [28] GSE18358 [10] GSE40230 [15] GSE15871 [18] GSE2527 [6] GSE34765 [6] GSE13563 [6] GSE38672 [6] GSE13421 [8] GSE4040 [6] GSE21755 [25] GSE17266 [59] GSE45143 [6] GSE27717 [11] GSE5891 [6] GSE23781 [6] GSE27159 [8] GSE6116 [70] GSE6875 [8] GSE4193 [8] GSE26308 [12] GSE58214 [6] GSE29648 [10] GSE57543 [6] GSE14007 [8] GSE35435 [6] GSE30873 [6] CEM+ CEM GSE11291 [60] GSE31208 [8] GSE31792 [18] GSE11572 [12] GSE4323 [6] GSE34839 [6] 0.0 GSE30863 [20] GSE40443 [6]

GSE9044 [6] Scale ofaveragePearsoncorrelations GSE7381 [6] GSE46209 [21] GSE28559 [30] GSE19338 [24] GSE39273 [6] GSE6285 [24] 0.2 GSE8024 [8] GSE8726 [7] GSE17553 [16] GSE13526 [6] GSE24207 [73] GSE4535 [6] GSE20570 [6] GSE40282 [6] GSE47872 [6] 0.4 GSE51608 [6] GSE6526 [16] GSE23600 [10] GSE17097 [20] GSE39391 [21] GSE10556 [6] GSE17886 [16] GSE15267 [8] GSE11386 [15] 0.6 GSE27378 [8] GSE15724 [9] GSE17112 [8] GSE13229 [6] GSE10113 [12] GSE43635 [9] GSE27261 [8] GSE46150 [8] GSE51108 [6] 0.8 GSE31938 [8] GSE8503 [6] GSE16874 [12] GSE46500 [6] Score 2.72 2.73 2.76 2.77 2.77 2.77 2.84 2.86 2.87 2.92 2.92 2.93 2.94 2.94 2.95 2.97 2.98 3.02 3.10 3.11 3.11 3.14 3.19 3.19 3.22 3.26 3.26 3.27 3.27 3.27 3.29 3.29 3.30 3.32 3.42 3.42 3.47 3.56 3.56 3.56 3.57 3.57 3.57 3.59 3.62 3.72 3.72 3.73 3.73 3.74 1.0 Notes 9230110C19Rik 4933427D14Rik Symbol Num ofCEMGenes:11.Predicted338.SelectedDatasets:19.Strength:0.3 CEM 1,Geneset"[G]TCTN-B9Dcomplex",Page5 Tmem218 AI429214 Fam185a Map3k12 Dcun1d2 Psmc3ip Tbc1d19 Zscan18 Flywch2 Pm20d2 Smim13 Dynlrb2 Wrap73 Ube2v2 Mrps33 Kbtbd7 Pard6a Hnrnpr Zfp523 Thnsl1 Zfp653 Rangrf Lancl1 Pacrgl Wdr48 Acyp1 Ppp5c C2cd5 Spa17 Thyn1 Hirip3 Pfdn4 Nicn1 Zfp61 Dhps Bod1 Vbp1 Stip1 Nek1 Poc5 Ppil6 Lmln Pask Orc2 Mlh3 Ofd1 Rfx2 Ift43 0.0 1.0

GSE31972 [6] GSE27630 [8]

GSE9441 [36] Only showingfirst200datasets-Seetxtoutputforfulldetails. GSE26299 [108] GSE29318 [9] GSE27605 [8] GSE15872 [18] GSE47196 [6] GSE31561 [36] GSE31797 [6] GSE34206 [8] GSE6540 [12] GSE28593 [9] GSE32529 [224] GSE16585 [31] GSE13106 [10] GSE21606 [6] GSE56777 [8] GSE45820 [6] GSE21568 [12] GSE32095 [24] GSE49346 [6] GSE23895 [18] GSE24726 [8] GSE27546 [51] GSE23408 [39] GSE4734 [61] GSE1871 [12] GSE54056 [12] GSE40087 [15] GSE22824 [24] GSE40412 [14] GSE10902 [6] GSE19729 [14] GSE49128 [17] GSE34126 [19] GSE16496 [102] GSE15760 [6] GSE9760 [12] GSE31940 [8] GSE53951 [10] GSE5245 [16] GSE51365 [28] GSE11165 [6] GSE34423 [40] GSE24695 [9] GSE34279 [30] GSE21193 [10] GSE12948 [9] GSE26476 [6] GSE27713 [7] GSE5671 [18] GSE5127 [18] GSE18396 [6] GSE31849 [18] GSE28457 [24] GSE40156 [42] GSE3181 [6] GSE21309 [9] GSE27195 [6] GSE50122 [10] GSE56482 [8] GSE7069 [8] GSE5313 [6] GSE15741 [6] GSE23200 [6] GSE4260 [6] GSE7141 [6] GSE28408 [6] GSE28823 [12] GSE20177 [14] GSE8357 [6] GSE40716 [12] GSE37431 [6] GSE33770 [8] GSE24813 [10] GSE13873 [27] GSE16110 [16] GSE17263 [6] GSE40856 [8] GSE17709 [18] GSE14004 [9] GSE38693 [8] GSE6383 [6] GSE16675 [72] GSE57425 [6] GSE29081 [6] GSE27675 [14] GSE36814 [20] GSE20954 [14] GSE22448 [6] GSE38215 [11] GSE21900 [12] GSE17794 [44] GSE36384 [12] GSE9338 [42] GSE6846 [6] GSE31744 [8] GSE32963 [6] GSE18010 [29] GSE31570 [6] GSE46797 [6] GSE30488 [52] GSE27568 [16] GSE15772 [8] GSE13227 [6] GSE27811 [9] GSE42601 [6] GSE45968 [6] GSE58296 [9] GSE42260 [6] GSE48203 [9] GSE13611 [8] GSE18907 [12] GSE14843 [6] GSE21393 [6] GSE11990 [20] GSE43713 [16] GSE48790 [8] GSE4695 [6] GSE18326 [8] GSE51483 [45] GSE47425 [7] GSE22073 [6] GSE48935 [12] GSE17316 [12] GSE39621 [51] GSE55238 [28] GSE18358 [10] GSE40230 [15] GSE15871 [18] GSE2527 [6] GSE34765 [6] GSE13563 [6] GSE38672 [6] GSE13421 [8] GSE4040 [6] GSE21755 [25] GSE17266 [59] GSE45143 [6] GSE27717 [11] GSE5891 [6] GSE23781 [6] GSE27159 [8] GSE6116 [70] GSE6875 [8] GSE4193 [8] GSE26308 [12] GSE58214 [6] GSE29648 [10] GSE57543 [6] GSE14007 [8] GSE35435 [6] GSE30873 [6] CEM+ CEM GSE11291 [60] GSE31208 [8] GSE31792 [18] GSE11572 [12] GSE4323 [6] GSE34839 [6] 0.0 GSE30863 [20] GSE40443 [6]

GSE9044 [6] Scale ofaveragePearsoncorrelations GSE7381 [6] GSE46209 [21] GSE28559 [30] GSE19338 [24] GSE39273 [6] GSE6285 [24] 0.2 GSE8024 [8] GSE8726 [7] GSE17553 [16] GSE13526 [6] GSE24207 [73] GSE4535 [6] GSE20570 [6] GSE40282 [6] GSE47872 [6] 0.4 GSE51608 [6] GSE6526 [16] GSE23600 [10] GSE17097 [20] GSE39391 [21] GSE10556 [6] GSE17886 [16] GSE15267 [8] GSE11386 [15] 0.6 GSE27378 [8] GSE15724 [9] GSE17112 [8] GSE13229 [6] GSE10113 [12] GSE43635 [9] GSE27261 [8] GSE46150 [8] GSE51108 [6] 0.8 GSE31938 [8] GSE8503 [6] GSE16874 [12] GSE46500 [6] Score 1.73 1.77 1.77 1.78 1.79 1.80 1.84 1.90 1.90 1.90 1.95 1.96 1.97 1.97 2.00 2.02 2.04 2.05 2.05 2.06 2.08 2.10 2.10 2.12 2.13 2.14 2.19 2.20 2.21 2.21 2.23 2.24 2.27 2.27 2.27 2.29 2.30 2.37 2.37 2.37 2.43 2.46 2.49 2.51 2.55 2.64 2.64 2.65 2.67 2.70 1.0 Notes 1700088E04Rik Symbol Num ofCEMGenes:11.Predicted338.SelectedDatasets:19.Strength:0.3 CEM 1,Geneset"[G]TCTN-B9Dcomplex",Page6 Camsap1 Fam154b Ccdc113 Camkk1 Katnal2 Rab39b Stk11ip Mettl16 Syngr1 Maneal Osgin2 Ruvbl2 Ppm1d Alkbh6 Zfp689 Tspyl5 Neurl4 Map10 Rhpn1 Abhd8 Wdr66 Rsph9 Mrgbp Erlec1 Senp8 Hdac6 Klhl12 Dmxl2 Ascc1 Mettl3 Prmt5 Dyrk3 Nupl1 Tbpl1 Tctn3 Krt10 Nprl2 Ncdn Hap1 Sun1 Uba2 Eml5 Fn3k Sltm Rtca Klc3 Ift27 Tub Ilf2 0.0 1.0

GSE31972 [6] GSE27630 [8]

GSE9441 [36] Only showingfirst200datasets-Seetxtoutputforfulldetails. GSE26299 [108] GSE29318 [9] GSE27605 [8] GSE15872 [18] GSE47196 [6] GSE31561 [36] GSE31797 [6] GSE34206 [8] GSE6540 [12] GSE28593 [9] GSE32529 [224] GSE16585 [31] GSE13106 [10] GSE21606 [6] GSE56777 [8] GSE45820 [6] GSE21568 [12] GSE32095 [24] GSE49346 [6] GSE23895 [18] GSE24726 [8] GSE27546 [51] GSE23408 [39] GSE4734 [61] GSE1871 [12] GSE54056 [12] GSE40087 [15] GSE22824 [24] GSE40412 [14] GSE10902 [6] GSE19729 [14] GSE49128 [17] GSE34126 [19] GSE16496 [102] GSE15760 [6] GSE9760 [12] GSE31940 [8] GSE53951 [10] GSE5245 [16] GSE51365 [28] GSE11165 [6] GSE34423 [40] GSE24695 [9] GSE34279 [30] GSE21193 [10] GSE12948 [9] GSE26476 [6] GSE27713 [7] GSE5671 [18] GSE5127 [18] GSE18396 [6] GSE31849 [18] GSE28457 [24] GSE40156 [42] GSE3181 [6] GSE21309 [9] GSE27195 [6] GSE50122 [10] GSE56482 [8] GSE7069 [8] GSE5313 [6] GSE15741 [6] GSE23200 [6] GSE4260 [6] GSE7141 [6] GSE28408 [6] GSE28823 [12] GSE20177 [14] GSE8357 [6] GSE40716 [12] GSE37431 [6] GSE33770 [8] GSE24813 [10] GSE13873 [27] GSE16110 [16] GSE17263 [6] GSE40856 [8] GSE17709 [18] GSE14004 [9] GSE38693 [8] GSE6383 [6] GSE16675 [72] GSE57425 [6] GSE29081 [6] GSE27675 [14] GSE36814 [20] GSE20954 [14] GSE22448 [6] GSE38215 [11] GSE21900 [12] GSE17794 [44] GSE36384 [12] GSE9338 [42] GSE6846 [6] GSE31744 [8] GSE32963 [6] GSE18010 [29] GSE31570 [6] GSE46797 [6] GSE30488 [52] GSE27568 [16] GSE15772 [8] GSE13227 [6] GSE27811 [9] GSE42601 [6] GSE45968 [6] GSE58296 [9] GSE42260 [6] GSE48203 [9] GSE13611 [8] GSE18907 [12] GSE14843 [6] GSE21393 [6] GSE11990 [20] GSE43713 [16] GSE48790 [8] GSE4695 [6] GSE18326 [8] GSE51483 [45] GSE47425 [7] GSE22073 [6] GSE48935 [12] GSE17316 [12] GSE39621 [51] GSE55238 [28] GSE18358 [10] GSE40230 [15] GSE15871 [18] GSE2527 [6] GSE34765 [6] GSE13563 [6] GSE38672 [6] GSE13421 [8] GSE4040 [6] GSE21755 [25] GSE17266 [59] GSE45143 [6] GSE27717 [11] GSE5891 [6] GSE23781 [6] GSE27159 [8] GSE6116 [70] GSE6875 [8] GSE4193 [8] GSE26308 [12] GSE58214 [6] GSE29648 [10] GSE57543 [6] GSE14007 [8] GSE35435 [6] GSE30873 [6] CEM+ CEM GSE11291 [60] GSE31208 [8] GSE31792 [18] GSE11572 [12] GSE4323 [6] GSE34839 [6] 0.0 GSE30863 [20] GSE40443 [6]

GSE9044 [6] Scale ofaveragePearsoncorrelations GSE7381 [6] GSE46209 [21] GSE28559 [30] GSE19338 [24] GSE39273 [6] GSE6285 [24] 0.2 GSE8024 [8] GSE8726 [7] GSE17553 [16] GSE13526 [6] GSE24207 [73] GSE4535 [6] GSE20570 [6] GSE40282 [6] GSE47872 [6] 0.4 GSE51608 [6] GSE6526 [16] GSE23600 [10] GSE17097 [20] GSE39391 [21] GSE10556 [6] GSE17886 [16] GSE15267 [8] GSE11386 [15] 0.6 GSE27378 [8] GSE15724 [9] GSE17112 [8] GSE13229 [6] GSE10113 [12] GSE43635 [9] GSE27261 [8] GSE46150 [8] GSE51108 [6] 0.8 GSE31938 [8] GSE8503 [6] GSE16874 [12] GSE46500 [6] Score 0.75 0.77 0.78 0.79 0.80 0.82 0.82 0.82 0.84 0.85 0.94 0.96 0.96 0.99 1.01 1.02 1.03 1.05 1.07 1.08 1.10 1.11 1.13 1.15 1.19 1.24 1.25 1.25 1.26 1.28 1.28 1.30 1.31 1.34 1.36 1.37 1.42 1.45 1.47 1.56 1.60 1.60 1.61 1.62 1.66 1.69 1.69 1.69 1.69 1.73 1.0 Notes 1700003M02Rik 2610524H06Rik 4930430F08Rik Symbol Num ofCEMGenes:11.Predicted338.SelectedDatasets:19.Strength:0.3 CEM 1,Geneset"[G]TCTN-B9Dcomplex",Page7 Mphosph6 Hist2h2be Arhgap39 Rbm12b2 Trp53bp1 Zfp322a Ndufaf3 Enoph1 Cacybp Ccdc64 Ccdc96 Zc3h14 Tardbp Bzrap1 Rbm48 Smim8 Ptp4a3 Pam16 Rasal2 Ttc30b Wdr16 Rpap3 Rsbn1 Acbd7 Spag6 Ewsr1 Wwox Dimt1 Fopnl Scaf8 Plch1 Lsm8 Taf1a Wdr6 Dph3 Sub1 Tbcc Rrn3 Adal Cdyl Syt9 Iffo1 Azi1 Ttll1 Pifo Itpa 0.0 1.0

GSE31972 [6] GSE27630 [8]

GSE9441 [36] Only showingfirst200datasets-Seetxtoutputforfulldetails. GSE26299 [108] GSE29318 [9] GSE27605 [8] GSE15872 [18] GSE47196 [6] GSE31561 [36] GSE31797 [6] GSE34206 [8] GSE6540 [12] GSE28593 [9] GSE32529 [224] GSE16585 [31] GSE13106 [10] GSE21606 [6] GSE56777 [8] GSE45820 [6] GSE21568 [12] GSE32095 [24] GSE49346 [6] GSE23895 [18] GSE24726 [8] GSE27546 [51] GSE23408 [39] GSE4734 [61] GSE1871 [12] GSE54056 [12] GSE40087 [15] GSE22824 [24] GSE40412 [14] GSE10902 [6] GSE19729 [14] GSE49128 [17] GSE34126 [19] GSE16496 [102] GSE15760 [6] GSE9760 [12] GSE31940 [8] GSE53951 [10] GSE5245 [16] GSE51365 [28] GSE11165 [6] GSE34423 [40] GSE24695 [9] GSE34279 [30] GSE21193 [10] GSE12948 [9] GSE26476 [6] GSE27713 [7] GSE5671 [18] GSE5127 [18] GSE18396 [6] GSE31849 [18] GSE28457 [24] GSE40156 [42] GSE3181 [6] GSE21309 [9] GSE27195 [6] GSE50122 [10] GSE56482 [8] GSE7069 [8] GSE5313 [6] GSE15741 [6] GSE23200 [6] GSE4260 [6] GSE7141 [6] GSE28408 [6] GSE28823 [12] GSE20177 [14] GSE8357 [6] GSE40716 [12] GSE37431 [6] GSE33770 [8] GSE24813 [10] GSE13873 [27] GSE16110 [16] GSE17263 [6] GSE40856 [8] GSE17709 [18] GSE14004 [9] GSE38693 [8] GSE6383 [6] GSE16675 [72] GSE57425 [6] GSE29081 [6] GSE27675 [14] GSE36814 [20] GSE20954 [14] GSE22448 [6] GSE38215 [11] GSE21900 [12] GSE17794 [44] GSE36384 [12] GSE9338 [42] GSE6846 [6] GSE31744 [8] GSE32963 [6] GSE18010 [29] GSE31570 [6] GSE46797 [6] GSE30488 [52] GSE27568 [16] GSE15772 [8] GSE13227 [6] GSE27811 [9] GSE42601 [6] GSE45968 [6] GSE58296 [9] GSE42260 [6] GSE48203 [9] GSE13611 [8] GSE18907 [12] GSE14843 [6] GSE21393 [6] GSE11990 [20] GSE43713 [16] GSE48790 [8] GSE4695 [6] GSE18326 [8] GSE51483 [45] GSE47425 [7] GSE22073 [6] GSE48935 [12] GSE17316 [12] GSE39621 [51] GSE55238 [28] GSE18358 [10] GSE40230 [15] GSE15871 [18] GSE2527 [6] GSE34765 [6] GSE13563 [6] GSE38672 [6] GSE13421 [8] GSE4040 [6] GSE21755 [25] GSE17266 [59] GSE45143 [6] GSE27717 [11] GSE5891 [6] GSE23781 [6] GSE27159 [8] GSE6116 [70] GSE6875 [8] GSE4193 [8] GSE26308 [12] GSE58214 [6] GSE29648 [10] GSE57543 [6] GSE14007 [8] GSE35435 [6] GSE30873 [6] CEM+ CEM GSE11291 [60] GSE31208 [8] GSE31792 [18] GSE11572 [12] GSE4323 [6] GSE34839 [6] 0.0 GSE30863 [20] GSE40443 [6]

GSE9044 [6] Scale ofaveragePearsoncorrelations GSE7381 [6] GSE46209 [21] GSE28559 [30] GSE19338 [24] GSE39273 [6] GSE6285 [24] 0.2 GSE8024 [8] GSE8726 [7] GSE17553 [16] GSE13526 [6] GSE24207 [73] GSE4535 [6] GSE20570 [6] GSE40282 [6] GSE47872 [6] 0.4 GSE51608 [6] GSE6526 [16] GSE23600 [10] GSE17097 [20] GSE39391 [21] GSE10556 [6] GSE17886 [16] GSE15267 [8] GSE11386 [15] 0.6 GSE27378 [8] GSE15724 [9] GSE17112 [8] GSE13229 [6] GSE10113 [12] GSE43635 [9] GSE27261 [8] GSE46150 [8] GSE51108 [6] 0.8 GSE31938 [8] GSE8503 [6] GSE16874 [12] GSE46500 [6] Score 0.01 0.02 0.05 0.05 0.06 0.07 0.08 0.09 0.11 0.13 0.13 0.14 0.17 0.17 0.18 0.19 0.22 0.23 0.24 0.24 0.26 0.36 0.36 0.37 0.38 0.38 0.38 0.41 0.42 0.46 0.47 0.48 0.48 0.49 0.50 0.51 0.52 0.54 0.55 0.56 0.56 0.60 0.61 0.61 0.64 0.68 0.72 0.73 0.74 1.0 Notes 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 (0.210893)OE MmICAM1-positive-2 (0.147735) OE MmICAM1-negative-3 (0.125148)OE ICAM1-positive-3 (0.202064) (0.209495) (0.104666)[ min ] [ medium ] [ max ] CEM 1 Tmem231 347.0 718.9 1098.8 P ( S | Z, I ) = 1.00 B9d1 313.9 1540.2 1855.4 Mean Corr = 0.78178Tmem216 346.5 697.5 749.3 Tctn2 492.9 605.3 802.0 Cep290 260.1 415.1 975.8 Cc2d2a 1128.5 1364.5 1504.6 Mks1 167.7 380.6 416.6 Tmem17 36.9 106.6 189.5 B9d2 330.0 735.8 894.8 Ahi1 1.7 20.1 78.7 Tmem67 4.6 69.2 108.5 Nphp1 416.9 799.9 946.3 Tmem107 2422.0 9119.1 11899.8 Ttc26 240.7 823.9 1062.5 Arl6 1086.0 5848.6 6608.4 Ccdc173 83.0 242.6 620.6 CEM 1 + Enkd1 154.8 399.2 432.1 Top 10 Genes Bbs2 520.5 808.0 916.2 Wdr34 465.6 1348.5 1653.1 Bbs1 488.8 2231.1 2829.3 Rabl2 278.0 1756.2 2102.2

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 (0.178016) [biological atwildtype min replicate miceE13,from 2 (0.147957) biologicalatwildtype replicate miceE13, ]3 (0.0669719) biologicalat mice E13, replicate4 (0.0913978) biologicalat[ E13, replicatemedium 1 (0.0682207) biological replicate 2 (0.0788559) replicate 3 (0.181084)] 4 (0.187496)[ max ] CEM 1 Tmem231 780.2 1026.0 1178.2 P ( S | Z, I ) = 1.00 B9d1 1601.5 2397.0 3121.8 Mean Corr = 0.73250Tmem216 426.1 607.7 704.1 Tctn2 708.8 1239.4 1373.4 Cep290 129.2 190.9 230.7 Cc2d2a 641.7 940.1 1081.7 Mks1 323.1 375.6 395.1 Tmem17 165.4 255.5 347.8 B9d2 558.7 635.7 696.6 Ahi1 36.8 45.5 64.3 Tmem67 51.3 61.0 72.9 Nphp1 1459.9 2484.8 2721.1 Tmem107 4945.1 8498.7 10972.3 Ttc26 472.6 696.2 796.0 Arl6 3500.6 5879.9 6761.4 Ccdc173 279.2 433.1 538.4 CEM 1 + Enkd1 330.0 431.3 502.2 Top 10 Genes Bbs2 498.1 787.0 838.1 Wdr34 773.3 1301.0 1446.1 Bbs1 694.9 1312.3 1441.1 Rabl2 2052.7 2301.5 2689.9

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(0.0445791) 6_2 B_AK_SleepDep_ZT(0.023594) 6_3 B_AK_SleepDep_ZT(0.0411282) 6_1B_B6_Control_ZT (0.0357606) 6_2B_B6_Control_ZT (0.03197) 6_3B_B6_Control_ZT (0.0304651) 6_1 B_B6_SleepDep_ZT(0.0217034) 6_2 B_B6_SleepDep_ZT(0.0263846) 6_3 B_B6_SleepDep_ZT(0.0202418) 6_1B_D2_Control_ZT (0.0551248) 6_2B_D2_Control_ZT (0.0167682) 6_3B_D2_Control_ZT (0.0427211) 6_1 B_D2_SleepDep_ZT(0.0264715) 6_2 B_D2_SleepDep_ZT(0.0279572) 6_3 B_D2_SleepDep_ZT(0.015292) 6_1L_AK_Control_ZT (0.0254471) 6_2L_AK_Control_ZT (0.021607) 6_3L_AK_Control_ZT (0.021841) 6_1 L_AK_SleepDep_ZT(0.0156891) 6_2 L_AK_SleepDep_ZT(0.0245138) 6_3 L_AK_SleepDep_ZT(0.0193419) 6_1L_B6_Control_ZT (0.0255837) 6_2L_B6_Control_ZT (0.026283) 6_3L_B6_Control_ZT (0.0273437) 6_1 (0.0186895)L_B6_SleepDep_ZT 6_2 (0.0243818)L_B6_SleepDep_ZT 6_3 (0.0232809)L_B6_SleepDep_ZT 6_1L_D2_Control_ZT (0.0268826) 6_2L_D2_Control_ZT (0.0231893) 6_3L_D2_Control_ZT (0.0270014) 6_1 (0.0231343)L_D2_SleepDep_ZT 6_2 (0.0412535)L_D2_SleepDep_ZT 6_3 (0.0228319)L_D2_SleepDep_ZT 6_1 (0.0252181) 6_2 (0.0459176) 6_3 (0.0304071)[ min ] [ medium ] [ max ] CEM 1 Tmem231 119.4 378.2 477.9 P ( S | Z, I ) = 1.00 B9d1 91.8 417.0 781.7 Mean Corr = 0.71805Tmem216 64.6 167.7 251.8 Tctn2 50.8 182.1 307.6 Cep290 32.2 50.4 93.4 Cc2d2a 96.1 308.5 471.1 Mks1 104.3 135.9 196.3 Tmem17 33.9 59.3 75.0 B9d2 229.6 530.3 698.8 Ahi1 37.3 183.8 1021.7 Tmem67 42.9 55.9 73.9 Nphp1 216.4 399.8 569.9 Tmem107 381.9 699.3 1157.4 Ttc26 38.9 100.5 176.3 Arl6 103.8 597.3 1129.9 Ccdc173 36.6 47.9 72.8 CEM 1 + Enkd1 56.7 146.2 273.7 Top 10 Genes Bbs2 79.8 337.0 621.8 Wdr34 135.7 488.2 721.2 Bbs1 46.8 312.9 435.5 Rabl2 108.6 617.8 909.4

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 "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 (0.266846) cellsretinal biologicalsorted PN0 repliacteFAC positive2 (0.178022) cellsretinal biologicalsorted repliacte positive3 FAC (0.165721)cells biological sortedrepliacte positive 1FAC [(0.0935248) min biological sortedrepliacte 2FAC (0.0592561) biologicalsorted] 3repliacte (0.0394425) biological repliacte 1 (0.0694124)[ medium repliacte 2 (0.0573105) 3 (0.0704647) ] [ max ] CEM 1 Tmem231 515.2 597.2 1093.0 P ( S | Z, I ) = 1.00 B9d1 671.9 927.1 2388.4 Mean Corr = 0.64276Tmem216 488.5 534.2 733.0 Tctn2 306.6 383.5 718.1 Cep290 223.2 398.2 1755.9 Cc2d2a 770.6 910.4 2629.0 Mks1 452.0 604.5 1011.2 Tmem17 99.3 117.9 292.1 B9d2 904.1 1200.9 1631.1 Ahi1 43.5 68.4 212.6 Tmem67 49.5 58.8 90.1 Nphp1 661.1 806.0 1123.6 Tmem107 2685.3 3846.6 7186.7 Ttc26 346.6 483.2 598.7 Arl6 1520.8 2413.8 11871.2 Ccdc173 125.4 209.9 389.9 CEM 1 + Enkd1 259.7 487.7 836.0 Top 10 Genes Bbs2 703.4 946.9 2068.0 Wdr34 475.9 625.8 1231.2 Bbs1 712.6 894.2 2609.1 Rabl2 1821.6 2350.0 3583.1

Null module GEO Series "GSE27605" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 8 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

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

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

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

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

0.614 Kernel fit Pairwise Correlations Normal fit

Density 0.307

0.000 CEM 1

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

Pre-normalization Quantiles

intestine-Lgr5High-R1intestine-Lgr5Low-R1intestine-EphB2High-R1 intestine-EphB2Medium-R1(0.205157) (0.0480076)intestine-EphB2Low-R1intestine-EphB2High-R2 (0.126699)intestine-EphB2Medium-R2 (0.0254021)intestine-EphB2Low-R2 (0.181618) (0.130999) (0.0512126) (0.230905)[ min ] [ medium ] [ max ] CEM 1 Tmem231 18.4 61.3 128.7 P ( S | Z, I ) = 1.00 B9d1 75.9 372.2 634.0 Mean Corr = 0.62142Tmem216 216.8 500.6 691.4 Tctn2 72.3 113.0 175.2 Cep290 77.9 112.0 143.9 Cc2d2a 127.5 600.0 1001.6 Mks1 89.3 246.0 314.4 Tmem17 46.3 133.9 184.1 B9d2 49.3 85.7 132.1 Ahi1 8.0 11.1 12.1 Tmem67 6.2 9.4 11.8 Nphp1 62.8 125.4 203.5 Tmem107 175.0 921.1 1330.1 Ttc26 12.8 49.7 83.1 Arl6 32.7 63.3 106.8 Ccdc173 16.0 36.1 60.1 CEM 1 + Enkd1 33.1 200.8 308.0 Top 10 Genes Bbs2 343.5 576.4 738.7 Wdr34 87.8 440.5 677.8 Bbs1 17.7 32.2 61.0 Rabl2 71.1 156.4 269.5

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(0.0452044) rep2pylorus at biological E14.5, (0.0335729) rep3duodenum at biological E14.5, (0.0492371) rep1duodenum biological(0.00872245) at rep2 E14.5,duodenum (0.0612993) at rep3biological E14.5,stomach (0.0298568) at biological E14.5,stomach rep1 at E16.5, biological(0.0470015)stomach rep2 at biological E16.5, (0.0376932)pylorus rep3 at biological E16.5, (0.065255)rep1pylorus at E16.5, biological(0.0405818) rep2pylorus at biological E16.5, (0.0314829) rep3duodenum at biological E16.5, (0.0221392) rep1duodenum biological(0.028053) at rep2 E16.5,duodenum (0.0242746) at rep3biological E16.5, (0.0482833) at biological E16.5, rep1 biological(0.184299) rep2 (0.103472)[ rep3 min (0.139571) ] [ medium ] [ max ] CEM 1 Tmem231 125.9 249.0 315.6 P ( S | Z, I ) = 1.00 B9d1 178.5 515.5 796.9 Mean Corr = 0.61174Tmem216 152.2 430.5 507.8 Tctn2 58.9 139.9 209.1 Cep290 57.3 109.3 136.6 Cc2d2a 241.5 551.3 665.9 Mks1 99.3 187.1 230.2 Tmem17 27.5 39.1 44.8 B9d2 253.7 411.1 497.4 Ahi1 23.4 38.0 57.2 Tmem67 20.2 26.6 27.9 Nphp1 257.0 533.7 580.9 Tmem107 692.5 1486.0 1812.8 Ttc26 68.1 191.3 289.9 Arl6 209.4 613.8 824.4 Ccdc173 22.2 34.6 45.5 CEM 1 + Enkd1 75.1 225.8 283.2 Top 10 Genes Bbs2 145.4 287.7 335.9 Wdr34 111.1 276.7 374.1 Bbs1 43.9 108.6 166.0 Rabl2 231.3 616.5 697.8

Null module GEO Series "GSE47196" 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=GSE47196 Status: Public on May 23 2013 Title: Immunoglobulin-like domain receptor 1 mediates fat-stimulated cholecystokinin secretion. Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 23863714 Summary & Design: Summary: Cholecystokinin (CCK) is a satiety hormone produced by discrete enteroendocrine cells scattered among absorptive cells of the small intestine. CCK is released into blood following a meal; however, the mechanisms inducing hormone secretion are largely unknown. Ingested fat is the major stimulant of CCK secretion. We recently identified a novel member of the lipoprotein remnant receptor family known as immunoglobulin-like domain containing receptor 1 (ILDR1) in intestinal CCK cells and postulated that this receptor conveyed the signal for fat-stimulated CCK secretion. In the intestine, ILDR1 is expressed exclusively in CCK cells. Orogastric administration of fatty acids elevated blood levels of CCK in wild type but not ILDR1-deficient mice, although the CCK secretory response to trypsin inhibitor was retained. The uptake of fluorescently labeled lipoproteins in ILDR1-transfected CHO cells and release of CCK from isolated intestinal cells required a unique combination of fatty acid plus HDL. CCK secretion secondary to ILDR1 activation is associated with increased [Ca2+]i consistent with regulated hormone release. These findings demonstrate that ILDR1 regulates CCK release through a mechanism dependent on fatty acids and lipoproteins and that absorbed fatty acids regulate gastrointestinal hormone secretion.

Overall design: GFP positive cells from CCK-EGFP transgenic mice were isolated by FACS and the expression profile was compared with an equal number of non-fluorescent intestinal cells.

Background corr dist: KL-Divergence = 0.0167, L1-Distance = 0.0318, L2-Distance = 0.0015, Normal std = 0.7899

0.505 Kernel fit Pairwise Correlations Normal fit

Density 0.253

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

IntestinalIntestinal CCK-EGFPIntestinal non-EGFP cellsIntestinal CCK-EGFP rep1 cellsIntestinal (0.219743)non-EGFP rep1 cellsIntestinal (0.14141) non-EGFP rep2 cells (0.285424)CCK-EGFP rep2 cells (0.153181) rep3 cells (0.103304) rep3[ (0.0969383)min ] [ medium ] [ max ] CEM 1 Tmem231 15.4 134.8 197.9 P ( S | Z, I ) = 1.00 B9d1 47.2 715.6 1123.4 Mean Corr = 0.60964Tmem216 46.2 302.6 477.3 Tctn2 44.8 161.4 214.6 Cep290 38.1 172.5 808.1 Cc2d2a 28.6 584.9 1286.4 Mks1 78.8 164.5 282.3 Tmem17 12.5 46.0 71.5 B9d2 111.2 243.9 296.7 Ahi1 7.5 9.1 11.5 Tmem67 8.1 15.9 22.5 Nphp1 47.7 262.5 403.8 Tmem107 11.6 382.9 457.7 Ttc26 17.3 76.8 165.6 Arl6 10.8 167.2 305.7 Ccdc173 19.0 99.3 146.8 CEM 1 + Enkd1 23.2 54.6 84.2 Top 10 Genes Bbs2 332.5 992.0 1273.0 Wdr34 30.8 294.7 331.8 Bbs1 10.8 120.4 139.7 Rabl2 16.3 87.5 177.9

Null module GEO Series "GSE31561" 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=GSE31561 Status: Public on Feb 19 2013 Title: Transcriptional analysis of organ-specific toxicity induced by a panPPAR agonist in mice: Identification of organ-specific toxicity biomarkers Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 23272042 Summary & Design: Summary: In this study, we aim to identify candidate biomarkers which may be useful as surrogate indicators of toxicity for pre-clinical development of panPPAR-agonist drug candidates. Gene expression microarray, histopathology and clinical chemistry data were generated from liver, heart, kidney and skeletal muscles of three groups of mice administered with three different dosages of an experimental pan-peroxisome proliferator-activated receptor (pan-PPAR) agonist, PPM-201, for 14 days. The histopathology and clinical chemistry data were compared with the gene expression analysis and candidate biomarker genes were identified.

Overall design: Nine wild type mice (strain: C57BL/6J) were randomly divided into three groups - Group-I, II and III. PPM-201 in the vehicle base was administered daily for 14 days at 6 mg/kg body weight dose rate to each mouse in Group-II and at 20mg/kg body weight dose rate to each mouse in Group-III while the mice in Group-I received only the vehicle base. On 15th day, the mice were sacrificed to harvest blood, heart, skeletal muscle, liver and kidney tissues for clinical chemistry, microarray and histopathology analysis. In the clinical chemistry analysis, alanine aminotransferase (ALT, U/L), aspartate aminotransferase (AST, U/L), creatinine kinase (CK, U/L), blood urea nitrogen (BUN, mmol/L), creatinine (umol/L) and lactate dehydrogenase (LDH, U/L) were measured from the blood of each mouse. Two sections of liver, two sections of kidney, one or two sections of skeletal muscle, and one section of heart were prepared from each mouse, stained with hematoxylin and eosin (H&E), and examined by a veterinary pathologist. RNA was extracted and processed as per the established protocol from heart, skeletal muscle, liver and kidney tissue samples of all the 9 mice for profiling with Affymetrix Mouse Genome 430 2.0 Array and in total 36 chips were prepared. Using various quality control measures, the data was analysed for its quality. As it was found to be good in quality, the data from all the 36 chips were used for further analysis. The results from histopathology and clinical chemistry analysis were compared with the gene expression to determine if the dosages selected for the study were associated with findings in target organs.

Background corr dist: KL-Divergence = 0.0965, L1-Distance = 0.0540, L2-Distance = 0.0060, Normal std = 0.4768

0.888 Kernel fit Pairwise Correlations Normal fit

Density 0.444

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

Heart vehicleHeart vehiclerep1Heart (0.0046184) vehiclerep2Heart (0.00496528) 6mgkg-1rep3Heart (0.0069351) 6mgkg-1 Heartrep1 (0.017496) 6mgkg-1 Heartrep2 (0.00326426) 20mgkg-1 Heartrep3 (0.00847917) 20mgkg-1Heart rep1 20mgkg-1(0.00492547)Kidney rep2 (0.0100707) Kidneyvehicle rep3 (0.0108282) Kidneyvehiclerep1 (0.0556788) Kidneyvehiclerep2 (0.0382602) Kidney6mgkg-1rep3 (0.0387787) Kidney6mgkg-1 rep1 (0.0743557) Kidney6mgkg-1 rep2 (0.0641802) Kidney20mgkg-1 rep3 (0.0436576) Kidney20mgkg-1 rep1 Liver 20mgkg-1(0.0379202) rep2 vehicleLiver (0.0334698) rep3 vehiclerep1Liver (0.0391236) (0.0272618) vehiclerep2Liver (0.0327734) 6mgkg-1rep3Liver (0.0437709) 6mgkg-1 rep1Liver (0.0416532) 6mgkg-1 rep2Liver (0.0362388) 20mgkg-1 rep3Liver (0.0356319) 20mgkg-1Liver rep1 20mgkg-1(0.033244)Skeletal rep2 (0.0460562)Skeletal Musclerep3 (0.0283321)Skeletal MusclevehicleSkeletal Musclevehiclerep1 (0.0152503)Skeletal Musclevehiclerep2 (0.0310884)Skeletal Muscle6mgkg-1rep3 (0.0361635)Skeletal Muscle6mgkg-1 rep1Skeletal (0.0161389)Muscle6mgkg-1 rep2Skeletal (0.0206317)Muscle20mgkg-1 rep3 (0.0113441)Muscle20mgkg-1 rep1 20mgkg-1(0.0268169) rep2 (0.00987877) rep3[ (0.0107177)min ] [ medium ] [ max ] CEM 1 Tmem231 30.8 255.3 991.4 P ( S | Z, I ) = 1.00 B9d1 44.5 234.1 674.2 Mean Corr = 0.56919Tmem216 286.6 396.8 724.5 Tctn2 38.1 76.9 218.0 Cep290 74.5 184.4 305.5 Cc2d2a 166.6 575.1 900.7 Mks1 89.7 178.1 265.6 Tmem17 108.0 184.7 404.4 B9d2 138.0 227.9 309.2 Ahi1 11.5 15.5 38.2 Tmem67 9.0 13.5 18.6 Nphp1 127.2 627.4 1133.4 Tmem107 70.9 222.1 628.5 Ttc26 25.4 123.6 453.1 Arl6 194.2 422.6 1910.7 Ccdc173 42.2 144.3 376.4 CEM 1 + Enkd1 53.4 101.1 218.4 Top 10 Genes Bbs2 247.6 625.3 1289.3 Wdr34 214.1 339.9 777.3 Bbs1 24.5 97.6 415.5 Rabl2 132.3 180.6 496.7

Null module 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-/-(0.132827) InsigKO_C3 -/-/Insig2 InsigKO_E1/ (0.0480076) -/-/Insig2 InsigKO_E2 (0.420571) -/-(0.0882206) InsigKO_E3 (0.129375)[ min (0.180998) ] [ medium ] [ max ] CEM 1 Tmem231 458.1 592.8 764.8 P ( S | Z, I ) = 1.00 B9d1 638.1 723.7 1188.9 Mean Corr = 0.55583Tmem216 373.6 515.3 846.4 Tctn2 266.3 380.5 625.1 Cep290 174.3 263.7 474.4 Cc2d2a 691.1 756.1 1175.0 Mks1 247.1 313.7 335.8 Tmem17 3.1 60.1 74.0 B9d2 497.7 541.1 648.4 Ahi1 8.2 45.0 76.6 Tmem67 43.0 81.1 134.2 Nphp1 230.6 343.0 619.5 Tmem107 5561.7 6677.4 9385.4 Ttc26 282.4 387.2 597.6 Arl6 725.0 1109.6 1554.2 Ccdc173 125.9 190.2 364.8 CEM 1 + Enkd1 155.8 280.7 466.7 Top 10 Genes Bbs2 334.5 386.4 528.4 Wdr34 415.2 643.4 824.5 Bbs1 331.6 426.4 637.8 Rabl2 1280.0 1642.3 3140.0

Null module GEO Series "GSE34206" 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=GSE34206 Status: Public on Dec 07 2011 Title: Gene regulation in macrophages from irradiated tumors Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 22761754 Summary & Design: Summary: Tumors engender an environment dominated by M2 differentiated tumor macrophages that support tumor invasion, metastases and escape from immune control. In this study, we demonstrate that following radiation therapy of tumors in mice there is an influx of tumor macrophages that polarize towards wound repair and immune suppression.

To investigate changes in the phenotype of tumor macrophages following radiation therapy, we FACS sorted tumor macrophages from Panc02 tumors. We have previously shown that we can distinguish mature tumor macrophages from immature myeloid and MDSC populations by expression of Gr1 and IA (MHC class II). To isolate these sub-populations, we first gated CD11b+ cells in the untreated or irradiated tumors, then sorted the CD11b+IA+ macrophage population and the CD11b+Gr1hi MDSC population. Cytospins of the sorted populations demonstrates that the CD11b+Gr1hi MDSC predominantly have a granulocyte morphology and the CD11b+IA+ cells have a macrophage morphology in both the untreated and irradiated tumors. RNA was purified from CD11b+IA+ macrophages from untreated or irradiated tumors 1 day or 7 days following radiation therapy and Gene Expression Microarray analysis was performed.

Overall design: There are untreated and irradiated samples at time points 1 day and 7 days following radiation therapy. The experiment was repeated in entirety, generating a second gene array sample for each. For analysis, the untreated samples of 1 day and 7 days were grouped together.

Background corr dist: KL-Divergence = 0.0586, L1-Distance = 0.0288, L2-Distance = 0.0013, Normal std = 0.5440

0.756 Kernel fit Pairwise Correlations Normal fit

Density 0.378

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

Tumor MacrophageTumor MacrophageTumor Untreated MacrophageTumor Untreated MacrophageTumor d1 rep1 Untreated MacrophageTumor d1 (0.446832) rep2 Untreated MacrophageTumor d7 (0.0303935) rep1 Irradiated MacrophageTumor d7 (0.0733105) rep2 Irradiated Macrophage d1 (0.101061) rep1 Irradiated d1 (0.0894996) rep2 Irradiated d7 (0.103579) rep1 [d7 (0.0828768) min rep2 (0.0724477) ] [ medium ] [ max ] CEM 1 Tmem231 138.7 212.4 521.4 P ( S | Z, I ) = 1.00 B9d1 243.2 454.3 1098.1 Mean Corr = 0.52881Tmem216 213.3 398.5 799.1 Tctn2 57.6 108.4 206.3 Cep290 79.1 115.4 156.3 Cc2d2a 66.4 177.1 463.4 Mks1 107.9 168.9 241.7 Tmem17 123.9 161.8 254.0 B9d2 355.6 494.8 548.6 Ahi1 2.9 10.5 19.0 Tmem67 6.2 13.0 16.9 Nphp1 134.1 248.7 549.2 Tmem107 287.9 434.0 854.4 Ttc26 49.8 90.3 238.1 Arl6 211.1 298.3 389.3 Ccdc173 162.4 196.1 240.5 CEM 1 + Enkd1 134.6 279.6 483.1 Top 10 Genes Bbs2 230.8 343.6 706.2 Wdr34 215.6 402.5 712.8 Bbs1 27.2 60.4 107.7 Rabl2 140.6 198.2 433.1

Null module GEO Series "GSE6540" 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=GSE6540 Status: Public on Dec 14 2007 Title: Expression data from olfactory epithelium of Lip-C-treated mice compared to Lip-O-treated control mice Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 17848607 Summary & Design: Summary: Microarray analysis of gene expression in the olfactory epithelium of macrophage depleted mice to study the role of macrophages in regulating neurodegeneration, neuroprotection, and neurogenesis of olfactory sensory neurons

Keywords: comparison of gene expression level in sham and 48 hr OBX Lip-O mice versus Lip-C mice

Overall design: Olfactory epithelium from LIp-C-treated and Lip-O-treated mice was microdissected for RNA extraction and hybridization on Affymetrix microarrays. We compared levels of gene expression in macrophage-depleted and non-depleted sham and 48 hr OBX mice using a 2x2 ANOVA and pairwise comparisons to identify molecular mechanisms of macrophage-mediated neurodegeneration, neuroprotection, and neurogenesis and to validate the gene expression patterns using real-time RT-PCR and immunohistochemistry

Background corr dist: KL-Divergence = 0.1195, L1-Distance = 0.0264, L2-Distance = 0.0010, Normal std = 0.4100

0.973 Kernel fit Pairwise Correlations Normal fit

Density 0.487

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

Lip-C-treatedLip-C-treated 48Lip-C-treated hr OBX 48Lip-C-treated hrC57 OBX 48mouse,Lip-C-treated hrC57 OBX sham mouse,biolLip-C-treated C57 rep1 OBX sham mouse,biolLip-O-treated (0.115381) C57 rep2 OBX sham mouse,biolLip-O-treated (0.0220186) C57 rep3 OBX 48 mouse,Lip-O-treatedbiol (0.0123294)hr C57 rep1OBX 48 mouse,Lip-O-treatedbiol hr(0.0510505)C57 rep2OBX 48mouse, Lip-O-treatedbiol hr(0.108434)C57 rep3OBX sham mouse,biolLip-O-treated (0.10076)C57 rep1 OBX sham mouse,biol (0.166292) C57 rep2 OBX sham mouse,biol (0.0984179) C57 rep3 OBX mouse,biol (0.0701831) C57 rep1 mouse,[biol (0.113403)min rep2 biol (0.0610986) rep3] (0.080631)[ medium ] [ max ] CEM 1 Tmem231 715.4 1011.5 1209.7 P ( S | Z, I ) = 1.00 B9d1 755.7 960.3 1223.9 Mean Corr = 0.50919Tmem216 485.6 624.3 724.0 Tctn2 464.9 581.3 659.9 Cep290 434.4 767.8 892.3 Cc2d2a 812.4 869.5 995.4 Mks1 418.1 554.6 664.2 Tmem17 127.6 191.5 229.1 B9d2 639.5 833.0 1143.7 Ahi1 132.7 218.0 291.3 Tmem67 135.4 235.0 368.1 Nphp1 640.6 763.1 864.2 Tmem107 5101.5 6406.9 6935.8 Ttc26 638.0 973.5 1122.9 Arl6 2418.5 3644.4 4114.9 Ccdc173 297.9 393.3 501.7 CEM 1 + Enkd1 333.2 386.2 481.8 Top 10 Genes Bbs2 628.0 1069.9 1380.3 Wdr34 651.1 887.4 1056.7 Bbs1 655.8 1062.9 1377.7 Rabl2 1760.8 2704.2 3059.7

Null module GEO Series "GSE28593" 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=GSE28593 Status: Public on Apr 15 2011 Title: KMT1E Mediated H3K9 Methylation Is Required for the Maintenance of Embryonic Stem Cells by Repressing Trophectoderm Differentiation Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 20014010 Summary & Design: Summary: Dynamic regulation of histone methylation by methyltransferases and demethylases plays a central role in regulating the fate of embryonic stem (ES) cells. The histone H3K9 methyltransferase KMT1E, formerly known as ESET or Setdb1, is essential to embryonic development as the ablation of the Setdb1 gene results in peri-implantation lethality and prevents the propagation of ES cells. However, Setdb1- null blastocysts do not display global changes in H3K9 methylation or DNA methylation, arguing against a genome- wide defect. Here we show that conditional deletion of the Setdb1 gene in ES cells results in the upregulation of lineage differentiation markers, especially trophectoderm-specific factors, similar to effects observed upon loss of Oct3/4 expression in ES cells. We demonstrate that KMT1E deficiency in ES cells leads to a decrease in histone H3K9 methylation at and derepression of trophoblast-associated genes such as Cdx2. Furthermore, we find genes that are derepressed upon Setdb1 deletion to overlap with known targets of polycomb mediated repression, suggesting that KMT1E mediated H3K9 methylation acts in concert with polycomb controlled H3K27 methylation. Our studies thus demonstrate an essential role for KMT1E in the control of developmentally regulated gene expression programs in ES cells.

Overall design: Analysis of KMT1E-deficiency in mouse embryonic stem cells using a Setdb1 conditional allele and tamoxifen-inducible Cre/loxP recombination

Background corr dist: KL-Divergence = 0.0295, L1-Distance = 0.0506, L2-Distance = 0.0029, Normal std = 0.7544

0.581 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

Setdb1 Setdb12lox/1lox Setdb12lox/1lox plus tamoxifenSetdb12lox/1lox plus tamoxifenSetdb12lox/1lox/Cre plus1 (0.101163) tamoxifenSetdb12lox/1lox/Cre 2 (0.0794632) minus Setdb12lox/1lox/Cre 3 (0.0279862) tamoxifen minus Setdb12lox/1lox/Cre tamoxifen minus Setdb12lox/1lox/Cre 1 (0.0808182) tamoxifen plus 2lox/1lox/Cre 2 (0.110168) tamoxifen plus 3 (0.169472) tamoxifen plus1 (0.155678) tamoxifen 2[ (0.0938634) min 3 (0.181388) ] [ medium ] [ max ] CEM 1 Tmem231 349.4 545.9 729.8 P ( S | Z, I ) = 1.00 B9d1 932.6 1113.6 1605.6 Mean Corr = 0.60051Tmem216 421.4 462.1 905.7 Tctn2 171.0 211.8 246.2 Cep290 185.6 221.9 271.2 Cc2d2a 131.9 269.4 292.0 Mks1 244.2 396.5 466.1 Tmem17 23.9 30.0 36.6 B9d2 330.7 371.1 405.2 Ahi1 34.5 65.1 101.8 Tmem67 18.6 22.1 28.7 Nphp1 385.4 551.7 716.3 Tmem107 2594.0 3761.5 4580.0 Ttc26 167.0 369.2 456.2 Arl6 783.9 1282.3 1476.5 Ccdc173 46.2 72.1 118.1 CEM 1 + Enkd1 532.0 562.9 770.7 Top 10 Genes Bbs2 311.5 423.2 936.0 Wdr34 493.5 967.3 1139.8 Bbs1 74.7 84.7 125.9 Rabl2 452.2 572.3 759.5

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 "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,(0.0354229) rep2 Rorb-/- biologicalP14(0.0334615) rep3 Rorb-/-retina, P14(0.0207838) rep4 biologicalRorb-/- retina, P14(0.0389752) Rorb-/- biologicalretina, rep1P14 +/+;CrxpNrl (0.0244679)biologicalretina, rep2P14 +/+;CrxpNrl biological(0.0254562) rep3P14 retina, +/+;CrxpNrl (0.0256379) rep4P14 biologicalretina, +/+;CrxpNrl (0.0149059)P14 biologicalretina, rep1Rorb-/-;CrxpNrlP14 biologicalretina,(0.0310434) rep2Rorb-/-;CrxpNrlP14 biological(0.0389451) rep3Rorb-/-;CrxpNrl retina,P14 (0.0489413) rep4 Rorb-/-;CrxpNrl biologicalretina,P28 (0.0415707) +/+ biologicalretina, P28rep1retina, +/+ biologicalretina,(0.0179279) biologicalP28rep2retina, +/+ biological(0.0137652) biologicalP28rep3retina, rep1 +/+ (0.0132138) biologicalP28rep4retina,(0.0325804) rep2 Rorb-/- (0.0078791) biologicalP28(0.0143834) rep3 Rorb-/-retina, P28(0.0225475) rep4 biologicalRorb-/- retina, P28(0.0122586) Rorb-/- biologicalretina, rep1P28 +/+;CrxpNrl (0.0310682)biologicalretina, rep2P28 +/+;CrxpNrl biological(0.0331101) rep3P28 retina, +/+;CrxpNrl (0.0221361) rep4P28 biologicalretina, Rorb-/-;CrxpNrl (0.031831)P28 biologicalretina, rep1Rorb-/-;CrxpNrlP28 biological(0.0169705) rep2Rorb-/-;CrxpNrl retina,P28 (0.0271358) rep3 Rorb-/-;CrxpNrl biologicalretina, (0.0106126) biologicalretina, rep1 biologicalretina,(0.0396878) rep2 biological(0.0748627) [rep3 min (0.100754) rep4 ] (0.097664) [ medium ] [ max ] CEM 1 Tmem231 404.5 487.7 587.7 P ( S | Z, I ) = 1.00 B9d1 334.8 604.6 838.2 Mean Corr = 0.37481Tmem216 264.6 426.1 527.9 Tctn2 134.4 296.3 443.1 Cep290 619.2 1473.3 1945.6 Cc2d2a 755.8 1211.8 1809.1 Mks1 212.4 514.7 662.8 Tmem17 42.0 70.4 95.0 B9d2 636.1 774.4 906.4 Ahi1 249.7 549.3 1128.3 Tmem67 60.1 95.2 140.5 Nphp1 323.1 525.4 725.0 Tmem107 1200.5 2627.7 3913.9 Ttc26 162.8 299.3 376.4 Arl6 2431.0 8511.7 10146.9 Ccdc173 128.2 371.0 810.4 CEM 1 + Enkd1 123.3 303.6 471.7 Top 10 Genes Bbs2 878.3 1452.8 2139.5 Wdr34 357.0 589.6 697.7 Bbs1 691.0 1462.6 1885.2 Rabl2 1165.7 1713.8 2083.4

Null module GEO Series "GSE13106" 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=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 (0.0654476)mus-6dpp-50ng_activin-rep1 (0.0504557)mus-6dpp-50ng_activin-rep2 (0.0647435)mus-15dpp-0ng_activin-rep1 (0.0952483)mus-15dpp-0ng_activin-rep2 (0.0614973)mus-15dpp-5ng_activin-rep1 (0.0622208)mus-15dpp-5ng_activin-rep2 (0.133157) (0.139362) (0.22673) (0.101137)[ min ] [ medium ] [ max ] CEM 1 Tmem231 254.7 356.9 569.4 P ( S | Z, I ) = 1.00 B9d1 405.3 489.4 1333.6 Mean Corr = 0.44108Tmem216 341.3 451.2 575.5 Tctn2 430.0 545.9 674.0 Cep290 173.2 399.9 1311.4 Cc2d2a 171.2 392.3 531.4 Mks1 311.1 423.8 658.2 Tmem17 18.1 65.2 91.8 B9d2 407.5 500.5 630.6 Ahi1 136.4 159.3 217.2 Tmem67 44.6 85.2 394.1 Nphp1 400.8 573.5 3539.6 Tmem107 1956.2 2468.4 6316.5 Ttc26 180.3 276.2 866.7 Arl6 528.9 774.0 1559.0 Ccdc173 85.0 149.9 796.4 CEM 1 + Enkd1 203.4 274.8 676.1 Top 10 Genes Bbs2 235.8 340.0 817.8 Wdr34 313.3 365.9 840.5 Bbs1 141.0 191.2 548.6 Rabl2 949.3 1138.8 1774.2

Null module GEO Series "GSE21606" 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=GSE21606 Status: Public on Jul 07 2010 Title: Expression profiling of murine neonatal lung tissue from Carm1 knockouts and wild type controls Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 20530543 Summary & Design: Summary: Coactivator associated arginine methyltransferase I (CARM1, also known as Protein aRginine MethylTransferase 4, or PRMT4) regulates gene expression by multiple mechanisms including methylation of histones and coactivation of steroid receptor transcription. Mice lacking CARM1 are smaller than their littermates, fail to breath, and die shortly after birth, demonstrating the critical role of CARM1 in development.We performed gene expression analysis to identify genes that are responsible for hyperproliferaion in CARM1 knockout lung.

Overall design: RNA extracted from murine lung at E18.5 with carm1 knockouts and wild type controls was hybridised to Affymetrix mouse430.2 GeneChips to identify differentially expressed genes in the disease state.

Background corr dist: KL-Divergence = 0.0455, L1-Distance = 0.0209, L2-Distance = 0.0005, Normal std = 0.5932

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

WT1 (0.164959)WT2 (0.0892906)WT3 (0.180042)KN1 (0.0879936)KN2 (0.119011)KN3 (0.358703) [ min ] [ medium ] [ max ] CEM 1 Tmem231 281.8 331.9 392.7 P ( S | Z, I ) = 0.99 B9d1 773.1 1250.6 1727.2 Mean Corr = 0.51908Tmem216 461.3 527.2 567.4 Tctn2 305.1 359.2 446.5 Cep290 144.7 204.6 257.7 Cc2d2a 576.9 656.6 689.7 Mks1 227.8 261.0 291.7 Tmem17 110.3 136.1 159.0 B9d2 453.9 489.2 532.3 Ahi1 37.9 47.5 56.6 Tmem67 44.8 92.7 101.3 Nphp1 476.6 660.9 814.4 Tmem107 3364.4 3898.0 5772.9 Ttc26 264.4 313.0 419.6 Arl6 982.5 1193.8 1476.5 Ccdc173 116.7 173.6 243.5 CEM 1 + Enkd1 229.6 279.2 408.8 Top 10 Genes Bbs2 256.1 306.5 481.6 Wdr34 526.4 639.5 710.1 Bbs1 140.1 178.0 182.7 Rabl2 606.0 1000.2 1288.3

Null module GEO Series "GSE56777" 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=GSE56777 Status: Public on May 14 2014 Title: Expression data of E13.5 mouse Blood Brain Barrier and lung endothelial cells Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 24828040 Summary & Design: Summary: Following the identification of a critical time window of Blood Brain Barrier formation in the mouse embryo, we aimed to identify genes important for barriergenesis. To this end, we isolated cortical and lung E13.5 endothelial cells and compared expression between the two populations.

The working hypothesis was that endothelial cells which are actively building a barrier would have a uniqe pattern of gene expression that would be detectable in comparison to a non-barrier endothelial population that is also active in vasculogenesis.

Overall design: E13.5 Tie2-GFP embryos were micro-dissected for cortex and lungs. Cortex tissue was carefully cleared of the meninges and choroid plexus. FACS purification of GFP positive cells and GeneChip analysis was applied . All material from a single litter (10-13 embryos) was pooled and considered as a biological replicate. n=4 litters.

Background corr dist: KL-Divergence = 0.0382, L1-Distance = 0.0277, L2-Distance = 0.0012, Normal std = 0.6186

0.645 Kernel fit Pairwise Correlations Normal fit

Density 0.322

0.000 CEM 1

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

Pre-normalization Quantiles

Cortex_72Lung_72 (0.224247)Lung_22 (0.105538)Cortex_22 (0.190678)Lung_19 (0.0869575)Cortex_19 (0.0759311)Lung_18 (0.104628)Cortex_18 (0.103922) (0.108099) [ min ] [ medium ] [ max ] CEM 1 Tmem231 162.9 332.6 541.4 P ( S | Z, I ) = 0.99 B9d1 483.2 956.0 1772.9 Mean Corr = 0.47916Tmem216 323.5 617.2 729.8 Tctn2 120.1 187.4 236.6 Cep290 63.1 126.2 174.3 Cc2d2a 483.6 624.2 804.0 Mks1 95.2 153.2 211.7 Tmem17 75.1 166.2 287.8 B9d2 142.0 226.9 429.2 Ahi1 37.9 96.8 119.2 Tmem67 61.2 71.0 83.3 Nphp1 186.6 341.0 465.4 Tmem107 114.4 394.1 590.9 Ttc26 67.6 194.8 239.9 Arl6 134.1 516.6 618.8 Ccdc173 44.8 159.2 318.9 CEM 1 + Enkd1 383.6 492.1 683.0 Top 10 Genes Bbs2 250.3 743.1 1086.1 Wdr34 155.8 401.1 1155.0 Bbs1 47.5 186.4 231.9 Rabl2 73.1 268.9 425.5

Null module GEO Series "GSE45820" 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=GSE45820 Status: Public on May 19 2014 Title: Expression data from murine cardiac fibroblasts and endothelial cells following Transverse Aortic Constriction Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: Accumulation of activated cardiac fibroblasts plays a key role in heart failure progression. These cells deposit excessive extracellular matrix that leads to mechanical stiffness, myocyte uncoupling and ischemia. To investigate whether two developmentally distinct cardiac fibroblast populations exhibit distinct expression profiles in response to cardiac injury, and therefore might necessitate distinct therapeutic targeting, we performed microarray analysis on FACS sorted cells. Tie2cre lineage traced CFs, non Tie2cre lineage traced cardiac fibroblasts and endothelial cells were isolated from left ventricle of SHAM operated and banded hearts at the onset of fibrosis, one week after surgery.

We used microarrays to detail the global programme of gene expression in cardiac fibroblasts and endothelium following pressure overload. Tie2cre lineage traced, non-tie2cre lineage traced fibroblasts and endothelial cells were sorted from left ventricle of 3 SHAM operated and 3 TAC operated adult male Black Swiss mice.

Overall design: Tie2cre lineage traced, non-tie2cre lineage traced fibroblasts and endothelial cells were sorted from left ventricle of 3 SHAM operated and 3 Transaortic Constriction (TAC) operated adult male Black Swiss mice for RNA extraction and Affymetrix microarray analysis. Hypertrophy in TAC animals, an lack of hypertrophy in SHAM operated animals, was evaluated by hemodynamic measurements before surgery and one week after surgery. Cells were isolated one week after surgery.

Background corr dist: KL-Divergence = 0.0132, L1-Distance = 0.0279, L2-Distance = 0.0011, Normal std = 0.8360

0.477 Kernel fit Pairwise Correlations Normal fit

Density 0.239

0.000 CEM 1

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

Pre-normalization Quantiles

Tie2cre Tie2crelineage Tie2cre lineagetraced Tie2cre fibroblastnon-lineagetraced Endothelialfibroblastnon-lineage SHAM, tracedEndothelial BiologicalTAC, cells fibroblasttraced Biological SHAM, cellsfibroblast Replicate SHAM, BiologicalTAC, Replicate BiologicalTAC, 1 (0.0842658) ReplicateBiological 1[ (0.0821212) minReplicate 1 Replicate (0.439805) ] 1 (0.0602496)(0.171314) 1 (0.162245)[ medium ] [ max ] CEM 1 Tmem231 64.8 303.3 335.3 P ( S | Z, I ) = 0.98 B9d1 218.8 818.8 915.5 Mean Corr = 0.45081Tmem216 148.1 455.9 541.7 Tctn2 145.3 240.6 323.5 Cep290 35.8 69.7 102.4 Cc2d2a 138.2 588.6 704.7 Mks1 146.6 218.5 234.6 Tmem17 43.7 130.4 180.5 B9d2 270.7 439.0 581.0 Ahi1 34.1 162.7 180.6 Tmem67 178.6 211.7 519.0 Nphp1 179.6 385.7 474.4 Tmem107 58.4 1447.0 1846.4 Ttc26 56.5 244.2 375.9 Arl6 179.1 732.5 1240.0 Ccdc173 53.1 91.9 132.8 CEM 1 + Enkd1 129.4 248.8 267.5 Top 10 Genes Bbs2 169.3 407.9 658.9 Wdr34 118.0 478.7 490.7 Bbs1 76.5 144.7 236.2 Rabl2 188.2 318.5 379.1

Null module GEO Series "GSE21568" 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=GSE21568 Status: Public on Jan 12 2011 Title: Mouse bulge (CD34+CD200+CD49+) versus secondary hair germ (CD34-CD200+CD49+) versus interfollicular epidermis (CD34-CD200-CD49+) Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21206086 Summary & Design: Summary: Mouse back skin was disassociated to single cells, sorted by cell surface markers and tested by microarrray

To compare the gene expression of mouse bulge (CD34+CD200+CD49+) versus secondary hair germ (CD34-CD200+CD49+) versus interfollicular epidermis (CD34-CD200-CD49+)

xx

Bald scalp retains hair follicle stem cells but lacks CD200-rich and CD34-positive hair follicle progenitor cells

Androgenetic alopecia (AGA) or common baldness results from a marked decrease in hair follicle size. This miniaturization may be related to loss of hair follicle stem or progenitor cells. To test this hypothesis, we analyzed bald and non-bald scalp from the same individuals for the presence of hair follicle stem and progenitor cells using flow cytometry to quantitate cells expressing CYTOKERATIN 15 (KRT15), CD200, CD34 and ALPHA-6-INTEGRIN (ITGA6). High levels of KRT15 expression correlated with stem cell properties of small cell size and quiescence. Cells with the highest level of KRT15 expression were maintained in bald scalp; however, distinct populations of CD200high ITGA6high cells and CD34-positive cells were markedly diminished. Consistent with a progenitor cell phenotype, the diminished populations localized closely to the stem-cell rich bulge area but were larger and more proliferative than the bulge stem cells. In functional assays, analogous CD200 high /Itga6 high cells from murine hair follicles were multipotent and generated new hair follicles in skin reconstitution assays. These findings suggest that a defect in stem cell activation plays a role in the pathogenesis of AGA.

Overall design: 4 independent biologic replicates (each pooled from 3 distinct mice) were sorted for Mouse bulge (CD34+CD200+CD49+) versus secondary hair germ (CD34-CD200+CD49+) versus interfollicular epidermis (CD34-CD200-CD49+)

Background corr dist: KL-Divergence = 0.0683, L1-Distance = 0.0257, L2-Distance = 0.0012, Normal std = 0.5061

0.788 Kernel fit Pairwise Correlations Normal fit

Density 0.394

0.000 CEM 1

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

Pre-normalization Quantiles

CD34+CD200+CD49+Replicate1CD34+CD200+CD49+Replicate2CD34+CD200+CD49+Replicate3CD34+CD200+CD49+Replicate4CD34-CD200+CD49+Replicate1 (0.331284)CD34-CD200+CD49+Replicate2 (0.0692741)CD34-CD200+CD49+Replicate3 (0.0257362)CD34-CD200+CD49+Replicate4 (0.0678677)CD34-CD200-CD49+Replicate1 (0.0557583)CD34-CD200-CD49+Replicate2 (0.0896859)CD34-CD200-CD49+Replicate3 (0.0831679)CD34-CD200-CD49+Replicate4 (0.0880491) (0.0514877) (0.0319838) (0.0830648)[ (0.0226409) min ] [ medium ] [ max ] CEM 1 Tmem231 201.4 331.2 659.5 P ( S | Z, I ) = 0.39 B9d1 179.3 283.2 443.8 Mean Corr = 0.49677Tmem216 741.5 906.6 1670.3 Tctn2 83.9 175.5 252.1 Cep290 225.8 271.7 347.4 Cc2d2a 487.8 1094.5 1760.8 Mks1 134.1 156.8 238.4 Tmem17 79.2 114.5 239.3 B9d2 96.1 193.0 371.9 Ahi1 16.7 19.8 29.4 Tmem67 6.9 8.2 10.2 Nphp1 303.8 521.9 969.7 Tmem107 549.9 815.5 1541.4 Ttc26 64.1 133.0 297.3 Arl6 352.1 435.3 615.7 Ccdc173 93.5 170.9 490.4 CEM 1 + Enkd1 127.2 203.6 365.1 Top 10 Genes Bbs2 515.0 1046.3 1745.6 Wdr34 373.4 603.3 1162.2 Bbs1 120.8 175.6 390.7 Rabl2 218.8 336.9 667.8

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 (0.03318)GPR120KO #427Liver HFD adipose (0.0334873)GPR120KO Epididymal#428 HFD (0.0237627)GPR120KO #428Liver HFD adipose (0.0161804)WT Epididymal#429 HFDHFD (0.0230543)WT #546#429Liver HFD adipose (0.0248563) (0.0179078)WT #546Epididymal HFD (0.0334492) WT #547Liver HFD adipose(0.0199012) WT #547Liver HFD (0.0189146) WT #560Epididymal HFDND (0.035269) #686 #560Liver (0.030041) adipose(0.0285289) WTEpididymal ND WT#687Liver ND (0.0174842) adipose #687WTEpididymal ND (0.054803) WT#690Liver ND (0.0566774) adipose #690GPR120KOEpididymal (0.0456283) GPR120KOLiver ND adipose GPR120KO#718Epididymal ND (0.0271461) GPR120KO#718Liver ND (0.0562793)adipose GPR120KO#719Epididymal ND (0.0371629) GPR120KO#719 ND (0.0543863)adipose #720 ND (0.0435231) WT#720 ND (0.0432577) #686[ min(0.225119) ] [ medium ] [ max ] CEM 1 Tmem231 63.9 153.9 470.6 P ( S | Z, I ) = 0.03 B9d1 15.6 144.1 1189.0 Mean Corr = 0.40712Tmem216 130.5 434.6 1169.6 Tctn2 7.0 92.3 340.5 Cep290 16.1 89.9 473.9 Cc2d2a 132.3 406.9 573.7 Mks1 76.0 220.9 509.9 Tmem17 5.0 33.3 85.8 B9d2 159.1 291.9 526.3 Ahi1 5.0 5.1 80.0 Tmem67 5.0 18.7 84.6 Nphp1 19.6 216.8 2433.9 Tmem107 275.2 680.4 2045.3 Ttc26 42.6 102.7 339.9 Arl6 103.7 609.4 1378.9 Ccdc173 5.0 86.4 1123.6 CEM 1 + Enkd1 16.8 76.7 438.0 Top 10 Genes Bbs2 16.4 159.5 637.0 Wdr34 103.4 183.1 545.1 Bbs1 5.0 115.4 258.3 Rabl2 119.6 286.5 679.6

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 (0.0805652)Lyz2+_EpCAM+_Adult-1 (0.0803764)Lyz2+_EpCAM+_Adult-2 (0.117754)Lyz2+_EpCAM+_Adult-3 (0.158503) (0.156987) (0.405814)[ min ] [ medium ] [ max ] CEM 1 Tmem231 169.6 292.8 560.8 P ( S | Z, I ) = 0.01 B9d1 56.9 247.9 1236.9 Mean Corr = 0.33954Tmem216 3.4 576.2 679.7 Tctn2 58.9 223.3 710.4 Cep290 48.7 144.4 584.5 Cc2d2a 165.9 745.5 867.6 Mks1 79.8 132.9 253.9 Tmem17 1.8 15.3 18.8 B9d2 413.3 819.1 1201.1 Ahi1 2.2 5.6 12.2 Tmem67 17.2 39.4 103.9 Nphp1 16.9 250.3 867.5 Tmem107 1421.1 4156.0 10521.2 Ttc26 35.8 127.8 553.9 Arl6 200.5 547.3 1812.1 Ccdc173 61.7 77.2 367.4 CEM 1 + Enkd1 4.6 106.4 312.3 Top 10 Genes Bbs2 52.6 155.9 533.7 Wdr34 84.6 289.7 1473.1 Bbs1 56.4 206.7 663.5 Rabl2 168.1 290.9 1531.9

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 (0.10496)MouseLiver_0.05ugSe_rep2 (0.0441027)MouseLiver_0.05ugSe_rep3 (0.0442605)MouseLiver_0.2ugSe_rep1 (0.0484879)MouseLiver_0.2ugSe_rep2 (0.0649553)MouseLiver_0.2ugSe_rep3 (0.0838522)MouseKidney_SeDef_rep1 (0.0425343)MouseKidney_SeDef_rep2 (0.0517911)MouseKidney_SeDef_rep3 (0.0409196)MouseKidney_0.05ugSe_rep1 (0.0585074)MouseKidney_0.05ugSe_rep2 (0.0356292)MouseKidney_0.05ugSe_rep3 (0.0305344)MouseKidney_0.2ugSe_rep1 MouseKidney_0.2ugSe_rep2(0.0803955) MouseKidney_0.2ugSe_rep3(0.0492695) (0.0494936) (0.056484) (0.0774175) (0.0364049)[ min ] [ medium ] [ max ] CEM 1 Tmem231 308.6 716.2 902.6 P ( S | Z, I ) = 0.00 B9d1 149.0 359.4 542.8 Mean Corr = 0.36521Tmem216 154.4 324.0 502.8 Tctn2 129.2 252.7 298.3 Cep290 21.7 37.2 49.1 Cc2d2a 178.9 608.3 734.9 Mks1 178.6 247.0 322.5 Tmem17 23.2 28.1 35.6 B9d2 329.3 423.9 549.4 Ahi1 43.7 49.3 61.5 Tmem67 31.1 42.1 49.4 Nphp1 332.9 1508.7 1754.4 Tmem107 301.6 954.5 1236.4 Ttc26 88.8 282.3 343.6 Arl6 188.7 1647.0 2239.9 Ccdc173 34.9 79.0 107.1 CEM 1 + Enkd1 78.7 146.8 202.9 Top 10 Genes Bbs2 73.9 219.7 324.4 Wdr34 136.4 195.4 287.1 Bbs1 100.7 323.5 398.9 Rabl2 312.8 442.0 529.3

Null module GEO Series "GSE24726" 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=GSE24726 Status: Public on Dec 21 2010 Title: Gene expression profile of mature plasmacytoid dendritic cells (PDC) after the deletion of transcription factor E2-2 Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21145760 Summary & Design: Summary: The interferon-producing plasmacytoid dendritic cells (PDC) share common progenitors with antigen-presenting classical dendritic cells (cDC), yet they possess distinct morphology and molecular features resembling those of lymphocytes. It is unclear whether the unique cell fate of PDC is actively maintained in the steady state. We report that the deletion of transcription factor E2-2 from mature peripheral PDC caused their spontaneous differentiation into cells with cDC properties. This included the loss of PDC markers, increase in MHC class II expression and T cell priming capacity, acquisition of dendritic morphology and induction of cDC signature genes. Genome-wide chromatin immunoprecipitation revealed direct binding of E2-2 to key PDC-specific and lymphoid genes, as well as to certain genes enriched in cDC. Thus, E2-2 actively maintains the cell fate of mature PDC and opposes the default cDC fate, in part through direct regulation of lineage-specific gene expression programs.

Overall design: Inducible deletion of E2-2 (Tcf4) has been performed by administering tamoxifen to conditional E2-2flox/flox Rosa26-CreER+ mice or to E2-2flox/flox Rosa26-CreER- control littermates. Four or six days later total splenocytes were isolated, pooled from 2-3 mice and PDC (CD11b- B220+ CD11clow Bst2+) were isolated by sorting. Global gene expression profiles of E2-2-deficient (null) and control (Ctrl) PDC were compared using Affymetrix microarrays (GPL1261).

Background corr dist: KL-Divergence = 0.0689, L1-Distance = 0.0375, L2-Distance = 0.0025, Normal std = 0.5200

0.771 Kernel fit Pairwise Correlations Normal fit

Density 0.385

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

PDC_control_day4_rep1PDC_control_day4_rep2PDC_control_day6_rep1PDC_control_day6_rep2 (0.0873522)PDC_null_day4_rep1 (0.0980413)PDC_null_day4_rep2 (0.0400395)PDC_null_day6_rep1 (0.0769067) (0.0450453)PDC_null_day6_rep2 (0.0772449) (0.462458) (0.112913)[ min ] [ medium ] [ max ] CEM 1 Tmem231 512.0 690.8 820.5 P ( S | Z, I ) = 0.00 B9d1 12.2 100.0 518.1 Mean Corr = 0.40641Tmem216 4.2 26.5 130.5 Tctn2 55.4 105.1 344.6 Cep290 26.1 137.9 164.0 Cc2d2a 5.3 65.6 243.8 Mks1 252.3 339.5 429.5 Tmem17 4.1 10.1 86.8 B9d2 548.9 743.4 1110.7 Ahi1 5.0 10.4 67.8 Tmem67 11.1 42.7 112.8 Nphp1 17.1 44.0 74.9 Tmem107 317.6 660.5 853.1 Ttc26 35.2 132.5 177.8 Arl6 204.7 320.0 378.6 Ccdc173 74.1 101.0 197.5 CEM 1 + Enkd1 34.7 186.2 211.6 Top 10 Genes Bbs2 7.5 29.5 297.0 Wdr34 73.9 101.1 186.7 Bbs1 24.6 213.1 244.3 Rabl2 180.1 401.4 453.6

Null module GEO Series "GSE27546" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 51 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27546 Status: Public on Feb 28 2011 Title: Effects of HMGN variants on cellular transcription profile Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21278158 Summary & Design: Summary: HMGN (high mobility group N) is a family of intrinsically disordered nuclear proteins that binds to nucleosomes, alters the structure of chromatin and affects transcription. A major unresolved question is the extent of functional specificity, or redundancy, between the various members of the HMGN protein family.

Here we analyze the transcriptional profile of cells in which the expression of various HMGN proteins has been either deleted or doubled. The results reveal an HMGN-variant specific effect on the fidelity of the cellular transcription profile, indicating that functionally, the various HMGN subtypes are not fully redundant.

Overall design: RNA was collected from either primary knock-out MEFs or SV40-transformed MEFs and MIN6 cells over expressing various HMGN proteins and mutants and hybridized to Affymetrix arrays. We obtained a double ammount of HMGN proteins in MEFs and MIN6 cells by retroviral infection and subsequent selection procedure. We collected all infected cells (pools, not clones) in order to eliminate the effect of viral integration in the genome.

Background corr dist: KL-Divergence = 0.0270, L1-Distance = 0.0406, L2-Distance = 0.0025, Normal std = 0.6975

0.572 Kernel fit Pairwise Correlations Normal fit

Density 0.286

0.000 CEM 1

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

Pre-normalization Quantiles

MEFs HMGN1MEFs HMGN1 knockMEFs outHMGN1 knockMEFs rep outHMGN1 1knockMEFs (0.0158166) rep outHMGN1 2WTMEFs (0.0157208) rep rep HMGN1 3WT MEFs 1(0.0129003) (0.014714) rep HMGN3 WT MEFs2 (0.0136639) rep HMGN3 knock MEFs3 (0.0164258) outHMGN3 knockMEFs rep outHMGN3 1knockMEFs (0.0165958) rep outHMGN3 2WTMEFs (0.0164346) rep rep HMGN3 3WT MEFs 1(0.0156081) (0.0173812) rep HMGN5 WT MEFs2 (0.0154972) rep HMGN5 knock MEFs3 (0.0167879) outHMGN5 knockMEFs rep outHMGN5 1knockMEFs (0.0156545) rep outHMGN5 2WTMEFs (0.0198928) rep rep HMGN5 3WT MEFs 1(0.0150984) (0.0144868) rep empty WT MEFs2 (0.012872) rep vector empty MEFs3 (0.0178141) OEvector emptyMEFs rep OE1vector HMGN1 (0.0121627)MEFs rep OE2 HMGN1 (0.00633549)OEMEFs rep rep 3 HMGN1 (0.00602029)OE1MEFs (0.00800287) rep HMGN2 OE2MEFs (0.00682085) rep HMGN2 OE3MEFs (0.0100228) rep HMGN2 OE1MEFs (0.00421957) rep HMGN3a OE2MEFs (0.0121297) rep HMGN3a 3MEFs OE (0.00573177) rep HMGN3aMEFs OE1 (0.0056631) rep HMGN5MEFs OE2 (0.00827976) rep HMGN5 OEMEFs 3 (0.00779322) rep HMGN5 OE1MEFs (0.00707001) rep HMGN5SE OE2MEFs (0.00864541) rep HMGN5SE 3MEFs (0.00474865) OE repHMGN5SEMEFs OE1 (0.00856902) repHMGN1_N2swapMEFs OE2 (0.00699548) repHMGN1_N2swapMEFs 3 (0.00883931) HMGN1_N2swapMEFs rep 1 HMGN1_N3swap (0.00927615)MEFs rep 2 HMGN1_N3swap (0.0109686)MEFs rep 3 HMGN1_N3swap (0.0121114)MIN6 rep 1empty (0.0128876)MIN6 rep vector 2empty (0.0194848)MIN6 rep OEvector 3empty (0.0150549)MIN6 rep OE1vector HMGN1 (0.0629567)MIN6 rep OE2 HMGN1 (0.0526241)OEMIN6 rep rep 3 HMGN1 (0.0668464)OE1MIN6 (0.0604439) rep HMGN3a OE2MIN6 (0.0467023) rep HMGN3a 3 MIN6OE (0.0524491) rep HMGN3a OE1 (0.048886) rep OE2 (0.055598) rep 3 (0.0522952)[ min ] [ medium ] [ max ] CEM 1 Tmem231 233.1 320.4 786.3 P ( S | Z, I ) = 0.00 B9d1 269.7 798.2 1143.2 Mean Corr = 0.43657Tmem216 257.4 533.5 964.4 Tctn2 54.6 258.3 399.0 Cep290 59.8 170.4 625.9 Cc2d2a 70.0 276.2 672.0 Mks1 47.5 96.7 286.4 Tmem17 24.1 33.7 41.3 B9d2 321.4 581.9 1099.6 Ahi1 34.8 62.3 270.1 Tmem67 24.7 33.0 143.5 Nphp1 390.8 652.8 1191.4 Tmem107 982.0 3270.2 8315.1 Ttc26 100.9 257.9 608.1 Arl6 601.9 1268.5 2608.4 Ccdc173 25.7 45.1 100.5 CEM 1 + Enkd1 132.6 584.7 769.4 Top 10 Genes Bbs2 38.3 182.1 848.5 Wdr34 127.2 310.8 551.5 Bbs1 34.7 140.6 572.2 Rabl2 232.1 468.3 823.3

Null module GEO Series "GSE23408" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 39 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23408 Status: Public on Aug 02 2011 Title: Global gene expression profiles and the progression of pro- and anti-inflammatory pathways in mouse models Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: Gaucher Disease (GD) is caused by defective glucocerebrosidase (GCase) activity and the consequent accumulation of its substrate, glucosylceramide (GC). This excess of accumulation of GC leads to broad functional impairments in multiple organs, but the pathogenic pathways leading to lipid laden macrophages (Gaucher cells) in visceral organs and their abnormal function is obscure. To understand the molecular pathogenesis of GD, developmental global gene expression was conducted by microarray analyses of total mRNAs from lung and liver of two distinct GCase point-mutated mice (V394L/V394L and D409V/null) and genetic background matched wild-type controls. INFg regulated pro-inflammatory and IL-4 regulated anti-inflammatory cytokine/mediator network were constructed in the lung and liver of GCase mutant mice. Progressive alterations of the INFg and IL-4 pathways were similar, but to different degrees, in visceral tissues from the two different GCase mutated mice. These analyses implicate IFNg regulated pro-inflammatory and IL-4 regulated anti-inflammatory networks in the differential pathophysiological progression.

Overall design: In order to understand the molecular pathogenesis of GD, the disease progression in those models were inverstigated in two visceral tissues (lung and liver) at four time points according to the genotypes. 9V/null: 4 weeks (4w), 12 weeks (12w), 18 weeks (18w), 28 weeks (28w); 4L: weeks (4w), 12 weeks (12w), 18 weeks (18w), 28 weeks (28w). The data from those models were analyzed relative to the adult wild type at 28 weeks.

Background corr dist: KL-Divergence = 0.0891, L1-Distance = 0.0753, L2-Distance = 0.0105, Normal std = 0.4948

0.925 Kernel fit Pairwise Correlations Normal fit

Density 0.463

0.000 CEM 1

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

Pre-normalization Quantiles

lung_9V/null_lung_9V/null_ 4w_rep1lung_9V/null_ 4w_rep2lung_9V/null_ (0.0463656) 12w_rep1lung_9V/null_ (0.0115145) 12w_rep2lung_9V/null_ (0.0248749) 18w_rep1lung_9V/null_ (0.0174708) 18w_rep2lung_9V/null_ (0.040351) 28w_rep1liver_9V/null_ (0.0569485) 28w_rep2liver_9V/null_ (0.0250315) 4w_rep1liver_9V/null_ (0.0130019) 4w_rep2liver_9V/null_ (0.0150004) 12w_rep1liver_9V/null_ (0.012929) 12w_rep2liver_9V/null_ (0.0189621) 18w_rep1liver_9V/null_ (0.0219091) 18w_rep2liver_9V/null_ (0.012458) 28w_rep1lung_4L_ (0.0224033) 28w_rep2lung_4L_ (0.012323)4w_rep1lung_4L_ (0.0223684)4w_rep2 (0.0321938)lung_4L_ 12w_rep1 (0.0293933)lung_4L_ 12w_rep2 (0.0382217)lung_4L_ 18w_rep1 (0.0536636)lung_4L_ 18w_rep2 (0.0328059)lung_4L_ 28w_rep1 (0.0201639)liver_4L_ 28w_rep2 (0.0707765)liver_4L_ 4w_rep1 (0.0401093)liver_4L_ 4w_rep2 (0.0194488)liver_4L_ 12w_rep1 (0.01658)liver_4L_ 12w_rep2 (0.0132613)liver_4L_ 18w_rep1 (0.0181537)liver_4L_ 18w_rep2 (0.026548)liver_4L_ 28w_rep1 (0.0233165)lung_WT_ 28w_rep2 (0.0163979)lung_WT_ 28w_rep1 (0.0236539)lung_WT_ 28w_rep2 (0.0489843)lung_WT_ 28w_rep3 (0.0178264)liver_WT_ 28w_rep4 (0.0130095)liver_WT_ 28w_rep1 (0.0178226)liver_WT_ 28w_rep2 (0.0173261) 28w_rep3 (0.0137685) (0.022662)[ min ] [ medium ] [ max ] CEM 1 Tmem231 26.8 280.2 671.5 P ( S | Z, I ) = 0.00 B9d1 27.0 358.3 1173.3 Mean Corr = 0.52036Tmem216 138.2 241.3 454.8 Tctn2 8.8 275.8 583.4 Cep290 0.4 38.5 267.0 Cc2d2a 96.8 356.0 733.2 Mks1 41.9 143.2 285.8 Tmem17 2.5 10.8 71.8 B9d2 186.7 395.6 1002.0 Ahi1 1.1 45.9 115.5 Tmem67 27.6 81.3 176.7 Nphp1 13.7 187.5 520.9 Tmem107 384.8 1759.8 6615.1 Ttc26 27.3 142.2 349.4 Arl6 89.9 385.5 1036.5 Ccdc173 4.6 41.9 111.8 CEM 1 + Enkd1 34.8 148.0 483.4 Top 10 Genes Bbs2 19.5 228.5 432.1 Wdr34 104.4 290.9 752.8 Bbs1 4.2 86.8 244.4 Rabl2 148.9 337.2 1697.4

Null module GEO Series "GSE4734" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 61 -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=GSE4734 Status: Public on Mar 05 2007 Title: Mouse brain region gene expression (430 2.0 Array) Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 17324278 Summary & Design: Summary: Gene expression patterns were determined from five brain regions (bed nucleus of the stria terminalis, hippocampus, hypothalamus, periaqueductal gray, and pituitary gland) in six mouse strains (129S6/SvEvTac, A/J, C57BL/6J, C3H/HeJ, DBA/2J, and FVB/NJ). At least two replicate samples per brain region/strain were analyzed using Affymetrix Mouse Genome 430 2.0 arrays.

Keywords: mouse strain and brain region comparison

Overall design: six mouse strains and five brain regions were analyzed

Background corr dist: KL-Divergence = 0.1388, L1-Distance = 0.0659, L2-Distance = 0.0086, Normal std = 0.4122

1.079 Kernel fit Pairwise Correlations Normal fit

Density 0.539

0.000 CEM 1

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

Pre-normalization Quantiles

129S6/SvEvTac129S6/SvEvTacA/J bed bed nucleusA/J nucleusbed bed nucleus ofC57BL/6J nucleus theof the stria ofC57BL/6J stria theof bedterminalis the striaterminalis nucleusC3H/HeJ stria bedterminalis terminalisrep1 nucleusC3H/HeJ of rep1bed the(430 rep2nucleus(430 striaC3H/HeJ of 2.0 rep2bed the(4302.0 Array)terminalis nucleus(430 striaofArray)DBA/2J 2.0 bedthe 2.0(0.00775514) Array)terminalis strianucleus(0.00577439) ofArray)DBA/2J rep1bed the terminalis(0.018846) nucleus(430 stria(0.0104295) ofFVB/NJ rep2bed the2.0 terminalis nucleus(430 ofstriaArray) rep1FVB/NJ bedthe 2.0 terminalis (430 strianucleus (0.0040315)ofArray) rep2129S6/SvEvTac bed the2.0 terminalis (430 strianucleusArray) (0.0051077)of rep3129S6/SvEvTac the2.0 terminalis (430(0.00868264) stria Array) rep1ofA/J hippocampusthe2.0 terminalis (430 hippocampus (0.0128566) stria Array)rep2 A/J2.0 hippocampus terminalis (430 hippocampus Array)(0.00518349) rep1 C57BL/6Jrep12.0 (430rep1(0.00786352) Array) (430rep2 C57BL/6J rep22.0(430 hippocampus2.0(430rep2(0.00693682) Array) (4302.0 Array) C3H/HeJ2.0(430 Array) hippocampus 2.0(0.00515029) Array) 2.0(0.012385) Array)C3H/HeJ (0.0146564) Array)hippocampusrep1 (0.00322612) (0.0174317) (430DBA/2J (0.0152615) hippocampusrep2 2.0 (430 DBA/2JArray) hippocampusrep1 2.0 (430 (0.0181087) FVB/NJArray) hippocampusrep2 2.0 (430 Array)(0.0164117)FVB/NJrep1 hippocampus 2.0 (430 (0.0158585) Array)129S6/SvEvTacrep2 hippocampus 2.0 (430 Array)(0.0172349) 129S6/SvEvTacrep1 2.0 (430(0.0181694) Array) A/Jrep2 hypothalamus 2.0 hypothalamus (430(0.0130107) Array)A/J hypothalamus 2.0 hypothalamus (0.0165409) Array)C57BL/6J rep1 rep1 (0.0161816) (430C57BL/6J rep2(430 hypothalamus 2.0rep2 (4302.0 Array)C3H/HeJ (430 Array)hypothalamus 2.0 2.0(0.0127344) Array)C3H/HeJ (0.00980279) hypothalamus Array)rep1 (0.0110717) DBA/2J(430 (0.00407415)hypothalamus rep2 2.0 DBA/2J (430 hypothalamusArray) rep1 2.0 (430 FVB/NJ(0.00963734) hypothalamusArray) rep2 2.0 (430 FVB/NJ Array)(0.00845225)rep1hypothalamus 2.0 (430 (0.00661904) 129S6/SvEvTac Array)rep2hypothalamus 2.0 (430 Array)(0.00788285)129S6/SvEvTac rep1 2.0 (430(0.0169097) Array)A/J rep2periaqueductal 2.0 periaqueductal (430(0.0167217) Array)A/J periaqueductal 2.0 periaqueductal (0.0164116) Array)C57BL/6J gray gray (0.0134873) rep1C57BL/6J grayrep1 periaqueductal (430gray rep2(430C3H/HeJ 2.0rep2 periaqueductal (4302.0 Array) (430 C3H/HeJArray) 2.0periaqueductal gray 2.0(0.00458515) Array) (0.00500922) DBA/2J Array)rep1 periaqueductal gray (0.0099837) (430 (0.00795534)DBA/2J periaqueductalrep2 gray 2.0 (430 Array) FVB/NJ rep1periaqueductal gray 2.0 (430 (0.00576646) Array) FVB/NJ rep2periaqueductal gray 2.0 (430 Array)(0.00909035)rep1129S6/SvEvTac periaqueductal gray 2.0 (430 (0.00518636) Array)rep2129S6/SvEvTac 2.0gray (430 Array)(0.00774636) rep1A/J pituitary2.0gray pituitary(430(0.00625338) Array) rep2A/J pituitary2.0 gland pituitary(430(0.0022938) Array)glandC57BL/6J 2.0rep1 gland rep1(0.0129319) Array)gland (430C57BL/6J rep2(430 pituitary 2.0rep2(0.00975949) (4302.0 Array)C3H/HeJ (430 Array)pituitary 2.0gland 2.0(0.045724) Array)C3H/HeJ pituitary(0.0523233) Array)rep1 gland (0.0439206) DBA/2J(430 pituitary(0.0369849) rep2gland 2.0 DBA/2J(430pituitary Array) rep1 gland 2.0 (430FVB/NJ pituitary(0.0363974) Array) rep2gland 2.0 (430 FVB/NJ Array)pituitary(0.0438809)rep1 gland 2.0 (430 (0.0288934) Array)pituitaryrep2 gland 2.0 (430 Array)(0.0312368) rep1 gland 2.0 (430(0.0385498) Array) rep2 2.0 (430(0.0395349) Array)[ min2.0 (0.0519419) Array) ] (0.0371513) [ medium ] [ max ] CEM 1 Tmem231 282.0 525.7 1278.7 P ( S | Z, I ) = 0.00 B9d1 281.5 442.2 1236.2 Mean Corr = 0.36380Tmem216 114.0 214.5 419.5 Tctn2 260.2 445.0 658.1 Cep290 21.9 90.0 167.4 Cc2d2a 458.9 692.9 1878.0 Mks1 107.8 241.0 928.4 Tmem17 3.3 35.8 143.5 B9d2 244.6 475.2 835.9 Ahi1 514.7 2358.1 5573.2 Tmem67 46.8 130.6 360.3 Nphp1 3.4 171.3 685.4 Tmem107 400.4 723.2 3485.5 Ttc26 198.9 323.4 714.5 Arl6 816.5 1194.6 1784.1 Ccdc173 54.8 142.5 342.6 CEM 1 + Enkd1 152.8 256.9 379.8 Top 10 Genes Bbs2 231.4 472.8 1581.3 Wdr34 205.2 473.0 860.4 Bbs1 343.8 578.1 790.6 Rabl2 360.3 868.3 1494.1

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 (0.35668)VehVeh3 (0.059909)VehLPS1 (0.0675322)VehLPS2 (0.0584877)VehLPS (0.0808699)SimvaVeh1 (0.0606359)SimvaVeh2 (0.0215888)SimvaVeh3 (0.0328006)SimvaLPS1 (0.0806879)SimvaLPS2 (0.041539)SimvaLPS3 (0.104021) (0.0352482) [ min ] [ medium ] [ max ] CEM 1 Tmem231 383.8 619.4 1302.1 P ( S | Z, I ) = 0.00 B9d1 236.9 484.3 718.4 Mean Corr = 0.33506Tmem216 161.6 217.5 328.4 Tctn2 242.8 304.2 524.3 Cep290 146.3 281.9 367.0 Cc2d2a 356.6 764.2 1093.1 Mks1 128.2 290.3 508.5 Tmem17 24.7 43.8 76.2 B9d2 456.3 614.3 728.1 Ahi1 13.7 49.8 73.5 Tmem67 38.1 78.2 218.5 Nphp1 131.0 344.6 735.0 Tmem107 1638.4 2712.3 4604.7 Ttc26 384.4 498.9 934.2 Arl6 388.0 691.7 875.2 Ccdc173 71.1 105.6 167.4 CEM 1 + Enkd1 161.1 218.7 357.9 Top 10 Genes Bbs2 96.9 290.3 421.4 Wdr34 220.1 276.9 573.7 Bbs1 306.3 463.4 708.7 Rabl2 762.0 1152.9 3000.5

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 (0.122992)intact three rep2 explantcultured for retinadays, (0.0910998)intact three cultured forbiologicalfrom retinadays,129 three 129 retinal forbiologicalfrom days mouse, 129rep1three 129 explantretinalwith (0.0743052) days mouse, 129biologicalrep2 chir99021, explantculturedretinalwith (0.0486527) 129biological chir99021, rep1 explantculturedretinal biologicalfor (0.127086) three rep2 explantcultured biologicalfor days, (0.0808528)rep1 three cultured for(0.111657)biological days, rep2 three for(0.111996)biological days[ rep1three min with (0.0492109) days rep2 chir99021, ]with (0.0326319) chir99021, biological[ mediumbiological rep1 (0.086095) rep2 (0.0634209) ] [ max ] CEM 1 Tmem231 384.2 463.4 517.4 P ( S | Z, I ) = 0.00 B9d1 538.4 754.9 868.7 Mean Corr = 0.40871Tmem216 401.4 566.6 658.4 Tctn2 190.2 235.8 337.6 Cep290 1028.5 1309.7 2072.1 Cc2d2a 712.7 1017.9 1511.7 Mks1 307.6 395.4 477.9 Tmem17 106.1 133.5 174.5 B9d2 565.0 695.1 806.3 Ahi1 53.0 102.6 152.6 Tmem67 32.7 40.9 45.8 Nphp1 522.2 677.9 820.8 Tmem107 2425.3 3889.0 6509.1 Ttc26 250.0 310.5 485.7 Arl6 6065.4 10215.2 17838.6 Ccdc173 376.4 487.1 687.2 CEM 1 + Enkd1 240.7 347.4 497.6 Top 10 Genes Bbs2 739.6 1667.8 2458.1 Wdr34 432.2 589.9 795.6 Bbs1 777.1 1021.4 1902.3 Rabl2 753.8 1229.5 1707.2

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 37ºC 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 (0.0698032)dayNTHi rep2N4 1, treated mouse,-daybio NTHi(0.035452) rep3N51, biotreated mouse,-day NTHi(0.0099685) rep1 N61, biotreated mouse, -day(0.054918) NTHi rep2 WT11, biotreated mouse, day(0.0917516) - rep3untreated WT27, bio mouse, day(0.0266961) - rep1untreated WT37, mouse, bio day(0.058038) - rep2untreated S47, mouse,bio -(0.0771906) saline reprep3S5 mouse,bio1 - treated(0.0845962) (0.0214467)saline repS6 bio2 - treatedmouse, (0.110085)saline rep 3 treatedmouse,(0.0850314)day7, bio mouse,day7, rep1 bio (0.114981)day7, rep2[ biomin (0.0514036) rep3 (0.108638)] [ medium ] [ max ] CEM 1 Tmem231 469.8 753.2 1077.0 P ( S | Z, I ) = 0.00 B9d1 683.3 1217.0 2022.7 Mean Corr = 0.43854Tmem216 139.0 294.7 447.8 Tctn2 391.2 772.8 1160.0 Cep290 230.1 687.8 1208.8 Cc2d2a 930.3 1785.2 2710.3 Mks1 220.9 384.8 693.0 Tmem17 23.2 66.6 111.1 B9d2 197.4 384.3 570.3 Ahi1 1.6 9.2 16.8 Tmem67 6.2 28.5 70.1 Nphp1 498.8 1010.9 1531.7 Tmem107 4123.0 10506.6 15739.8 Ttc26 391.9 693.9 1271.9 Arl6 1956.3 3230.6 4451.0 Ccdc173 392.6 849.9 2291.8 CEM 1 + Enkd1 94.7 199.7 282.0 Top 10 Genes Bbs2 165.1 351.6 454.7 Wdr34 322.2 952.4 2231.8 Bbs1 348.2 1125.1 1845.6 Rabl2 1294.8 2695.0 4728.7

Null module GEO Series "GSE22824" 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=GSE22824 Status: Public on Jan 01 2011 Title: Gene expression in retina and LGN of wild type and Chrnb2-/- mice Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21547082 Summary & Design: Summary: Mice lacking the beta 2 subunit (Chrnb2) of the neuronal nicotinic acetylcholine receptor display altered retinal waves and disorganized projections of the retinal ganglion cells to the lateral geniculate nucleus (LGN). mRNA populations from retinas and LGN from Chrnb2-/-and wild type (C57BL/6J) mice were compared at 4 days postnatal, when RGC segregation to the LGN begins in WT mice. Retinal mRNAs were also compared at adulthood.

Using microarray hybridization, we identified transcripts which are differentially expressed between Chrnb2-/- and wild type animals in these two tissues at these two ages.

Overall design: mRNA was isolated from retina and LGN of three male littermates each of WT and Chrnb2-/- mice at P4. mRNA from retinas of two adult male littermates of each type was also examined.

Background corr dist: KL-Divergence = 0.0272, L1-Distance = 0.0235, L2-Distance = 0.0007, Normal std = 0.6813

0.595 Kernel fit Pairwise Correlations Normal fit

Density 0.297

0.000 CEM 1

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

Pre-normalization Quantiles

PicciottoPicciotto b2 -/- Picciottoretina b2 -/- P4, Xuretina b2 mouseb2 -/- -/-P4, Xuretina retina Amouseb2 (0.034208) -/-P4, XuP4, retina Bmouseb2 mouse (0.0236926) -/- WildP4, retina C Amouse (0.0427016)type (0.0355649) WildP4, retina Bmouse type (0.0170578)Wild P4, retina C typemouse (0.0277877)Picciotto P4, retina Amouse (0.0184139)Picciotto P4, b2 B-/-LGNmouse (0.0406086)Picciotto b2 P4,C-/- (0.0300129)XuLGN mouse b2 b2 -/-P4, -/- XuLGN BLGNmouse (0.0319102)b2 P4, -/-P4,Xu LGNCmouse mouse b2(0.045774) -/-P4,Wild LGND Amouse (0.0459968) (0.0460643)type P4,Wild LGNBmouse (0.0312253)type WildP4, LGNC mouse (0.0358109)type PicciottoP4, LGN Amouse (0.0514477) PicciottoP4, b2 Dmouse -/- (0.0449435) Xuretina b2 b2E -/- (0.034579)-/-adult, Xuretina retina b2 mouse -/-adult, Wildadult, retina type1542mouse mouse Wildadult, retina(0.0767172) type1543 77mouse adult, (0.0287649) retina(0.0680333) 78 mouse adult,(0.0329511) 748mouse (0.0829039) 763[ min (0.07283) ] [ medium ] [ max ] CEM 1 Tmem231 451.3 571.2 682.8 P ( S | Z, I ) = 0.00 B9d1 143.3 445.2 1192.2 Mean Corr = 0.46961Tmem216 195.0 500.9 946.7 Tctn2 214.9 310.1 494.9 Cep290 28.0 375.4 978.9 Cc2d2a 250.0 1242.4 1743.6 Mks1 127.4 523.0 943.0 Tmem17 125.5 194.8 331.4 B9d2 416.0 725.6 1626.1 Ahi1 41.4 115.1 257.2 Tmem67 8.1 30.5 145.0 Nphp1 355.2 554.3 673.1 Tmem107 337.0 1494.3 3279.2 Ttc26 174.0 280.9 400.1 Arl6 1513.6 4976.6 7074.1 Ccdc173 19.2 225.4 426.4 CEM 1 + Enkd1 112.6 344.7 471.9 Top 10 Genes Bbs2 181.5 632.4 1754.1 Wdr34 582.8 1080.7 1672.5 Bbs1 477.9 721.8 1798.3 Rabl2 953.3 1439.4 2251.1

Null module GEO Series "GSE40412" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 14 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40412 Status: Public on Mar 04 2013 Title: Replication-coupled passive DNA demethylation for the erasure of genome imprints in mice Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 23241950 Summary & Design: Summary: Genome-wide DNA demethylation, including the erasure of genome imprints, in primordial germ cells (PGCs), is critical as a first step for creating the totipotent epigenome in the germ line. Here, we provide evidence that contrary to the prevailing model involving active DNA demethylation, imprint erasure in mouse PGCs occurs in a manner consistent with replication-coupled passive DNA demethylation: PGCs erase imprints during their rapid proliferation with little de novo as well as maintenance DNA methylation potential and no major chromatin alterations. Our findings necessitate the re-evaluation of and provide novel insights into the mechanism of genome-wide DNA demethylation in PGCs.

Overall design: We performed expression analysis of primordial germ cells (PGCs) at embryonic days 10.5-13.5. Because the number of PGCs available at these stages were low, cDNAs were amplified by the method that we previously published (Kurimoto et al. 2006, NAR 34: e42 (PMID 16547197)). To include analysis of PGC gene expression at E9.5, we re-normalized the data from our E9.5 PGC samples (GSM744103, GSM744104) from our previous publication (Hayashi et al., 2011, Cell 146: 519-32 (PMD 21820164)) together with the data from this submission.

Background corr dist: KL-Divergence = 0.1317, L1-Distance = 0.0284, L2-Distance = 0.0016, Normal std = 0.3977

1.003 Kernel fit Pairwise Correlations Normal fit

Density 0.502

0.000 CEM 1

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

Pre-normalization Quantiles

E9.5 primordialE9.5 primordialE10.5 germ primordialcells,E11.5 germ biological primordialcells,E12.5 germ biological primordial E12.5cells,rep1 germ (0.145084)primordialbiological E13.5cells,rep2 germ (0.0508121)primordialbiological E13.5cells, rep1germ primordial female,(0.0858455) E10.5cells, rep1germ primordialmale,biological(0.0213702) E11.5cells, germ biological primordialmale, E12.5cells, germrep1 biological primordialfemale, (0.0627682)E12.5rep1cells, germ (0.0274977) primordialbiologicalbiological E13.5rep1cells, germ (0.0322784) primordialbiological E13.5cells, rep2germrep1 primordial male, (0.0974264)(0.12286) cells, rep2germ biological female,(0.0770511) cells, germ male,biological rep2cells, biological(0.0318966) female,[ rep2min biological (0.0891402)rep2 ] (0.067556) rep2 (0.0884136)[ medium ] [ max ] CEM 1 Tmem231 1049.6 1272.6 1444.9 P ( S | Z, I ) = 0.00 B9d1 293.2 1407.5 2112.2 Mean Corr = 0.38707Tmem216 100.9 445.1 561.7 Tctn2 256.4 447.5 614.6 Cep290 106.3 128.5 360.7 Cc2d2a 60.4 306.9 778.1 Mks1 119.1 321.4 486.7 Tmem17 120.7 179.3 373.1 B9d2 823.5 1227.4 1668.7 Ahi1 12.9 42.8 68.2 Tmem67 19.6 46.3 69.9 Nphp1 123.9 320.4 696.8 Tmem107 1994.9 2496.5 4253.7 Ttc26 162.8 447.7 624.1 Arl6 399.5 1011.0 1644.7 Ccdc173 34.6 77.4 111.1 CEM 1 + Enkd1 763.0 927.5 1078.3 Top 10 Genes Bbs2 209.9 415.1 773.7 Wdr34 1984.4 2436.0 3371.0 Bbs1 31.2 105.3 219.0 Rabl2 187.7 344.1 557.8

Null module GEO Series "GSE10902" 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=GSE10902 Status: Public on Jun 06 2008 Title: Differential expression between FHL2-/- and WT MEFs. Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 19018287 Summary & Design: Summary: The LIM-only protein FHL2 acts as a transcriptional modulator that positively or negatively regulates multiple signaling pathways. We recently reported that FHL2 cooperates with CBP/p300 in the activation of ˆ-catenin/TCF target gene cyclin D1. In this paper, we demonstrate that FHL2 is associated with the cyclin D1 promoter at the TCF/CRE site, providing evidence that cyclin D1 is a direct target of FHL2. We show that deficiency of FHL2 greatly reduces the proliferative capacity of spontaneously immortalized mouse fibroblasts which is associated with decreased expression of cyclin D1 and p16INK4a, and hypophosphorylation of Rb. Reexpression of FHL2 in FHL2-null fibroblasts efficiently restores cyclin D1 levels and cell proliferative capacity, indicating that FHL2 is critical for cyclin D1 activation and cell growth. Moreover, ectopic cyclin D1 expression is sufficient to override growth inhibition of immortalized FHL2-null fibroblasts. Gene expression profiling revealed that FHL2 deficiency triggers a broad change of the cell cycle program that is associated with downregulation of several G1/S and G2/M cyclins, E2F transcription factors and DNA replication machinery, thus correlating with reduced cell proliferation. This change also involves downregulation of the negative cell cycle regulators, particularly INK4 inhibitors, which could counteract the decreased expression of cyclins, allowing cells to grow. Our study illustrates that FHL2 can act on different aspects of the cell cycle program to finely regulate cell proliferation.

Keywords: mouse embryonic fibroblasts derived from FHL2-/- and WT mouse embryos (14.5 days)

Overall design: Two biological genotypes, FHL2-/- and WT MEF cells. Three spontaneously immortalized clones of each genotype were analyzed using Affymetrix arrays.

Background corr dist: KL-Divergence = 0.0204, L1-Distance = 0.0119, L2-Distance = 0.0002, Normal std = 0.7307

0.546 Kernel fit Pairwise Correlations Normal fit

Density 0.273

0.000 CEM 1

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

Pre-normalization Quantiles

MEF.FHL2mutEMEF.FHL2mutHMEF.FHL2mutJ (0.253098)MEF.WT.E (0.152936)MEF.WT.F (0.172311) (0.129935)MEF.WT.I (0.126981) (0.16474) [ min ] [ medium ] [ max ] CEM 1 Tmem231 273.6 634.2 814.5 P ( S | Z, I ) = 0.00 B9d1 285.7 773.8 949.3 Mean Corr = 0.35829Tmem216 252.2 299.9 375.6 Tctn2 196.7 283.9 329.0 Cep290 42.2 52.3 60.1 Cc2d2a 466.4 647.6 964.9 Mks1 87.6 171.6 313.9 Tmem17 57.9 71.8 97.2 B9d2 323.3 393.9 448.8 Ahi1 67.1 79.5 86.1 Tmem67 32.3 41.0 46.3 Nphp1 489.9 555.1 601.9 Tmem107 706.5 1628.0 2154.7 Ttc26 66.9 109.4 128.3 Arl6 616.2 704.7 832.0 Ccdc173 32.2 41.6 49.6 CEM 1 + Enkd1 353.8 481.6 609.3 Top 10 Genes Bbs2 188.8 237.9 459.7 Wdr34 182.0 490.8 532.9 Bbs1 49.5 108.5 128.4 Rabl2 350.2 474.3 613.3

Null module GEO Series "GSE19729" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 14 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE19729 Status: Public on Jan 05 2010 Title: Interactions between developing B-lymphocytes and stromal cells reveal complex interactions and two-way communication Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 20152025 Summary & Design: Summary: Full title: Genomics based analysis of interactions between developing B-lymphocytes and stromal cells reveal complex interactions and two-way communication

In order to identify extra cellular signals that promote B lymphocyte development we created a database with approximately 400 receptor ligand pairs and software matching gene expression data from two cell populations to obtain information about possible communication pathways. Using this database and gene expression data from NIH3T3 cells (unable to support B cell development) and OP-9 cells (strongly supportive of B cell development) and data from pro-B and pre-B cells as well as mature peripheral B-lineage cells, we were able to identify a set of potential stage and stromal cell restricted communication pathways. Functional analysis of some of these potential ways of communication allowed us to identify BMP-4 as a potent stimulator of B-cell development in vitro. Further, the analysis suggested that there existed possibilities for progenitor B cells to send signals to the stroma. The functional consequences of this were investigated by co-culture experiments revealing that the co-incubation of stromal cells with pro-B cells altered both the morphology and the gene expression pattern in the stromal cells.

Overall design: OP9 Stromal cells has been cultured with and without primary PreB cells drived from LSK cells in culture or PreB cell lines 230-238. OP9 cells has been isolated by FACS and microarray performed to study the effect of PreB cells on OP9's at the level of RNA expression. The results have been compared with 3T3 and MC3T3 cells.

Background corr dist: KL-Divergence = 0.0722, L1-Distance = 0.0433, L2-Distance = 0.0037, Normal std = 0.5033

0.793 Kernel fit Pairwise Correlations Normal fit

Density 0.396

0.000 CEM 1

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

Pre-normalization Quantiles

NIH3T3 NIH3T3cells biological OP9cells with biologicalOP9 rep1 230-238 with (0.0237322)OP9 rep2 230-238 biological biological (0.030442)OP9 biological biological rep1 MC3T3rep1 (0.0754972) (0.0575495) rep2 MC3T3biologicalrep2 (0.056997) (0.0451074) PreBbiological rep1 cellsPreB (0.0904677) rep2biological cellsProB (0.0830296) biological cells rep1ProB biological(0.088784) cells rep2MatureB biological(0.106325) rep1MatureB cells (0.0564606) rep2biological cells (0.0451661) biological rep1 (0.0894851) rep2 (0.150957)[ min ] [ medium ] [ max ] CEM 1 Tmem231 108.0 262.4 387.1 P ( S | Z, I ) = 0.00 B9d1 82.2 484.8 794.0 Mean Corr = 0.30336Tmem216 95.5 398.0 916.8 Tctn2 42.9 125.4 305.7 Cep290 29.6 86.6 160.6 Cc2d2a 33.6 291.1 681.5 Mks1 114.0 267.8 624.7 Tmem17 33.0 52.1 98.5 B9d2 364.0 562.6 2327.3 Ahi1 28.8 56.6 113.1 Tmem67 30.6 41.2 53.0 Nphp1 82.1 500.7 953.8 Tmem107 297.4 1628.0 2290.5 Ttc26 29.3 148.6 229.5 Arl6 158.2 759.2 1547.7 Ccdc173 34.7 53.3 92.6 CEM 1 + Enkd1 209.5 326.4 1691.7 Top 10 Genes Bbs2 98.8 339.4 493.1 Wdr34 119.1 328.4 510.6 Bbs1 34.8 88.6 123.1 Rabl2 177.9 444.9 564.1

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 (0.127393) TTrep Hflu ME2 (0.0477607) controlrep ME1 (0.071807) controlrep ME3 (0.0244165) TTrep Hflu ME4 (0.0213933) controlrep ME2 (0.0418896) controlrep ME5 (0.0748767) controlrep ME6 (0.0784753) TTrep Hflu ME7 (0.0612505) TTrep Hflu ME3 (0.074736) TTrep Hflu ME4 (0.0658583) controlrep ME5 (0.0303988) TTrep Hflu ME8 (0.0351878) TTrep Hflu ME6 (0.0496347) TTrep Hflu ME7 (0.0484379) TTrep Hflu 8 (0.0612164) rep 9 (0.0852679) [ min ] [ medium ] [ max ] CEM 1 Tmem231 305.2 399.3 766.7 P ( S | Z, I ) = 0.00 B9d1 429.5 715.3 1121.3 Mean Corr = 0.30964Tmem216 950.1 1175.5 1454.0 Tctn2 140.3 194.2 298.0 Cep290 114.3 131.3 152.9 Cc2d2a 366.6 463.3 771.8 Mks1 86.8 113.6 141.9 Tmem17 143.4 190.3 255.2 B9d2 348.7 510.2 720.7 Ahi1 21.9 28.8 38.7 Tmem67 6.0 7.5 12.5 Nphp1 283.7 348.0 433.4 Tmem107 703.0 973.1 1516.0 Ttc26 70.5 104.2 149.3 Arl6 334.3 400.1 492.7 Ccdc173 101.8 165.3 264.3 CEM 1 + Enkd1 249.9 345.3 441.1 Top 10 Genes Bbs2 360.0 460.7 599.2 Wdr34 404.8 618.5 925.3 Bbs1 96.1 131.5 172.3 Rabl2 263.0 322.2 432.3

Null module GEO Series "GSE34126" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 19 -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=GSE34126 Status: Public on Dec 05 2011 Title: An Animal Model of Myc-driven medulloblastoma Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 22340590 Summary & Design: Summary: Medulloblastoma (MB) is the most common malignant brain tumor in children. Patients whose tumors exhibit overexpression or amplification of the MYC oncogene (c-MYC) usually have an extremely poor prognosis, but there are no animal models of this subtype of the disease. Here we show that cerebellar stem cells expressing Myc and mutant Trp53 (p53) generate aggressive tumors following orthotopic transplantation. These tumors consist of large, pleiomorphic cells and resemble human MYC-driven MB at a molecular level. Notably, antagonists of PI3K/mTOR signaling, but not Hedgehog signaling, inhibit growth of tumor cells. These findings suggest that cerebellar stem cells can give rise to MYC-driven MB, and identify a novel model that can be used to test therapies for this devastating disease.

To gain insight into the pathways that control growth of MYC-driven MB, we compared gene expression profiles of murine Myc/DNp53 (MP) tumor cells to those of freshly isolated cerebellar stem cells (Prom1+Lin- cells) and of tumors from Ptch1 mutant mice (a model for Sonic Hedgehog-associated MB). RNA was isolated from stem cells and tumor cells using the RNAqueous kit (Ambion). RNA was labeled and hybridized to Affymetrix Mouse Genome 430 2.0 arrays.

Overall design: 19 mouse cell samples (stem cells and tumor cells) were analyzed. There are four groups of samples, three with five biological replicates and the last with four (one outlier was removed). To gain insight into the mechanisms of transformation into tumors, we compared the gene expression profiles of MP tumor cells derived from stem cells (Myc/DNp53-infected Prom1+Lin- cells, designated MP-pl) or progenitors (Myc/DNp53-infected Prom1+ cells, designated MP-p) to gene expression profiles of uninfected stem cells (designated NSC) and profiles from a distinct model of medulloblastoma, the patched mutant mouse (designated ptch1).

Background corr dist: KL-Divergence = 0.1063, L1-Distance = 0.0311, L2-Distance = 0.0018, Normal std = 0.4292

0.929 Kernel fit Pairwise Correlations Normal fit

Density 0.465

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

normal normalstem cells normalstem rep1 cells normalstem (0.0495498) rep2 cells normalstem (0.0750714) rep3 cells stem (0.0298672) rep4 cell-derivedcellsstem (0.112886) rep5 cell-derivedstem (0.104683) tumors cell-derivedstem tumorsrep1 cell-derivedstem (0.026048) tumorsrep2 cell-derivedpatched (0.0343447) tumorsrep3patched (0.0243553)tumors tumorsrep4patched (0.0387583) tumorsrep1 rep5 (0.0538312)patched (0.00723544) tumorsrep2 (0.0930212)progenitor-derived tumorsrep3 (0.0271268)progenitor-derived rep4 (0.0711007)progenitor-derived tumorsprogenitor-derived tumorsrep1progenitor-derived (0.0181935) tumorsrep2 (0.0745795) tumorsrep3 (0.087557) tumorsrep4 (0.0388392) rep5[ (0.0329519)min ] [ medium ] [ max ] CEM 1 Tmem231 271.5 407.9 585.4 P ( S | Z, I ) = 0.00 B9d1 226.4 576.6 1230.6 Mean Corr = 0.39929Tmem216 173.1 429.6 526.4 Tctn2 104.4 134.6 245.6 Cep290 156.2 228.9 327.5 Cc2d2a 216.1 384.0 549.1 Mks1 222.1 322.4 451.2 Tmem17 43.6 63.6 110.1 B9d2 239.3 487.3 733.3 Ahi1 46.8 57.8 345.2 Tmem67 34.6 41.1 81.1 Nphp1 562.1 1216.5 3724.0 Tmem107 1300.1 3947.6 6013.8 Ttc26 244.3 334.8 473.4 Arl6 1275.5 2108.4 3957.6 Ccdc173 99.6 135.7 204.8 CEM 1 + Enkd1 383.8 665.5 1201.4 Top 10 Genes Bbs2 144.0 444.1 614.4 Wdr34 275.0 503.9 704.9 Bbs1 60.3 186.9 404.7 Rabl2 795.4 1191.4 2170.5

Null module GEO Series "GSE16496" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 102 -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=GSE16496

Background corr dist: KL-Divergence = 0.3007, L1-Distance = 0.0716, L2-Distance = 0.0154, Normal std = 0.2865 GEO Series "GSE15760" 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=GSE15760 Status: Public on Apr 01 2010 Title: Comparative transcriptional profiling of tumor-associated and normal lymphatic endothelial cells Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: In the past decade, the relevance of tumor-induced lymphangiogenesis for the metastatic spread of tumor cells has been demonstrated, thus indicating the potential of targeting tumor lymphangiogenesis to treat cancer. Whereas numerous preclinical studies demonstrated that blocking angiogenesis or lymphangiogenesis could inhibit tumor metastasis, the scarcity of highly selective targeting candidates hampers their translation to the clinic.

We employed a new approach consisting of immuno-laser capture microdissection (i-LCM) and transcriptional profiling by means of microarrays in order to identify novel tumor-specific endothelial markers.

Overall design: By using short immunostainings prior to microdissection, specific identification of lymphatic (LECs) and blood (BECs) endothelial cells was allowed. For the subsequent gene expression profiling, a single round of the Ribo-Spia amplification method in combination with the Affymterix microarray platform was used. Comparison of gene expression profiles of tumor-associated and normal LECs resulted in the identification of differentially expressed genes in tumor-associated lymphatic vasculature.

Background corr dist: KL-Divergence = 0.0432, L1-Distance = 0.0637, L2-Distance = 0.0065, Normal std = 0.6547

0.609 Kernel fit Pairwise Correlations Normal fit

Density 0.305

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

LECs fromLECs healthy fromLECs healthytissue, fromtumor-associated healthybiologicaltissue,tumor-associated biologicaltissue, replicatetumor-associated LECs, biological replicate 1 biological (0.13206)LECs, replicate 2 biological (0.107081)LECs, replicate 3 biological (0.276943) replicate 1[ (0.0959842) min replicate 2 (0.0940688) ] 3 (0.293863)[ medium ] [ max ] CEM 1 Tmem231 61.1 89.4 112.4 P ( S | Z, I ) = 0.00 B9d1 325.9 563.4 614.9 Mean Corr = 0.34800Tmem216 92.2 200.3 345.2 Tctn2 105.7 293.3 425.9 Cep290 34.1 54.6 71.9 Cc2d2a 75.1 236.3 489.5 Mks1 582.0 1001.0 1365.6 Tmem17 102.2 171.9 227.3 B9d2 547.0 904.3 1402.5 Ahi1 388.2 519.7 1032.6 Tmem67 73.4 122.5 256.0 Nphp1 232.5 465.3 661.2 Tmem107 44.5 49.1 84.2 Ttc26 135.7 146.3 349.9 Arl6 95.9 176.4 268.5 Ccdc173 74.9 93.4 362.6 CEM 1 + Enkd1 271.2 483.5 594.0 Top 10 Genes Bbs2 452.1 759.2 1925.6 Wdr34 180.9 206.3 308.7 Bbs1 68.2 90.9 103.3 Rabl2 309.0 678.4 993.2

Null module GEO Series "GSE9760" 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=GSE9760 Status: Public on Dec 04 2007 Title: Embryonic stem cells with expanded CAG repeats (lorin-affy-mouse-501743) Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: Huntington´s disease (HD) is a devastating neurodegenerative disease, with out effective treatment. Despite significant advances, our understanding of how an expanded CAG repeat in the amino terminus of the large ubiquitously expressed HD gene product remains incomplete. Augmented adult neurogenesis in response to acute and chronic injury, including Huntington´s disease, has been demonstrated, but its role development, disease, and recovery is largely unknown, as are the factors controlling it. The HD gene product, huntingtin (htt) is know to interact with a number of transcription factors which subsequently influence gene expression. Understanding the factors involved in controlling neurogenesis in response to disease would bridge a significant knowledge gap and have tremendous therapeutic potential.

We propose to identify transcripts responsible for CAG repeat facilitated neurogenesis.

Our hypothesis is that expanded CAG repeats in the Huntington´s disease gene facilitates neurogenesis by altering transcription of genes critical in neurogenesis.

We have developed a model in which mouse embryonic stem cells (ESC) with expanded CAG repeats have facilitated neurogenesis. In this model more ESC with expanded CAG repeats transition to neuronal precursors and then develop into mature neurons more rapidly than control ESC. We propose to compare the gene expression profiles between ESC with expanded CAG repeats and control ESCs on days 4 and 6 of neuronal differentiation. Initial studies indicate that key transcriptional differences are occurring at these time points. Control ECS and a an ESC line with150 CAG repeats will be differentiated in triplicate, and RNA isolated form each replicate. It is anticipated that comparison of gene expression between the control and CAG repeat lines at each time point will identify transcripts involved in CAG repeat facilitated neurogenesis. Observed differences at day 4 may be more relevant to the transition from ESC to neuronal precursor whereas differences at day 6 may be more relevant to the neuronal precursor to neuron transition.

Keywords: time-course

Overall design:

Background corr dist: KL-Divergence = 0.0981, L1-Distance = 0.0297, L2-Distance = 0.0012, Normal std = 0.4524

0.899 Kernel fit Pairwise Correlations Normal fit

Density 0.450

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

nervousnervous system:nervous system: HM1 nervousday system: HM1 4 replicate nervousday system: HM1 4 replicate nervousday1_le1 system: CAG150 4 replicate(0.0804149) nervous2_le1 system: CAG day (0.0759227) nervous1503_le14 system: replicateCAG day (0.0690203) nervous150 4system: CAGreplicate 1_le1day nervous150 4system: CAG(0.0468323)replicate day2_le1 nervous150 6system: CAGreplicate(0.143185) day3_le1 nervous150 6system: HM1replicate(0.10531) day1_le1 day 6system: HM1replicate(0.0883242) 62_le1 replicate day HM1 (0.101335) 63_le1 replicate day1_le1 (0.0220937) 6 replicate(0.1231) [2_le1 min (0.0954049) 3_le1 ] (0.0490564) [ medium ] [ max ] CEM 1 Tmem231 432.3 628.8 772.2 P ( S | Z, I ) = 0.00 B9d1 1540.9 2240.0 2546.4 Mean Corr = 0.39842Tmem216 591.2 742.1 830.6 Tctn2 350.5 432.4 627.9 Cep290 202.4 342.0 443.7 Cc2d2a 121.6 191.1 270.5 Mks1 294.6 512.7 713.3 Tmem17 39.4 91.4 165.7 B9d2 258.6 351.0 433.6 Ahi1 113.0 177.9 204.6 Tmem67 33.0 68.6 99.7 Nphp1 462.2 525.8 648.1 Tmem107 2168.8 3690.1 4326.0 Ttc26 354.7 418.6 518.6 Arl6 1942.5 2317.2 2531.6 Ccdc173 97.8 179.8 227.8 CEM 1 + Enkd1 458.4 615.7 926.6 Top 10 Genes Bbs2 270.1 326.4 501.1 Wdr34 348.1 474.1 577.9 Bbs1 220.3 343.7 644.1 Rabl2 608.8 829.9 1021.7

Null module GEO Series "GSE31940" 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=GSE31940 Status: Public on Mar 01 2012 Title: White adipose tissue from aP2-Pex5 knockout and control mice Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: These arrays contain data from gonodal adipose tissue of aP2-Pex5 -/- male mice

Overall design: 4 arrays from gonadal adipose tissue from control mice (Swiss background) are compared with 4 arrays from gonadal adipose tissue of aP2-Pex5 knockout mice. The latter lack functional peroxisomes in adipose tissue.

Background corr dist: KL-Divergence = 0.0585, L1-Distance = 0.0201, L2-Distance = 0.0006, Normal std = 0.5314

0.751 Kernel fit Pairwise Correlations Normal fit

Density 0.375

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

WAT1-ctWAT6-ko (0.03047)WAT2-ct (0.0688384)WAT8-ko (0.267305)WAT3-ctr (0.160798)WAT9-ko (0.208881)WAT4-ct (0.0358343)WAT10-ko (0.18001) (0.0478642) [ min ] [ medium ] [ max ] CEM 1 Tmem231 292.4 393.3 518.8 P ( S | Z, I ) = 0.00 B9d1 369.7 495.1 579.9 Mean Corr = 0.38758Tmem216 524.7 734.2 814.2 Tctn2 195.3 256.0 307.0 Cep290 161.7 209.5 236.9 Cc2d2a 636.2 723.9 794.3 Mks1 235.9 291.6 300.9 Tmem17 40.9 48.3 62.3 B9d2 283.4 369.6 396.7 Ahi1 54.9 73.7 85.9 Tmem67 45.9 65.6 78.4 Nphp1 608.5 811.5 892.2 Tmem107 521.2 1462.6 2142.5 Ttc26 108.4 219.8 286.2 Arl6 813.1 1051.4 1096.0 Ccdc173 68.7 106.5 121.9 CEM 1 + Enkd1 159.4 212.5 229.7 Top 10 Genes Bbs2 359.0 550.6 613.9 Wdr34 300.3 457.2 521.6 Bbs1 186.6 300.0 334.8 Rabl2 361.9 446.1 530.2

Null module GEO Series "GSE53951" 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=GSE53951 Status: Public on Jan 10 2014 Title: Gene expression after type-I interferon treatment in primary neurons, primary fibroblasts and L929 cells Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 24453359 Summary & Design: Summary: Microarray expression profilling of mouse primary mixed cortical/hippocampal neurons, primary fibroblasts and L929 cells to compare ISGs signature in disctinct cell types

Overall design: Primary mixed cortical/hippocampal neurons, primary fibroblasts (MEFs) and L929 cells were mock-treated or treated with 5U/mL of IFN-beta and RNA was harvested after 24 hours. For neurons and fibroblast, 2 samples were analyzed for each condition.

Background corr dist: KL-Divergence = 0.0405, L1-Distance = 0.0863, L2-Distance = 0.0101, Normal std = 0.7845

0.611 Kernel fit Pairwise Correlations Normal fit

Density 0.305

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

neurons_mock_sample1neurons_IFNb_sample1neurons_mock_sample2neurons_IFNb_sample2 (0.0475392)MEFs_mock_sample1 (0.0792548)MEFs_IFNb_sample1 (0.0662684)MEFs_mock_sample2 (0.0701512) MEFs_IFNb_sample2(0.0326571) (0.0539497)L929_mock L929_IFNb(0.0491383) (0.277013) (0.0507857) (0.273242) [ min ] [ medium ] [ max ] CEM 1 Tmem231 194.3 266.3 401.5 P ( S | Z, I ) = 0.00 B9d1 463.0 584.9 1186.0 Mean Corr = 0.31552Tmem216 285.2 358.4 960.4 Tctn2 114.1 172.7 227.1 Cep290 120.5 221.1 520.1 Cc2d2a 223.4 357.7 639.7 Mks1 95.4 131.6 256.3 Tmem17 13.6 66.3 107.9 B9d2 201.8 280.9 533.7 Ahi1 5.0 37.7 120.5 Tmem67 6.0 26.1 67.3 Nphp1 174.2 298.0 918.6 Tmem107 871.6 1319.9 6890.4 Ttc26 173.3 218.9 871.9 Arl6 754.4 1819.5 2693.1 Ccdc173 39.7 69.8 155.3 CEM 1 + Enkd1 169.2 279.3 890.0 Top 10 Genes Bbs2 58.8 246.0 372.1 Wdr34 221.1 723.2 1115.4 Bbs1 39.2 253.8 455.9 Rabl2 325.2 812.4 953.3

Null module GEO Series "GSE5245" 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=GSE5245 Status: Public on Apr 03 2008 Title: Profiling of CD4+ T cells responding to transient or persistent antigen presented by dendritic cells in vivo Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 17881563 Summary & Design: Summary: These experiments were done to compare the gene expression profiles in CD4+ T cells responding to antigen presented by dendritic cells transiently or persistently. Some treatments include the activation of the dendritic cells by CD40 engagement.

Keywords: immune response

Overall design: 2-4x106 lymph node cells from AND TCR-transgenic animals that expressed the congenic marker CD90.1 were transferred into double-transgenic (Ii-rTA/TIM) recipient animals that expressed the corresponding peptide from moth cytochrome c under a doxycycline-controllable promoter and were FACS-sorted 60 hours later. Recipients expressed the antigen not at all (ctrl), transiently (short) or throughout the experiment (long) due to different doxycycline treatment protocols. A second variable tested was the activation status of the dendritic cells: recipients were either injected by the stimulatory antibody FGK45.5 targeting CD40 (FGK) or PBS (PBS).

Background corr dist: KL-Divergence = 0.0477, L1-Distance = 0.0650, L2-Distance = 0.0079, Normal std = 0.5996

0.665 Kernel fit Pairwise Correlations Normal fit

Density 0.333

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

AND T cells-noAND T cells-noAND dox, TPBS-rep1 cells-noAND dox, TPBS-rep2 cells-noAND dox,(0.0257861) TPBS-rep3 cells-noAND dox,(0.12553) TFGK-rep1 cells-shortAND dox,(0.0223871) TFGK-rep2 cells-shortAND (0.0124393) dox, T cells-shortAND PBS-rep1(0.289734) dox, T cells-shortAND PBS-rep2 dox,(0.0259828) T cells-shortAND PBS-rep3 dox,(0.0969895) T cells-longAND FGK-rep1 dox,(0.0322284) T cells-longAND FGK-rep2 dox, (0.0721804) T cells-longANDPBS-rep1 dox, (0.0630986) T cells-longANDPBS-rep2 dox,(0.0607801) T cells-longANDPBS-rep3 dox,(0.0401827) T cells-longFGK-rep1 dox,(0.0433012) FGK-rep2 dox,(0.030721) FGK-rep3 (0.0250228)[ (0.0336366)min ] [ medium ] [ max ] CEM 1 Tmem231 141.9 190.3 371.1 P ( S | Z, I ) = 0.00 B9d1 61.6 86.9 103.8 Mean Corr = 0.50067Tmem216 73.0 91.2 127.5 Tctn2 74.3 85.6 129.6 Cep290 28.1 32.6 47.1 Cc2d2a 79.0 123.1 217.9 Mks1 166.9 245.9 581.2 Tmem17 44.6 54.0 75.8 B9d2 192.4 247.3 348.4 Ahi1 35.5 43.1 61.8 Tmem67 30.7 42.2 66.7 Nphp1 129.8 153.2 187.1 Tmem107 52.7 122.7 303.6 Ttc26 51.8 70.5 122.7 Arl6 61.1 81.0 139.2 Ccdc173 41.9 57.3 88.5 CEM 1 + Enkd1 93.4 107.0 139.7 Top 10 Genes Bbs2 39.9 51.9 105.9 Wdr34 106.6 131.0 194.3 Bbs1 59.4 77.2 164.2 Rabl2 71.7 102.0 181.4

Null module GEO Series "GSE51365" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 28 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE51365 Status: Public on Oct 18 2013 Title: Latent gammaherpesvirus 68 infection induces distinct transcriptional changes in different organs Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 24155394 Summary & Design: Summary: Previous studies identified a role for latent herpesvirus infection in cross-protection to infection and exacerbation of chronic inflammatory diseases. Here, we compared the gene expression signature from livers, spleens and brains of mice infected with wild-type gammaherpesvirus 68 (MHV68), a mutant virus defective in the establishment of latency (ORF73.stop) or mockulum. We identified over 600 genes differentially expressed in organs of mice latently infected with MHV68 and found distinct sets of genes linked to different pathways were altered in spleen compared to liver. Several of the most differentially expressed latency-specific genes (e.g. IFNγ, Cxcl9, Ccl5) are associated with known latency-specific phenotypes.

Overall design: RNA was extracted from livers, spleens and brains of 7-9 week old male C57Bl/6 mice infected with gammaherpesvirus 68 (MHV68), a virus defective in establishment of latency (ORF73.stop) or mockulum. RNA from 3-4 mice per treatment was pooled and analyzed by M430 2.0 Affymetrix Gene Chip. Three biologic replicates were analyzed for all conditions, except mock livers, for which four biologic replicates were analyzed.

Background corr dist: KL-Divergence = 0.0674, L1-Distance = 0.0734, L2-Distance = 0.0082, Normal std = 0.6075

0.657 Kernel fit Pairwise Correlations Normal fit

Density 0.328

0.000 CEM 1

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

Pre-normalization Quantiles

LIVER|MOCK|SC1LIVER|MOCK|SC2LIVER|MOCK|SC3 (0.0303434)LIVER|MOCK|SC019 (0.0239749)LIVER|MHV-68|SC3 (0.0226881)LIVER|MHV-68|SC2 (0.0331734)LIVER|MHV-68|SC019 (0.0173315)LIVER|ORF73|SC2 (0.0240922)LIVER|ORF73|SC3 (0.027821)LIVER|ORF73|SC019 (0.0234102)SPLEEN|MOCK|SC2 (0.0266679)SPLEEN|MOCK|SC3 (0.0257074)SPLEEN|MOCK|SC019 (0.0077797)SPLEEN|MHV-68|SC2 (0.0134747)SPLEEN|MHV-68|SC3SPLEEN|MHV-68|SC019 (0.0303091) (0.0223724)SPLEEN|ORF73|SC2 (0.0108309)SPLEEN|ORF73|SC3SPLEEN|ORF73|SC019 (0.0418026) (0.023463)BRAIN|MOCK|SC017 (0.0477853)BRAIN|MOCK|SC018BRAIN|MOCK|SC019 (0.0403607) (0.0458302)BRAIN|MHV-68|SC017 (0.0365614)BRAIN|MHV-68|SC018 (0.0622158)BRAIN|MHV-68|SC019 BRAIN|ORF73|SC017(0.0715087) BRAIN|ORF73|SC018(0.0445302) BRAIN|ORF73|SC019(0.0533584) (0.0993955) (0.0377595) (0.0554519)[ min ] [ medium ] [ max ] CEM 1 Tmem231 74.8 115.2 254.7 P ( S | Z, I ) = 0.00 B9d1 36.5 51.8 177.1 Mean Corr = 0.30639Tmem216 11.8 18.2 23.5 Tctn2 17.1 27.1 67.7 Cep290 19.6 49.9 289.8 Cc2d2a 118.9 182.0 746.2 Mks1 17.5 24.2 36.6 Tmem17 15.9 22.3 36.2 B9d2 148.4 315.1 581.2 Ahi1 8.1 12.5 41.0 Tmem67 12.9 16.5 25.8 Nphp1 10.9 15.1 28.2 Tmem107 359.6 738.1 1647.7 Ttc26 25.0 34.9 119.2 Arl6 59.9 169.8 1942.7 Ccdc173 13.4 20.1 70.6 CEM 1 + Enkd1 18.3 26.1 39.5 Top 10 Genes Bbs2 20.6 37.1 149.6 Wdr34 34.9 89.9 392.0 Bbs1 14.3 26.6 604.2 Rabl2 32.5 69.6 223.1

Null module GEO Series "GSE11165" 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=GSE11165 Status: Public on Apr 15 2008 Title: Genes regulated by GATA6 in the lung Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 18536717 Summary & Design: Summary: Epithelial organs including the lung are known to possess regenerative abilities through activation of endogenous stem cell populations but the molecular pathways regulating stem cell expansion and regeneration are not well understood. Here we show that Gata6 regulates the temporal appearance and number of bronchioalveolar stem cells (BASCs) in the lung leading to the precocious appearance of BASCs and concurrent loss in epithelial differentiation in Gata6 null lung epithelium. This expansion of BASCs is the result of a dramatic increase in canonical Wnt signaling in lung epithelium upon loss of Gata6. Expression of the non-canonical Wnt receptor Fzd2 is down-regulated in Gata6 mutants and increased Fzd2 or decreased β-catenin expression rescues, in part, the lung epithelial defects in Gata6 mutants. During lung epithelial regeneration, we show that canonical Wnt signaling is activated in the niche containing BASCs and forced activation of Wnt signaling leads to a dramatic increase in BASC numbers. Moreover, Gata6 is required for proper lung epithelial regeneration and postnatal loss of Gata6 leads to increased BASC expansion and decreased differentiation. Together, these data demonstrate that Gata6 regulated Wnt signaling controls the balance between stem/progenitor expansion and epithelial differentiation required for both lung development and regeneration.

Keywords: gene targets in knockout mouse model

Overall design: 3 replicates of each condition-wild-type and GATA6 null tissue. 6 total samples.

Background corr dist: KL-Divergence = 0.0496, L1-Distance = 0.0769, L2-Distance = 0.0084, Normal std = 0.7206

0.624 Kernel fit Pairwise Correlations Normal fit

Density 0.312

0.000 CEM 1

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

Pre-normalization Quantiles

wild-typewild-type #1 (0.278282)wild-type #2 (0.133157)GATA6 #3 (0.089612) GATA6KO #1 (0.125197) GATA6KO #2 (0.135459) KO #3 (0.238293) [ min ] [ medium ] [ max ] CEM 1 Tmem231 23.1 62.4 106.4 P ( S | Z, I ) = 0.00 B9d1 554.8 912.9 925.7 Mean Corr = 0.47331Tmem216 313.1 406.8 440.2 Tctn2 71.9 133.8 219.8 Cep290 211.0 318.6 426.8 Cc2d2a 431.1 658.5 751.7 Mks1 141.7 183.8 232.2 Tmem17 68.1 94.2 107.9 B9d2 115.2 117.5 121.3 Ahi1 7.9 8.1 8.4 Tmem67 26.9 31.2 32.8 Nphp1 350.7 481.2 541.8 Tmem107 2879.6 4385.9 5649.7 Ttc26 178.6 257.9 323.1 Arl6 698.7 912.9 1038.8 Ccdc173 98.4 176.4 424.5 CEM 1 + Enkd1 132.8 152.8 197.9 Top 10 Genes Bbs2 176.4 193.2 271.2 Wdr34 250.7 259.6 383.6 Bbs1 33.9 57.1 142.7 Rabl2 394.0 490.7 620.4

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(0.0362715) PB_Kidney_Control_10(0.0322842) PB_Kidney_Control_8(0.032518) PB_Kidney_Control_3(0.0188283)PB_Kidney_Control_7 (0.016635) PB_Kidney_Control_2(0.0806352) PB_Kidney_Control_6(0.0119376) PB_Liver_Control_10(0.034553) PB_Liver_Control_9(0.0234439) PB_Liver_Control_2(0.0357882) (0.018018)PB_Liver_Control_3 (0.0297707)PB_Liver_Control_6 (0.0227939)PB_Liver_Control_5 (0.0261111)PB_Liver_Control_4 (0.0174944)PB_Liver_Control_8 (0.0141807)PB_Liver_Control_1 (0.0275779)PB_Liver_Control_7 (0.0322857)PB_Kidney_treated_20 (0.0182928)PB_Kidney_treated_18 (0.0289904)PB_Kidney_treated_12PB_Kidney_treated_11 (0.0131895)PB_Kidney_treated_17 (0.0145741)PB_Kidney_treated_16 (0.0275159)PB_Kidney_treated_14 (0.0165372)PB_Kidney_treated_15 (0.019897)PB_Kidney_treated_13 (0.0171688)PB_Kidney_treated_19 (0.0287434)PB_Liver_treated_12 (0.0126333)PB_Liver_treated_13 (0.0234277)PB_Liver_treated_14 (0.0288182) (0.0257587)PB_Liver_treated_15 (0.0145336)PB_Liver_treated_11 (0.0357593)PB_Liver_treated_16 (0.0184319)PB_Liver_treated_18 (0.0166044)PB_Liver_treated_19 (0.0478935)PB_Liver_treated_20 (0.0181668)PB_Liver_treated_17 (0.0221404) (0.0266716) (0.0131243)[ min ] [ medium ] [ max ] CEM 1 Tmem231 114.7 302.8 544.5 P ( S | Z, I ) = 0.00 B9d1 6.0 276.0 427.0 Mean Corr = 0.38392Tmem216 109.7 200.0 322.5 Tctn2 16.4 128.8 248.5 Cep290 15.1 125.6 320.9 Cc2d2a 151.3 344.4 509.3 Mks1 22.8 154.5 219.4 Tmem17 3.3 10.4 67.3 B9d2 64.1 384.2 567.6 Ahi1 3.4 17.8 74.7 Tmem67 3.3 51.0 104.3 Nphp1 14.1 235.2 510.9 Tmem107 457.1 1430.2 1985.6 Ttc26 22.1 277.9 374.6 Arl6 172.1 1166.1 1519.4 Ccdc173 6.7 77.3 171.2 CEM 1 + Enkd1 14.8 100.3 176.6 Top 10 Genes Bbs2 9.4 231.1 407.5 Wdr34 103.7 247.6 377.2 Bbs1 6.4 251.6 408.0 Rabl2 226.4 444.1 569.1

Null module GEO Series "GSE24695" 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=GSE24695 Status: Public on Oct 15 2010 Title: Transcription Factor Redundancy Ensures Induction of the Antiviral State Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 20943654 Summary & Design: Summary: Transcriptional response to virus infection in mice lacking type I and type III signaling

The transcriptional response to virus infection is thought to be predominantly induced by interferon (IFN) signaling. Here we demonstrate that, in the absence of IFN signaling, an IFN-like transcriptome is still maintained. This transcriptional activity is mediated from IFN-stimulated response elements (ISREs) that bind to both the IFN stimulated gene factor 3 (ISGF3) as well as to IFN response factor 7 (IRF7). Through a combination of both in vitro biochemistry and in vivo transcriptional profiling, we have dissected what constitutes IRF-specific, ISGF3-specific, or universal ISREs. Taken together, the data presented here suggests that IRF7 can induce an IFN-like transcriptome in the absence of type-I or -III signaling and therefore provides a level of redundancy to cells to ensure the induction of the antiviral state.

Overall design: Human: Analysis of IRF7 transcriptome in U3A cell line was performed in duplicates.

Background corr dist: KL-Divergence = 0.0750, L1-Distance = 0.0207, L2-Distance = 0.0006, Normal std = 0.4869

0.819 Kernel fit Pairwise Correlations Normal fit

Density 0.410

0.000 CEM 1

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

Pre-normalization Quantiles

whole lungswhole (pooled lungswhole (pooled inlungswhole triplicate) (pooled inlungswhole triplicate) mock (pooled inlungswhole triplicate) treated PR/8/34/A (pooled inlungswhole triplicate) 12hpi PR/8/34/AdeltaNS1 (pooled intreatedlungswhole triplicate)(0.088979) mock (pooled inlungs12hpiwhole triplicate) treated PR/8/34/A (pooled(0.10833) inlungs treatedtriplicate) 24hpi PR/8/34/AdeltaNS1 (pooled intreated 12hpitriplicate)(0.069789) mock in 24hpi(0.137351) triplicate) treated PR/8/34/A (0.0958701) [treated 48hpimin PR/8/34/AdeltaNS1 treated 24hpi(0.0940159) ] 48hpi(0.0356584) (0.190535) treated[ medium 48hpi (0.179472) ] [ max ] CEM 1 Tmem231 219.2 325.2 383.2 P ( S | Z, I ) = 0.00 B9d1 190.1 578.3 704.2 Mean Corr = 0.28853Tmem216 321.1 436.0 549.0 Tctn2 108.7 155.7 267.7 Cep290 130.3 279.1 381.0 Cc2d2a 315.8 442.1 600.5 Mks1 121.8 148.3 183.5 Tmem17 22.7 51.3 66.3 B9d2 410.7 475.9 709.7 Ahi1 4.1 34.3 45.1 Tmem67 33.9 66.6 89.2 Nphp1 344.2 379.6 459.5 Tmem107 712.7 2030.2 2434.9 Ttc26 198.6 324.3 385.1 Arl6 797.7 1054.0 1148.1 Ccdc173 35.5 105.2 135.4 CEM 1 + Enkd1 120.2 140.2 162.4 Top 10 Genes Bbs2 103.5 166.4 259.4 Wdr34 134.6 167.8 211.8 Bbs1 97.0 171.6 196.4 Rabl2 231.0 557.0 749.8

Null module GEO Series "GSE34279" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 30 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE34279 Status: Public on Dec 20 2012 Title: Retinoic acid (RA) induction time-course to profile gene expression during mES cell differentiation Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 23260668 Summary & Design: Summary: Murine ES cell gene expression before RA induction are used to compare gene expression for time-points of 8, 12, 16, 24, 36, 48, 60 and 72 hours post-induction.

Overall design: KH2 ES Cell RA Differentiation Time-course

Background corr dist: KL-Divergence = 0.0761, L1-Distance = 0.0220, L2-Distance = 0.0006, Normal std = 0.4833

0.825 Kernel fit Pairwise Correlations Normal fit

Density 0.413

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

08hr-A (0.0362292)08hr-B (0.0407738)08hr-C (0.0267156)12hr-A (0.0407994)12hr-B (0.0350685)12hr-C (0.0714292)12hr-D (0.0392668)12hr-E (0.0353069)12hr-F (0.0255779)16hr-A (0.0631958)16hr-B (0.0350664)16hr-C (0.0427016)24hr-A (0.0463124)24hr-B (0.0126701)24hr-C (0.0216149)24hr-D (0.0106608)24hr-E (0.0172961)24hr-F (0.0127118)36hr-A (0.015056)36hr-B (0.0204266)36hr-C (0.0163366)48hr-A (0.0353519)48hr-B (0.0252932)48hr-C (0.0295352)60hr-A (0.0423594)60hr-B (0.056067)60hr-C (0.0559181)72hr-A (0.0419451)72hr-B (0.0252122)72hr-C (0.0231016) [ min ] [ medium ] [ max ] CEM 1 Tmem231 490.6 561.7 908.1 P ( S | Z, I ) = 0.00 B9d1 694.9 1032.5 1319.2 Mean Corr = 0.39968Tmem216 221.9 265.0 317.4 Tctn2 168.3 210.6 232.8 Cep290 135.9 206.3 285.9 Cc2d2a 198.4 333.6 432.5 Mks1 216.4 299.1 482.5 Tmem17 51.5 66.2 82.6 B9d2 235.7 306.2 360.3 Ahi1 37.3 58.4 88.1 Tmem67 21.4 29.6 39.0 Nphp1 549.7 657.1 828.8 Tmem107 2274.1 2855.8 4769.3 Ttc26 321.8 413.5 574.2 Arl6 1167.0 1947.9 2390.1 Ccdc173 39.3 57.3 69.6 CEM 1 + Enkd1 384.6 529.6 758.2 Top 10 Genes Bbs2 344.0 522.5 745.2 Wdr34 327.6 505.4 834.0 Bbs1 131.2 167.7 235.9 Rabl2 737.2 921.8 1146.6

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 (0.163408)FB_0_12wk_4-2_AsDW_MusLung_Mouse430_2_HJCENV601_2 (0.0856959) (0.152818) (0.0397919) (0.191957)[ min (0.153369) ] (0.0169597) (0.146933)[ (0.0147894) medium (0.0342781) ] [ max ] CEM 1 Tmem231 150.9 183.5 284.4 P ( S | Z, I ) = 0.00 B9d1 464.2 743.3 1005.3 Mean Corr = 0.40376Tmem216 285.4 334.8 480.0 Tctn2 180.9 289.4 458.6 Cep290 16.8 20.1 33.4 Cc2d2a 137.1 238.8 344.4 Mks1 41.5 44.8 56.8 Tmem17 46.4 57.5 77.4 B9d2 77.5 88.0 113.0 Ahi1 6.1 6.4 8.6 Tmem67 36.8 54.6 65.7 Nphp1 102.3 158.5 253.7 Tmem107 4066.6 7294.9 10031.8 Ttc26 135.2 244.8 349.3 Arl6 803.8 1075.4 1239.8 Ccdc173 10.5 11.8 12.4 CEM 1 + Enkd1 43.1 61.0 84.4 Top 10 Genes Bbs2 134.0 195.4 251.9 Wdr34 142.1 213.1 325.3 Bbs1 83.9 120.9 175.7 Rabl2 837.7 1275.6 1773.7

Null module GEO Series "GSE12948" 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=GSE12948 Status: Public on Oct 27 2008 Title: Oncogenesis of T-ALL and non-malignant consequences of overexpressing NOTCH1 Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 20007543 Summary & Design: Summary: We have determined the consequences of ICN1 overexpression from retroviral vectors introduced into bone marrow cells.

Even though the tumors consist of phenotypically heterogeneous cells, no evidence for tumor stem cells was found.

Overall design: Expression analysis, array-based comparative genomic hybridization and spectral karyotyping.

Background corr dist: KL-Divergence = 0.0309, L1-Distance = 0.0439, L2-Distance = 0.0027, Normal std = 0.6826

0.584 Kernel fit Pairwise Correlations Normal fit

Density 0.292

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

ControlAbnormal 2 (0.0599077)Abnormal non-malignantControl non-malignantControl 3 (0.046339) 2 (0.0892832)Abnormal 1 (0.0502632) 3 (0.0624457)NIC non-malignant TumorNIC 1Tumor (0.0782977)NIC 1 2Tumor (0.115437) (0.2832) 3 (0.214826) [ min ] [ medium ] [ max ] CEM 1 Tmem231 163.3 188.6 434.7 P ( S | Z, I ) = 0.00 B9d1 140.2 178.5 335.2 Mean Corr = 0.30424Tmem216 130.0 162.7 228.0 Tctn2 71.5 75.4 141.8 Cep290 22.2 26.6 35.5 Cc2d2a 51.8 61.3 157.3 Mks1 102.6 129.2 285.8 Tmem17 25.4 28.6 47.5 B9d2 638.9 995.6 1202.4 Ahi1 68.4 114.9 188.6 Tmem67 43.6 58.2 61.3 Nphp1 146.8 223.4 405.9 Tmem107 249.0 517.0 922.8 Ttc26 53.9 71.1 124.5 Arl6 87.7 159.5 1053.6 Ccdc173 63.4 74.0 98.1 CEM 1 + Enkd1 475.8 545.2 806.3 Top 10 Genes Bbs2 103.6 129.2 311.2 Wdr34 80.1 114.9 503.3 Bbs1 96.3 130.6 148.0 Rabl2 143.6 219.7 637.0

Null module GEO Series "GSE26476" 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=GSE26476 Status: Public on Jan 07 2011 Title: Smooth muscle IL-4 receptor activation induces airway hyper-responsiveness Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21464224 Summary & Design: Summary: Selective stimulation of IL-4 receptor on smooth muscle induces airway hyper-responsiveness in mice.

Abstract: Production of the cytokines IL-4 and IL-13 is increased in both human asthma and mouse asthma models and Stat6 activation by the common IL-4/IL-13R drives most mouse model pathophysiology, including airway hyperresponsiveness (AHR). However, the precise cellular mechanisms through which IL-4Rα induces AHR remain unclear. Overzealous bronchial smooth muscle constriction is thought to underlie AHR in human asthma, but the smooth muscle contribution to AHR has never been directly assessed. Furthermore, differences in mouse vs. human airway anatomy and observations that selective IL-13 stimulation of Stat6 in airway epithelium induces murine AHR raise questions about the importance of direct IL-4R effects on smooth muscle in murine asthma models and relevance of these models to human asthma. Using transgenic mice in which smooth muscle is the only cell type that expresses or fails to express IL-4Rα, we demonstrate that direct smooth muscle activation by IL-4, IL-13, or allergen is sufficient, but not necessary, to induce AHR and show that 5 genes known to promote smooth muscle migration, proliferation and contractility are activated by IL-13 in smooth muscle in vivo. These observations demonstrate that IL-4Rα promotes AHR through multiple mechanisms and provide a model for testing smooth muscle-directed asthma therapeutics.

Overall design: Gene transcripts were identified that differed in their relative expression as a function of IL4R expression on the smooth muscle cells.

Background corr dist: KL-Divergence = 0.0370, L1-Distance = 0.0163, L2-Distance = 0.0003, Normal std = 0.6281

0.640 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

Adult Lung_IL4RA-ko-SMP8-IL4RA-het+IL13_rep1Adult Lung_IL4RA-ko-SMP8-IL4RA-het+IL13_rep2Adult Lung_IL4RA-ko+IL13_rep1Adult Lung_IL4RA-ko+IL13_rep2Adult Lung_wt1+IL13_rep1Adult Lung_wt1+IL13_rep2 (0.208193) (0.159319) (0.355352) (0.0951448)(0.121868) (0.0601227)[ min ] [ medium ] [ max ] CEM 1 Tmem231 503.8 553.5 581.1 P ( S | Z, I ) = 0.00 B9d1 384.4 428.1 478.0 Mean Corr = 0.38837Tmem216 267.1 274.9 319.1 Tctn2 262.8 303.6 333.2 Cep290 108.8 126.1 141.8 Cc2d2a 597.1 686.3 735.2 Mks1 169.8 200.0 210.1 Tmem17 40.3 42.7 55.4 B9d2 325.0 334.1 371.5 Ahi1 70.3 77.4 93.8 Tmem67 70.5 79.9 84.6 Nphp1 409.2 476.6 493.2 Tmem107 2559.6 2776.8 3023.9 Ttc26 200.7 225.5 234.2 Arl6 696.3 805.0 833.1 Ccdc173 52.8 58.7 69.6 CEM 1 + Enkd1 207.9 230.5 231.7 Top 10 Genes Bbs2 341.0 379.9 547.3 Wdr34 201.9 224.8 263.8 Bbs1 224.4 275.6 293.8 Rabl2 792.9 900.5 955.9

Null module