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

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

Dataset: Num of genes in input gene set: 13 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. Dync2li1 Dnah17 Dnah11 Dnah7a Dnaic2 Dnah9 Dnah5 Dnah8 Dnah1 Dnah2 Dnah6 Dnali1 Dnal4 Num ofGenesinQueryGeneset:13.CEMs:1. Overview ofCo-ExpressionModules(CEMs)withDatasetWeighting

Dnah6 Dnali1 Dnah7a Dnah2 Dnah1 Dnah8 Dnah5 Dnah9 Dnal4 Dnah11 Dnaic2 Dync2li1 Dnah17 CEM 1(36datasets) 0.0 Scale ofaveragePearsoncorrelations 0.2 0.4 0.6 0.8 1.0 1700003M02Rik 1700012B09Rik 1700088E04Rik 4930444P10Rik 1700019L03Rik 1700001L19Rik Symbol Num ofCEMGenes:13.Predicted1063.SelectedDatasets:36.Strength:0.7 CEM 1,Geneset"[G]axonemaldyneincomplex",Page1 Tsnaxip1 Dync2li1 Dynlrb2 Mapk15 Dnah17 Dnah11 Dnah7a Dnah12 Akap14 Ccdc11 Ccdc19 Maats1 B3gnt4 Gm101 Dnaic2 Ttc21a Armc4 Lrrc48 Lrrc23 Wdr63 Wdr65 Dnah9 Dnah5 Dnah8 Dnah1 Dnah2 Dnah6 Spag8 Dnali1 Fank1 Lrguk Dnal4 Stk33 Tcte1 Ttc29 Fsip1 Foxj1 Tekt4 Rtdr1 Eno4 Zbbx Mak Pifo Ak7 0.0 1.0

GSE40939 [10] GSE10813 [12]

GSE8726 [7] Only showingfirst200datasets-Seetxtoutputforfulldetails. GSE10192 [24] GSE50122 [10] GSE32020 [26] GSE30865 [68] GSE15401 [18] GSE39391 [21] GSE17923 [6] GSE12769 [20] GSE31972 [6] GSE7831 [14] GSE23908 [31] GSE9038 [24] GSE42601 [6] GSE9977 [24] GSE56236 [12] GSE1871 [12] GSE27630 [8] GSE9743 [12] GSE18534 [15] GSE31013 [12] GSE27568 [16] GSE29081 [6] GSE9954 [70] GSE10246 [182] GSE24207 [73] GSE13106 [10] GSE3100 [23] GSE17097 [20] GSE1983 [6] GSE8498 [6] GSE17373 [24] GSE10849 [6] GSE45487 [9] GSE28664 [17] GSE49128 [17] GSE18765 [14] GSE34765 [6] GSE7275 [8] GSE31940 [8] GSE32330 [12] GSE35435 [6] GSE35436 [6] GSE33770 [8] GSE6837 [8] GSE14481 [12] GSE5128 [18] GSE23408 [39] GSE14843 [6] GSE13103 [8] GSE19517 [6] GSE22448 [6] GSE35219 [6] GSE10528 [6] GSE25029 [56] GSE23600 [10] GSE40655 [6] GSE7809 [8] GSE27261 [8] GSE27987 [31] GSE50123 [6] GSE22527 [6] GSE26476 [6] GSE40261 [8] GSE55607 [18] GSE31208 [8] GSE9735 [9] GSE36336 [6] GSE12536 [6] GSE23505 [10] GSE9330 [8] GSE10989 [6] GSE30655 [35] GSE32422 [6] GSE4260 [6] GSE13149 [25] GSE29145 [10] GSE27717 [11] GSE57425 [6] GSE3889 [20] GSE20260 [48] GSE23584 [36] GSE4193 [8] GSE34807 [20] GSE27546 [51] GSE18704 [9] GSE13306 [17] GSE38215 [11] GSE18660 [10] GSE47425 [7] GSE23200 [6] GSE11982 [6] GSE7605 [18] GSE24295 [7] GSE41807 [6] GSE10639 [8] GSE33101 [8] GSE25778 [6] GSE14354 [6] GSE20954 [14] GSE17745 [6] GSE32681 [61] GSE18551 [18] GSE11759 [6] GSE49283 [12] GSE13225 [6] GSE19668 [50] GSE19194 [14] GSE35091 [11] GSE35226 [12] GSE33341 [227] GSE17096 [20] GSE31797 [6] GSE22034 [8] GSE15724 [9] GSE13229 [6] GSE27675 [14] GSE27720 [6] GSE15458 [8] GSE21193 [10] GSE7020 [8] GSE9443 [24] GSE22180 [60] GSE4765 [6] GSE4230 [8] GSE20366 [23] GSE21546 [24] GSE10239 [12] GSE19338 [24] GSE7699 [6] GSE17553 [16] GSE8407 [17] GSE7333 [6] GSE26461 [6] GSE20390 [6] GSE25640 [12] GSE54976 [17] GSE7596 [6] GSE43635 [9] GSE23081 [6] GSE5298 [8] GSE8349 [10] GSE17783 [19] GSE20152 [8] GSE33134 [31] GSE18745 [6] GSE19997 [9] GSE32963 [6] GSE20426 [35] GSE18341 [30] GSE18993 [13] GSE10478 [6] CEM+ CEM GSE22989 [10] GSE58915 [21] GSE55028 [6] GSE12465 [14] GSE18010 [29] GSE28417 [12] 0.0 GSE52101 [17] GSE13526 [6]

GSE7958 [12] Scale ofaveragePearsoncorrelations GSE13753 [10] GSE42008 [6] GSE23016 [9] GSE8249 [46] GSE11259 [9] GSE5763 [9] 0.2 GSE36378 [20] GSE5891 [6] GSE37301 [20] GSE9975 [36] GSE9338 [42] GSE17112 [8] GSE22140 [13] GSE19079 [6] GSE34863 [8] 0.4 GSE38672 [6] GSE24614 [6] GSE45044 [12] GSE17404 [9] GSE16564 [15] GSE29382 [36] GSE46496 [9] GSE35761 [6] GSE46150 [8] 0.6 GSE16874 [12] GSE24489 [14] GSE43197 [27] GSE6675 [8] GSE8488 [15] GSE18597 [42] GSE9441 [36] GSE11818 [6] GSE10904 [6] 0.8 GSE13148 [10] GSE19925 [6] GSE40087 [15] GSE29082 [6] Score 13.78 13.84 13.91 13.97 14.38 14.48 14.66 14.75 14.76 14.82 14.83 15.01 15.05 15.16 15.21 15.37 15.43 15.51 15.62 15.62 15.75 15.78 15.87 15.99 16.11 16.22 16.61 16.62 16.72 17.14 17.14 17.25 17.51 17.55 17.63 17.88 18.35 1.0 Notes 1700007G11Rik 6820408C15Rik 1700026D08Rik 4930430A15Rik 1700016K19Rik 1700028P14Rik 1700023E05Rik 4933412E24Rik 1700013F07Rik Symbol Num ofCEMGenes:13.Predicted1063.SelectedDatasets:36.Strength:0.7 CEM 1,Geneset"[G]axonemaldyneincomplex",Page2 Zmynd12 Zmynd10 Fam179a Fam227a Rsph10b Ccdc176 Ccdc74a Ccdc113 Ccdc146 Ccdc103 Ppp1r42 Efcab10 Spata33 Ccdc13 Ccdc96 Dnaic1 Zfp474 Mdh1b Vwa3b Got1l1 Lrrc34 Wdr96 Wdr16 Wdr66 Wdr27 Riiad1 Dydc2 Spag6 Caps2 Morn5 Styxl1 Enkur Nme5 Cdkl4 Ttc16 Btg4 Efhb Ulk4 Iqcd Ttll6 Kif9 0.0 1.0

GSE40939 [10] GSE10813 [12]

GSE7958 [12] Scale ofaveragePearsoncorrelations GSE13753 [10] GSE42008 [6] GSE23016 [9] GSE8249 [46] GSE11259 [9] GSE5763 [9] 0.2 GSE36378 [20] GSE5891 [6] GSE37301 [20] GSE9975 [36] GSE9338 [42] GSE17112 [8] GSE22140 [13] GSE19079 [6] GSE34863 [8] 0.4 GSE38672 [6] GSE24614 [6] GSE45044 [12] GSE17404 [9] GSE16564 [15] GSE29382 [36] GSE46496 [9] GSE35761 [6] GSE46150 [8] 0.6 GSE16874 [12] GSE24489 [14] GSE43197 [27] GSE6675 [8] GSE8488 [15] GSE18597 [42] GSE9441 [36] GSE11818 [6] GSE10904 [6] 0.8 GSE13148 [10] GSE19925 [6] GSE40087 [15] GSE29082 [6] Score 11.66 11.69 11.71 11.72 11.80 11.86 11.87 11.88 11.91 11.91 11.93 11.98 12.05 12.06 12.08 12.08 12.09 12.10 12.13 12.50 12.58 12.60 12.65 12.69 12.81 12.89 12.92 12.98 12.99 13.09 13.12 13.15 13.20 13.22 13.23 13.28 13.37 13.37 13.41 13.47 13.48 13.50 13.50 13.55 13.56 13.63 13.68 13.70 13.71 13.76 1.0 Notes E230008N13Rik 1110017D15Rik 4921536K21Rik 1700129C05Rik 4932418E24Rik 1700009P17Rik 2410004P03Rik Symbol Num ofCEMGenes:13.Predicted1063.SelectedDatasets:36.Strength:0.7 CEM 1,Geneset"[G]axonemaldyneincomplex",Page3 Tmem30c Fam183b Mycbpap Trpd52l3 Ccdc151 Ccdc108 Ccdc110 Ssmem1 Ccdc114 Ankrd45 Ppp1r36 Efcab12 Spata18 Lrrc10b Ubxn10 Mroh2b Spag17 Spag16 Ccdc40 Ccdc67 Ccdc89 Fbxo36 Gm884 Dnaaf1 Spats1 Spata4 Efcab6 Ttc39d Tcam1 Armc3 Adad1 Dydc1 Tcp11 Odf3b Stpg1 Tdrd5 Efhc1 Ribc1 Spef2 Lrrc6 Cib4 Frs3 Acr 0.0 1.0

GSE40939 [10] GSE10813 [12]

GSE7958 [12] Scale ofaveragePearsoncorrelations GSE13753 [10] GSE42008 [6] GSE23016 [9] GSE8249 [46] GSE11259 [9] GSE5763 [9] 0.2 GSE36378 [20] GSE5891 [6] GSE37301 [20] GSE9975 [36] GSE9338 [42] GSE17112 [8] GSE22140 [13] GSE19079 [6] GSE34863 [8] 0.4 GSE38672 [6] GSE24614 [6] GSE45044 [12] GSE17404 [9] GSE16564 [15] GSE29382 [36] GSE46496 [9] GSE35761 [6] GSE46150 [8] 0.6 GSE16874 [12] GSE24489 [14] GSE43197 [27] GSE6675 [8] GSE8488 [15] GSE18597 [42] GSE9441 [36] GSE11818 [6] GSE10904 [6] 0.8 GSE13148 [10] GSE19925 [6] GSE40087 [15] GSE29082 [6] Score 9.76 9.81 9.82 9.84 9.85 9.85 9.94 9.97 10.02 10.08 10.10 10.13 10.13 10.21 10.22 10.24 10.29 10.32 10.35 10.37 10.41 10.46 10.48 10.51 10.52 10.67 10.71 10.74 10.77 10.79 10.87 10.90 10.92 10.92 11.00 11.07 11.29 11.29 11.39 11.40 11.43 11.46 11.48 11.50 11.53 11.54 11.57 11.59 11.61 11.63 1.0 Notes 4930544G11Rik 4930485B16Rik 4921511H03Rik 4921501E09Rik 4930415F15Rik 4931429L15Rik Spata31d1d Symbol Num ofCEMGenes:13.Predicted1063.SelectedDatasets:36.Strength:0.7 CEM 1,Geneset"[G]axonemaldyneincomplex",Page4 Pom121l12 Tmem232 Rnf138rt1 Fam154b Catsper2 Apobec4 Zdhhc11 Adam21 Slco6d1 Slco6c1 Pabpc6 Fbxo24 Tsga13 Enthd1 Atp8b3 Rmdn2 Gm732 Ptchd3 Zfp541 Vwa3a Bpifb2 Lrrc46 Lrrc69 Lrrc18 Rsph1 Nsun7 Akap3 Morn3 Lypd4 Meig1 Prok2 Tdrd9 Ctag2 Poteg Efhc2 Stk30 Tbata Tekt1 Ttc34 Nmbr Pbp2 Kif17 Iqch 0.0 1.0

GSE40939 [10] GSE10813 [12]

GSE7958 [12] Scale ofaveragePearsoncorrelations GSE13753 [10] GSE42008 [6] GSE23016 [9] GSE8249 [46] GSE11259 [9] GSE5763 [9] 0.2 GSE36378 [20] GSE5891 [6] GSE37301 [20] GSE9975 [36] GSE9338 [42] GSE17112 [8] GSE22140 [13] GSE19079 [6] GSE34863 [8] 0.4 GSE38672 [6] GSE24614 [6] GSE45044 [12] GSE17404 [9] GSE16564 [15] GSE29382 [36] GSE46496 [9] GSE35761 [6] GSE46150 [8] 0.6 GSE16874 [12] GSE24489 [14] GSE43197 [27] GSE6675 [8] GSE8488 [15] GSE18597 [42] GSE9441 [36] GSE11818 [6] GSE10904 [6] 0.8 GSE13148 [10] GSE19925 [6] GSE40087 [15] GSE29082 [6] Score 8.53 8.53 8.56 8.58 8.59 8.59 8.60 8.63 8.66 8.66 8.69 8.69 8.72 8.73 8.73 8.76 8.78 8.81 8.82 8.83 8.85 8.85 8.92 8.93 8.95 8.98 9.00 9.05 9.13 9.16 9.16 9.18 9.22 9.28 9.31 9.31 9.33 9.34 9.34 9.36 9.38 9.43 9.46 9.48 9.52 9.52 9.54 9.61 9.66 9.74 1.0 Notes 4932414N04Rik 4930412D23Rik 4931423N10Rik 1700018C11Rik 4930505A04Rik 4930435E12Rik 1700074P13Rik 4921524L21Rik 1700106J16Rik LOC101055837 4933416I08Rik Symbol Num ofCEMGenes:13.Predicted1063.SelectedDatasets:36.Strength:0.7 CEM 1,Geneset"[G]axonemaldyneincomplex",Page5 BC030307 AK129341 Tmem210 Fam216b Ccdc175 Zdhhc25 Adam18 Pla2g2c Slc6a16 Fam209 Glipr1l2 Mageb3 Rimbp3 Ms4a13 Ccdc87 Galntl5 Adam3 Adam2 Prss45 Pnma1 Igbp1b Fbxl13 Cox8c Sh2d6 Actl11 Pdzd9 Piwil1 Pacrg Rxfp2 Nme8 Hyal5 Gfra4 Tekt3 Ttc18 Tktl2 Ica1l Mael Drc1 Mtl5 0.0 1.0

GSE40939 [10] GSE10813 [12]

GSE7958 [12] Scale ofaveragePearsoncorrelations GSE13753 [10] GSE42008 [6] GSE23016 [9] GSE8249 [46] GSE11259 [9] GSE5763 [9] 0.2 GSE36378 [20] GSE5891 [6] GSE37301 [20] GSE9975 [36] GSE9338 [42] GSE17112 [8] GSE22140 [13] GSE19079 [6] GSE34863 [8] 0.4 GSE38672 [6] GSE24614 [6] GSE45044 [12] GSE17404 [9] GSE16564 [15] GSE29382 [36] GSE46496 [9] GSE35761 [6] GSE46150 [8] 0.6 GSE16874 [12] GSE24489 [14] GSE43197 [27] GSE6675 [8] GSE8488 [15] GSE18597 [42] GSE9441 [36] GSE11818 [6] GSE10904 [6] 0.8 GSE13148 [10] GSE19925 [6] GSE40087 [15] GSE29082 [6] Score 7.59 7.59 7.62 7.62 7.64 7.67 7.69 7.70 7.71 7.79 7.83 7.84 7.85 7.85 7.86 7.86 7.93 7.94 7.94 7.95 7.95 7.97 7.98 7.98 8.02 8.03 8.03 8.06 8.07 8.08 8.08 8.09 8.11 8.11 8.12 8.19 8.20 8.21 8.21 8.22 8.22 8.24 8.27 8.30 8.30 8.31 8.31 8.40 8.40 8.50 1.0 Notes 1700057G04Rik 4930558K02Rik 4930524B15Rik 4930480E11Rik 1700034F02Rik 4933421I07Rik 4430402I18Rik 1700011I03Rik 4933434I20Rik Symbol Num ofCEMGenes:13.Predicted1063.SelectedDatasets:36.Strength:0.7 CEM 1,Geneset"[G]axonemaldyneincomplex",Page6 Catsperg1 BC051142 Fam181a Wbscr28 Ccdc150 Ankrd55 Gm5142 Slc13a5 Dbndd1 Henmt1 Ccdc39 Epha10 Ccdc81 Spaca7 Txndc8 Syngr4 Gtf2a1l Kctd16 Efcab3 Smc1b Mfsd6l Lrrc63 Adad2 Wdr31 Ccna1 Rab36 Sox30 Fhad1 Ttc23l Lrriq4 Prox2 Ndst4 Cfhr3 Prr22 Msh4 Elfn2 Rfx8 Iqub Tpte Ift88 Zan 0.0 1.0

GSE40939 [10] GSE10813 [12]

GSE7958 [12] Scale ofaveragePearsoncorrelations GSE13753 [10] GSE42008 [6] GSE23016 [9] GSE8249 [46] GSE11259 [9] GSE5763 [9] 0.2 GSE36378 [20] GSE5891 [6] GSE37301 [20] GSE9975 [36] GSE9338 [42] GSE17112 [8] GSE22140 [13] GSE19079 [6] GSE34863 [8] 0.4 GSE38672 [6] GSE24614 [6] GSE45044 [12] GSE17404 [9] GSE16564 [15] GSE29382 [36] GSE46496 [9] GSE35761 [6] GSE46150 [8] 0.6 GSE16874 [12] GSE24489 [14] GSE43197 [27] GSE6675 [8] GSE8488 [15] GSE18597 [42] GSE9441 [36] GSE11818 [6] GSE10904 [6] 0.8 GSE13148 [10] GSE19925 [6] GSE40087 [15] GSE29082 [6] Score 6.93 6.95 6.96 6.97 6.98 7.03 7.04 7.07 7.08 7.08 7.09 7.12 7.13 7.16 7.17 7.18 7.19 7.20 7.20 7.21 7.21 7.23 7.23 7.23 7.24 7.24 7.25 7.26 7.29 7.33 7.35 7.36 7.37 7.37 7.38 7.40 7.42 7.43 7.43 7.44 7.45 7.46 7.48 7.51 7.52 7.53 7.54 7.55 7.56 7.56 1.0 Notes 4930519G04Rik 4933427G17Rik 9530077C05Rik 4930432K09Rik 1700007K13Rik 4930547C10Rik 4930488N24Rik 4930468A15Rik 4930404A10Rik 4922502D21Rik 4930524N10Rik 1700019N19Rik 1700024P04Rik 4930503E14Rik 1700018F24Rik 4930407I10Rik Symbol Num ofCEMGenes:13.Predicted1063.SelectedDatasets:36.Strength:0.7 CEM 1,Geneset"[G]axonemaldyneincomplex",Page7 Tmem239 Tomm20l Wfdc15a Tmem89 March10 Gm8140 Tmbim7 Slc25a2 Slc26a8 Glipr1l1 Prps1l1 Abca16 Ccdc54 Mroh2a Gm626 Dnajb8 Prss58 Prss42 Slc2a5 Arl13a Lrrc52 Ube2u Spdya Actl7a Lrriq3 Wnk2 Ttc25 Sec1 Agr3 Ftmt Syt5 Iqca Iqce Ak8 0.0 1.0

GSE40939 [10] GSE10813 [12]

GSE7958 [12] Scale ofaveragePearsoncorrelations GSE13753 [10] GSE42008 [6] GSE23016 [9] GSE8249 [46] GSE11259 [9] GSE5763 [9] 0.2 GSE36378 [20] GSE5891 [6] GSE37301 [20] GSE9975 [36] GSE9338 [42] GSE17112 [8] GSE22140 [13] GSE19079 [6] GSE34863 [8] 0.4 GSE38672 [6] GSE24614 [6] GSE45044 [12] GSE17404 [9] GSE16564 [15] GSE29382 [36] GSE46496 [9] GSE35761 [6] GSE46150 [8] 0.6 GSE16874 [12] GSE24489 [14] GSE43197 [27] GSE6675 [8] GSE8488 [15] GSE18597 [42] GSE9441 [36] GSE11818 [6] GSE10904 [6] 0.8 GSE13148 [10] GSE19925 [6] GSE40087 [15] GSE29082 [6] Score 6.23 6.27 6.28 6.28 6.28 6.31 6.32 6.34 6.35 6.37 6.37 6.39 6.41 6.41 6.41 6.42 6.45 6.45 6.47 6.49 6.49 6.51 6.52 6.52 6.55 6.56 6.56 6.57 6.58 6.58 6.58 6.64 6.67 6.68 6.69 6.69 6.70 6.71 6.77 6.77 6.78 6.78 6.79 6.81 6.83 6.84 6.85 6.85 6.87 6.93 1.0 Notes 4930444G20Rik 4933413G19Rik 1700020D05Rik 4930522H14Rik 1700012P22Rik 1700025F22Rik LOC101055670 4933430I17Rik Symbol Num ofCEMGenes:13.Predicted1063.SelectedDatasets:36.Strength:0.7 CEM 1,Geneset"[G]axonemaldyneincomplex",Page8 Fancd2os Tmem190 Tmem225 Gm10044 Tctex1d1 Arhgef33 Slc22a16 Fam71e1 Fam122c Ccdc172 Zc2hc1c Cmtm2b Adam1b Dnajc5g Adam32 Dnajb13 Slc5a4b Fam83e Dcdc2b Dusp18 Abcc12 Ccdc70 Spesp1 Ccdc65 Plac8l1 Sptbn4 Ccser2 Ankef1 Pih1d3 Prame Pdha2 Samt4 Nek11 Fabp9 Acrv1 Hsfy2 Sun5 Spz1 Clgn Cpvl Ttll9 Dll3 0.0 1.0

GSE40939 [10] GSE10813 [12]

GSE7958 [12] Scale ofaveragePearsoncorrelations GSE13753 [10] GSE42008 [6] GSE23016 [9] GSE8249 [46] GSE11259 [9] GSE5763 [9] 0.2 GSE36378 [20] GSE5891 [6] GSE37301 [20] GSE9975 [36] GSE9338 [42] GSE17112 [8] GSE22140 [13] GSE19079 [6] GSE34863 [8] 0.4 GSE38672 [6] GSE24614 [6] GSE45044 [12] GSE17404 [9] GSE16564 [15] GSE29382 [36] GSE46496 [9] GSE35761 [6] GSE46150 [8] 0.6 GSE16874 [12] GSE24489 [14] GSE43197 [27] GSE6675 [8] GSE8488 [15] GSE18597 [42] GSE9441 [36] GSE11818 [6] GSE10904 [6] 0.8 GSE13148 [10] GSE19925 [6] GSE40087 [15] GSE29082 [6] Score 5.69 5.71 5.71 5.71 5.72 5.72 5.73 5.74 5.74 5.76 5.80 5.80 5.81 5.81 5.83 5.84 5.85 5.85 5.86 5.86 5.87 5.89 5.89 5.89 5.93 5.93 5.94 5.96 5.96 5.98 6.01 6.02 6.03 6.03 6.03 6.04 6.05 6.07 6.10 6.14 6.16 6.16 6.16 6.17 6.18 6.19 6.19 6.20 6.21 6.23 1.0 Notes 1700007K09Rik 4930550C14Rik 1700093K21Rik 1700019B03Rik 1700042B14Rik 4921504E06Rik 1700006E09Rik 4921530L21Rik 1700021F07Rik 1700015F17Rik 4930579F01Rik 4930519F16Rik 9530057J20Rik Symbol Num ofCEMGenes:13.Predicted1063.SelectedDatasets:36.Strength:0.7 CEM 1,Geneset"[G]axonemaldyneincomplex",Page9 Pom121l2 Gm11992 Fam221b Slc25a54 Fam187a Catsper3 Als2cr12 Zcchc13 Tsc22d4 Spata16 Fam71d Fbxw10 Galntl6 Kdm4d Gm128 Spata3 Mmel1 Kcnu1 Spdyb Rsph9 Asb17 Capzb Tex35 Tex36 Aurkc Tdrd1 Stk36 Adgb Lyzl6 Ybx2 Tnp1 Odf4 Cyct Fhl5 Art5 Gk2 Boll 0.0 1.0

GSE40939 [10] GSE10813 [12]

GSE7958 [12] Scale ofaveragePearsoncorrelations GSE13753 [10] GSE42008 [6] GSE23016 [9] GSE8249 [46] GSE11259 [9] GSE5763 [9] 0.2 GSE36378 [20] GSE5891 [6] GSE37301 [20] GSE9975 [36] GSE9338 [42] GSE17112 [8] GSE22140 [13] GSE19079 [6] GSE34863 [8] 0.4 GSE38672 [6] GSE24614 [6] GSE45044 [12] GSE17404 [9] GSE16564 [15] GSE29382 [36] GSE46496 [9] GSE35761 [6] GSE46150 [8] 0.6 GSE16874 [12] GSE24489 [14] GSE43197 [27] GSE6675 [8] GSE8488 [15] GSE18597 [42] GSE9441 [36] GSE11818 [6] GSE10904 [6] 0.8 GSE13148 [10] GSE19925 [6] GSE40087 [15] GSE29082 [6] Score 5.05 5.07 5.08 5.09 5.10 5.12 5.13 5.14 5.14 5.17 5.18 5.18 5.19 5.20 5.22 5.23 5.25 5.27 5.27 5.29 5.32 5.32 5.33 5.33 5.33 5.36 5.37 5.38 5.39 5.39 5.40 5.42 5.42 5.43 5.47 5.48 5.52 5.53 5.54 5.54 5.57 5.59 5.62 5.62 5.64 5.64 5.64 5.65 5.67 5.69 1.0 Notes 4930474N05Rik 2900092C05Rik 4933422H20Rik 1700003E16Rik 4933415F23Rik 1700011L22Rik 4933402J07Rik Symbol Num ofCEMGenes:13.Predicted1063.SelectedDatasets:36.Strength:0.7 CEM 1,Geneset"[G]axonemaldyneincomplex",Page10 Tmem217 Fam170a Catsper1 Ppp1r32 Ppp1r1c Cmtm2a Gm4871 Adam34 Slc35g3 Fbxw27 Pmfbp1 Rsph6a Capn11 Ccdc30 Abca14 Morc2b Spaca3 Spaca4 Ppp4r4 Cyb5r2 Trim42 Trim69 Zfp352 Nmur1 Hdgfl1 Actl7b Samt3 Fscn3 Actrt1 Gtsf1l Cct6b Slfnl1 Ttbk1 Lrrc9 Nbas Sgca Hils1 Grk4 Hsf5 Plb1 Iqcg Zic5 Lhb 0.0 1.0

GSE40939 [10] GSE10813 [12]

GSE7958 [12] Scale ofaveragePearsoncorrelations GSE13753 [10] GSE42008 [6] GSE23016 [9] GSE8249 [46] GSE11259 [9] GSE5763 [9] 0.2 GSE36378 [20] GSE5891 [6] GSE37301 [20] GSE9975 [36] GSE9338 [42] GSE17112 [8] GSE22140 [13] GSE19079 [6] GSE34863 [8] 0.4 GSE38672 [6] GSE24614 [6] GSE45044 [12] GSE17404 [9] GSE16564 [15] GSE29382 [36] GSE46496 [9] GSE35761 [6] GSE46150 [8] 0.6 GSE16874 [12] GSE24489 [14] GSE43197 [27] GSE6675 [8] GSE8488 [15] GSE18597 [42] GSE9441 [36] GSE11818 [6] GSE10904 [6] 0.8 GSE13148 [10] GSE19925 [6] GSE40087 [15] GSE29082 [6] Score 4.51 4.51 4.52 4.52 4.55 4.55 4.56 4.56 4.56 4.56 4.57 4.57 4.59 4.59 4.59 4.60 4.60 4.63 4.64 4.65 4.65 4.68 4.69 4.71 4.71 4.74 4.75 4.76 4.77 4.78 4.78 4.79 4.79 4.79 4.80 4.81 4.81 4.86 4.89 4.90 4.91 4.91 4.92 4.94 4.94 4.98 4.98 5.01 5.02 5.03 1.0 Notes A330021E22Rik 4921506M07Rik 1700034O15Rik 1700013D24Rik 1700001C02Rik 1700037C18Rik 4933417A18Rik 4930563D23Rik 4931417E11Rik 4933405L10Rik 4922501L14Rik 1700029I15Rik Symbol Num ofCEMGenes:13.Predicted1063.SelectedDatasets:36.Strength:0.7 CEM 1,Geneset"[G]axonemaldyneincomplex",Page11 BC048671 BC027072 AF366264 Tmem247 Adam26a Marveld3 Dync2h1 Ccdc105 Fam71f1 Ankrd66 Gm6772 Adam25 Spata19 Tmco5b Zswim5 Capza3 Ppp3r2 Prdx6b Cmtm1 Dnajb7 Ptpn20 Papolb Prss39 Nmur2 Mesp2 Lrrc36 Glb1l3 Mroh9 Snx29 Cabyr Gsto2 Hmx1 Prm3 Iqcf4 Tbx5 Ccin Daf2 Phf7 0.0 1.0

GSE40939 [10] GSE10813 [12]

GSE7958 [12] Scale ofaveragePearsoncorrelations GSE13753 [10] GSE42008 [6] GSE23016 [9] GSE8249 [46] GSE11259 [9] GSE5763 [9] 0.2 GSE36378 [20] GSE5891 [6] GSE37301 [20] GSE9975 [36] GSE9338 [42] GSE17112 [8] GSE22140 [13] GSE19079 [6] GSE34863 [8] 0.4 GSE38672 [6] GSE24614 [6] GSE45044 [12] GSE17404 [9] GSE16564 [15] GSE29382 [36] GSE46496 [9] GSE35761 [6] GSE46150 [8] 0.6 GSE16874 [12] GSE24489 [14] GSE43197 [27] GSE6675 [8] GSE8488 [15] GSE18597 [42] GSE9441 [36] GSE11818 [6] GSE10904 [6] 0.8 GSE13148 [10] GSE19925 [6] GSE40087 [15] GSE29082 [6] Score 4.02 4.02 4.04 4.05 4.05 4.06 4.08 4.09 4.12 4.12 4.12 4.14 4.14 4.15 4.16 4.17 4.17 4.19 4.20 4.21 4.22 4.22 4.23 4.23 4.25 4.25 4.26 4.27 4.27 4.28 4.29 4.29 4.29 4.30 4.34 4.34 4.34 4.38 4.39 4.40 4.41 4.42 4.46 4.48 4.48 4.49 4.49 4.50 4.50 4.50 1.0 Notes 1700008O03Rik 4930571K23Rik 1700015E13Rik 1700029P11Rik 1700026L06Rik 4921528I07Rik Symbol Num ofCEMGenes:13.Predicted1063.SelectedDatasets:36.Strength:0.7 CEM 1,Geneset"[G]axonemaldyneincomplex",Page12 Tmem231 Gm17455 Slc22a14 Fam217a Fam154a Fam166a Ccdc116 Ccdc153 Zcwpw2 Nup210l Slco6b1 Dpy19l2 Fam47c Armc12 Ccdc57 Ccdc33 Ccdc83 Pabpc2 Necab2 C87436 Olfr480 Dmrtc2 Prss54 Hs6st3 Slc4a8 Nutm1 Erich2 Lrrc73 Cct8l1 Lyrm7 Klhl35 Cdhr4 Gbgt1 Cylc1 Gtsf1 Kif2b Rhcg Gsc2 Actl9 Pbx4 Theg Dlx6 Ggn Allc 0.0 1.0

GSE40939 [10] GSE10813 [12]

GSE7958 [12] Scale ofaveragePearsoncorrelations GSE13753 [10] GSE42008 [6] GSE23016 [9] GSE8249 [46] GSE11259 [9] GSE5763 [9] 0.2 GSE36378 [20] GSE5891 [6] GSE37301 [20] GSE9975 [36] GSE9338 [42] GSE17112 [8] GSE22140 [13] GSE19079 [6] GSE34863 [8] 0.4 GSE38672 [6] GSE24614 [6] GSE45044 [12] GSE17404 [9] GSE16564 [15] GSE29382 [36] GSE46496 [9] GSE35761 [6] GSE46150 [8] 0.6 GSE16874 [12] GSE24489 [14] GSE43197 [27] GSE6675 [8] GSE8488 [15] GSE18597 [42] GSE9441 [36] GSE11818 [6] GSE10904 [6] 0.8 GSE13148 [10] GSE19925 [6] GSE40087 [15] GSE29082 [6] Score 3.61 3.61 3.61 3.61 3.62 3.62 3.63 3.63 3.65 3.65 3.65 3.66 3.66 3.67 3.67 3.68 3.68 3.69 3.70 3.71 3.71 3.72 3.73 3.73 3.76 3.76 3.76 3.76 3.77 3.79 3.80 3.82 3.84 3.87 3.88 3.88 3.91 3.91 3.93 3.95 3.96 3.96 3.96 3.96 3.97 3.97 3.98 3.98 4.00 4.01 1.0 Notes 1700016G14Rik 4933403O08Rik 4933402N03Rik 1700016C15Rik 4930564B18Rik 4933433C11Rik 9230104L09Rik 2200002J24Rik 4931429I11Rik 4933436I01Rik Symbol Num ofCEMGenes:13.Predicted1063.SelectedDatasets:36.Strength:0.7 CEM 1,Geneset"[G]axonemaldyneincomplex",Page13 BC051628 Ppapdc1a Abhd16b Mettl7a1 Ldhal6b Speer4f Hdhd1a Chchd6 D1Pas1 Adcy10 Adora3 Izumo1 Rnf148 Nt5c1b Adam5 Dnaja3 Grin2b Zfp600 Nupr1l Mesp1 Dpep3 Cage1 Morn1 Naa11 Sycp2 Foxh1 Agbl5 Park2 Dnal1 Vsig1 Ttbk2 Plcz1 Rps3 Irgc1 Nek5 Odf1 Pfn4 Rfx3 Tut1 T2 0.0 1.0

GSE40939 [10] GSE10813 [12]

GSE7958 [12] Scale ofaveragePearsoncorrelations GSE13753 [10] GSE42008 [6] GSE23016 [9] GSE8249 [46] GSE11259 [9] GSE5763 [9] 0.2 GSE36378 [20] GSE5891 [6] GSE37301 [20] GSE9975 [36] GSE9338 [42] GSE17112 [8] GSE22140 [13] GSE19079 [6] GSE34863 [8] 0.4 GSE38672 [6] GSE24614 [6] GSE45044 [12] GSE17404 [9] GSE16564 [15] GSE29382 [36] GSE46496 [9] GSE35761 [6] GSE46150 [8] 0.6 GSE16874 [12] GSE24489 [14] GSE43197 [27] GSE6675 [8] GSE8488 [15] GSE18597 [42] GSE9441 [36] GSE11818 [6] GSE10904 [6] 0.8 GSE13148 [10] GSE19925 [6] GSE40087 [15] GSE29082 [6] Score 3.22 3.24 3.25 3.28 3.28 3.28 3.29 3.29 3.29 3.30 3.30 3.30 3.30 3.31 3.34 3.34 3.35 3.35 3.36 3.36 3.37 3.38 3.39 3.39 3.40 3.40 3.40 3.41 3.41 3.46 3.46 3.46 3.47 3.47 3.48 3.50 3.50 3.51 3.51 3.51 3.53 3.53 3.53 3.54 3.55 3.56 3.56 3.56 3.57 3.57 1.0 Notes 1700110M21Rik 1700009N14Rik 4921517D22Rik 1700067P10Rik 4921539E11Rik 1700011E24Rik 4933425L06Rik 1700034J05Rik Symbol Num ofCEMGenes:13.Predicted1063.SelectedDatasets:36.Strength:0.7 CEM 1,Geneset"[G]axonemaldyneincomplex",Page14 Nipsnap3a BC049762 Tmem212 Hepacam Fam187b Aldoart2 Adam6a Acsbg2 Rbmxl2 Ccdc73 Fbxo15 Olfr672 Olfr544 Bdkrb2 Izumo3 Srgap1 Ubqln3 Spatc1 Pkd2l1 Pkdrej Lrrc72 Wdr64 Dand5 Spag4 Mroh4 Morn4 Sel1l2 Cdhr3 Tssk2 Atp7b Best1 Hyal6 Pdcl2 Spert Kif27 Sun3 Zpbp Iqcf3 Insl5 Ntn5 Ddi1 Mgll 0.0 1.0

GSE40939 [10] GSE10813 [12]

GSE7958 [12] Scale ofaveragePearsoncorrelations GSE13753 [10] GSE42008 [6] GSE23016 [9] GSE8249 [46] GSE11259 [9] GSE5763 [9] 0.2 GSE36378 [20] GSE5891 [6] GSE37301 [20] GSE9975 [36] GSE9338 [42] GSE17112 [8] GSE22140 [13] GSE19079 [6] GSE34863 [8] 0.4 GSE38672 [6] GSE24614 [6] GSE45044 [12] GSE17404 [9] GSE16564 [15] GSE29382 [36] GSE46496 [9] GSE35761 [6] GSE46150 [8] 0.6 GSE16874 [12] GSE24489 [14] GSE43197 [27] GSE6675 [8] GSE8488 [15] GSE18597 [42] GSE9441 [36] GSE11818 [6] GSE10904 [6] 0.8 GSE13148 [10] GSE19925 [6] GSE40087 [15] GSE29082 [6] Score 2.77 2.77 2.77 2.78 2.83 2.84 2.85 2.85 2.89 2.89 2.90 2.91 2.91 2.92 2.92 2.92 2.92 2.92 2.93 2.97 2.99 2.99 3.00 3.01 3.03 3.03 3.06 3.08 3.08 3.10 3.11 3.11 3.12 3.12 3.12 3.13 3.13 3.13 3.14 3.14 3.16 3.16 3.16 3.17 3.18 3.19 3.19 3.20 3.20 3.21 1.0 Notes D130043K22Rik 4930451C15Rik 1600014K23Rik 1700123K08Rik 4933411K16Rik 4930451I11Rik 1700123I01Rik Symbol Num ofCEMGenes:13.Predicted1063.SelectedDatasets:36.Strength:0.7 CEM 1,Geneset"[G]axonemaldyneincomplex",Page15 BC089491 Mapk8ip2 AI429214 Als2cr11 Ccdc157 Tbc1d21 Gm8267 Rnf144a Klk1b24 Klk1b21 Lpcat2b Wbp2nl Spatc1l Olfr701 Tex13a Hmgb4 H2afb1 Prss56 Prss52 Trim17 Tmco5 Zfp597 Nlrp14 Osbp2 Hrasls Hspb9 Cabs1 Olfr64 Olfr66 Dhrs2 Ccer1 Gja10 Gykl1 P2rx2 Ribc2 Coa4 Iqcf1 Ifna2 Odf2 Ksr2 Npb Lipf Fev 0.0 1.0

GSE40939 [10] GSE10813 [12]

GSE7958 [12] Scale ofaveragePearsoncorrelations GSE13753 [10] GSE42008 [6] GSE23016 [9] GSE8249 [46] GSE11259 [9] GSE5763 [9] 0.2 GSE36378 [20] GSE5891 [6] GSE37301 [20] GSE9975 [36] GSE9338 [42] GSE17112 [8] GSE22140 [13] GSE19079 [6] GSE34863 [8] 0.4 GSE38672 [6] GSE24614 [6] GSE45044 [12] GSE17404 [9] GSE16564 [15] GSE29382 [36] GSE46496 [9] GSE35761 [6] GSE46150 [8] 0.6 GSE16874 [12] GSE24489 [14] GSE43197 [27] GSE6675 [8] GSE8488 [15] GSE18597 [42] GSE9441 [36] GSE11818 [6] GSE10904 [6] 0.8 GSE13148 [10] GSE19925 [6] GSE40087 [15] GSE29082 [6] Score 2.27 2.28 2.33 2.33 2.35 2.35 2.35 2.37 2.38 2.40 2.40 2.40 2.41 2.42 2.43 2.43 2.43 2.46 2.47 2.48 2.48 2.51 2.54 2.54 2.54 2.56 2.56 2.57 2.58 2.59 2.59 2.60 2.60 2.60 2.62 2.62 2.62 2.63 2.64 2.64 2.67 2.68 2.69 2.69 2.70 2.70 2.75 2.75 2.75 2.76 1.0 Notes A930018P22Rik 1810046K07Rik 1700020A23Rik 4931440L10Rik 1700003F12Rik Symbol Num ofCEMGenes:13.Predicted1063.SelectedDatasets:36.Strength:0.7 CEM 1,Geneset"[G]axonemaldyneincomplex",Page16 Ceacam2 Fam194a Fam228a Scgb3a2 Zdhhc19 Osbpl10 Rbm15b Umodl1 Dusp13 Dcdc2a Slc35f4 Gabra2 Olfr156 Mbd3l1 Lrp2bp Gm166 Prss55 Smco2 Arrdc5 Muc20 Tgfbr2 Lrrc51 Kcnh3 Kcnn3 Sftpa1 Usp50 Wfdc3 Pde3a Gpr33 Tex37 Gzmn Stag3 Htr5b Znrf4 Klf17 Nell2 Ppil6 Iqcf5 Fa2h Fech Fbll1 Gja5 Eid3 Kif6 Klb 0.0 1.0

GSE40939 [10] GSE10813 [12]

GSE7958 [12] Scale ofaveragePearsoncorrelations GSE13753 [10] GSE42008 [6] GSE23016 [9] GSE8249 [46] GSE11259 [9] GSE5763 [9] 0.2 GSE36378 [20] GSE5891 [6] GSE37301 [20] GSE9975 [36] GSE9338 [42] GSE17112 [8] GSE22140 [13] GSE19079 [6] GSE34863 [8] 0.4 GSE38672 [6] GSE24614 [6] GSE45044 [12] GSE17404 [9] GSE16564 [15] GSE29382 [36] GSE46496 [9] GSE35761 [6] GSE46150 [8] 0.6 GSE16874 [12] GSE24489 [14] GSE43197 [27] GSE6675 [8] GSE8488 [15] GSE18597 [42] GSE9441 [36] GSE11818 [6] GSE10904 [6] 0.8 GSE13148 [10] GSE19925 [6] GSE40087 [15] GSE29082 [6] Score 1.82 1.82 1.83 1.85 1.86 1.86 1.87 1.88 1.89 1.89 1.89 1.91 1.95 1.95 1.97 1.98 1.98 1.98 1.98 1.99 2.03 2.04 2.05 2.05 2.06 2.08 2.08 2.09 2.10 2.10 2.11 2.11 2.12 2.13 2.13 2.14 2.15 2.16 2.16 2.17 2.17 2.18 2.19 2.20 2.20 2.21 2.22 2.22 2.26 2.27 1.0 Notes 1700007B14Rik 4930503B20Rik 1700029H14Rik 4933406J08Rik 1700010I14Rik Symbol Num ofCEMGenes:13.Predicted1063.SelectedDatasets:36.Strength:0.7 CEM 1,Geneset"[G]axonemaldyneincomplex",Page17 BC048562 Ube2d2b Ccdc169 Dnajc5b Nsmce1 Fam50b Fam71b Fam47e Stmnd1 Ccdc63 Cep112 Laptm5 Pde10a Pip5kl1 Dmrtb1 Olfr976 Mbd3l2 Htatip2 Rnf133 Rnf151 Efcab9 Sept12 Eps8l3 Bpifb5 Rhpn1 Cdh26 Usp9y Socs7 Pcsk1 Actrt2 Tex26 Pmp2 Klkb1 Ascl3 Oprl1 Trhr2 Gsg1 Lyzl1 Cd46 Exd1 Satl1 Itga2 Lhx3 Brs3 Zp3r 0.0 1.0

GSE40939 [10] GSE10813 [12]

GSE7958 [12] Scale ofaveragePearsoncorrelations GSE13753 [10] GSE42008 [6] GSE23016 [9] GSE8249 [46] GSE11259 [9] GSE5763 [9] 0.2 GSE36378 [20] GSE5891 [6] GSE37301 [20] GSE9975 [36] GSE9338 [42] GSE17112 [8] GSE22140 [13] GSE19079 [6] GSE34863 [8] 0.4 GSE38672 [6] GSE24614 [6] GSE45044 [12] GSE17404 [9] GSE16564 [15] GSE29382 [36] GSE46496 [9] GSE35761 [6] GSE46150 [8] 0.6 GSE16874 [12] GSE24489 [14] GSE43197 [27] GSE6675 [8] GSE8488 [15] GSE18597 [42] GSE9441 [36] GSE11818 [6] GSE10904 [6] 0.8 GSE13148 [10] GSE19925 [6] GSE40087 [15] GSE29082 [6] Score 1.38 1.41 1.41 1.43 1.44 1.46 1.46 1.47 1.48 1.49 1.49 1.49 1.50 1.53 1.54 1.54 1.54 1.55 1.56 1.57 1.57 1.58 1.58 1.58 1.61 1.62 1.62 1.63 1.64 1.65 1.65 1.66 1.66 1.67 1.68 1.69 1.71 1.74 1.74 1.74 1.76 1.76 1.77 1.78 1.78 1.79 1.80 1.80 1.80 1.82 1.0 Notes 1700019O17Rik 4930526D03Rik 1700016H13Rik 2310003H01Rik 1700020L24Rik D7Ertd443e Symbol Num ofCEMGenes:13.Predicted1063.SelectedDatasets:36.Strength:0.7 CEM 1,Geneset"[G]axonemaldyneincomplex",Page18 Vmn1r13 Vmn1r41 Hspa12a Onecut3 Klk1b27 Spata21 Slc30a3 Gapdhs Gucy2g Dusp21 Ccdc62 Wfdc6a Tex101 Bzrap1 Angel1 Serac1 Prss40 Col6a4 Spam1 Pcnxl2 Syce1l Amer2 Trpm6 Nkpd1 Kcnc1 Becn1 Fndc8 Gpr12 Chrne Oscar Dido1 Pomc Hyal4 Ccl28 Tescl Muc3 Adh4 Yipf7 Scgn Msi1 Safb Tal2 Rho Zp2 0.0 1.0

GSE40939 [10] GSE10813 [12]

GSE7958 [12] Scale ofaveragePearsoncorrelations GSE13753 [10] GSE42008 [6] GSE23016 [9] GSE8249 [46] GSE11259 [9] GSE5763 [9] 0.2 GSE36378 [20] GSE5891 [6] GSE37301 [20] GSE9975 [36] GSE9338 [42] GSE17112 [8] GSE22140 [13] GSE19079 [6] GSE34863 [8] 0.4 GSE38672 [6] GSE24614 [6] GSE45044 [12] GSE17404 [9] GSE16564 [15] GSE29382 [36] GSE46496 [9] GSE35761 [6] GSE46150 [8] 0.6 GSE16874 [12] GSE24489 [14] GSE43197 [27] GSE6675 [8] GSE8488 [15] GSE18597 [42] GSE9441 [36] GSE11818 [6] GSE10904 [6] 0.8 GSE13148 [10] GSE19925 [6] GSE40087 [15] GSE29082 [6] Score 0.98 1.00 1.03 1.03 1.04 1.05 1.05 1.07 1.07 1.07 1.08 1.08 1.09 1.10 1.12 1.12 1.13 1.13 1.13 1.15 1.15 1.17 1.18 1.18 1.19 1.19 1.20 1.21 1.21 1.21 1.22 1.22 1.25 1.25 1.25 1.26 1.28 1.29 1.29 1.29 1.29 1.30 1.31 1.32 1.33 1.33 1.34 1.34 1.36 1.37 1.0 Notes C530008M17Rik 4833427G06Rik 4931406B18Rik 1700017N19Rik 1700001P01Rik 4931431F19Rik Symbol Num ofCEMGenes:13.Predicted1063.SelectedDatasets:36.Strength:0.7 CEM 1,Geneset"[G]axonemaldyneincomplex",Page19 Rab11fip2 Gm11487 Aldh7a1 Fam13c Katnal2 Pcdhb1 Cd209c Chmp7 Bhlha9 Cldn26 Bcmo1 Pnpla5 Efcab1 Lingo2 Mtnr1a Pla2g6 Zfp943 Zfp961 Qrich2 Crisp2 Kcng4 Triml1 Exoc1 Casz1 Olfr16 Tex14 A4gnt Nr4a3 Cecr6 Zfp13 Grik3 Glra3 Chml Dpp3 Klf12 Rgs9 Zhx3 Nol4 Cst8 Pdilt Crot Ctrc Abo Ubc 0.0 1.0

GSE40939 [10] GSE10813 [12]

GSE7958 [12] Scale ofaveragePearsoncorrelations GSE13753 [10] GSE42008 [6] GSE23016 [9] GSE8249 [46] GSE11259 [9] GSE5763 [9] 0.2 GSE36378 [20] GSE5891 [6] GSE37301 [20] GSE9975 [36] GSE9338 [42] GSE17112 [8] GSE22140 [13] GSE19079 [6] GSE34863 [8] 0.4 GSE38672 [6] GSE24614 [6] GSE45044 [12] GSE17404 [9] GSE16564 [15] GSE29382 [36] GSE46496 [9] GSE35761 [6] GSE46150 [8] 0.6 GSE16874 [12] GSE24489 [14] GSE43197 [27] GSE6675 [8] GSE8488 [15] GSE18597 [42] GSE9441 [36] GSE11818 [6] GSE10904 [6] 0.8 GSE13148 [10] GSE19925 [6] GSE40087 [15] GSE29082 [6] Score 0.62 0.62 0.64 0.64 0.66 0.67 0.67 0.68 0.70 0.70 0.71 0.71 0.71 0.74 0.74 0.75 0.76 0.76 0.76 0.76 0.79 0.80 0.82 0.82 0.83 0.83 0.84 0.85 0.85 0.85 0.85 0.87 0.87 0.88 0.88 0.88 0.89 0.90 0.90 0.91 0.91 0.91 0.91 0.91 0.93 0.93 0.93 0.95 0.97 0.98 1.0 Notes 4930402K13Rik 4930568D16Rik 1700001K19Rik 1300017J02Rik Symbol Num ofCEMGenes:13.Predicted1063.SelectedDatasets:36.Strength:0.7 CEM 1,Geneset"[G]axonemaldyneincomplex",Page20 BC100451 Tmem38b Timm8a2 Tctex1d4 Slc16a11 Fam131c Ccdc166 Zscan5b Aldoart1 Adam24 Spata25 Slc36a3 Slc24a4 Slc5a12 Phyhipl Sh3d21 Mboat4 Cmklr1 Nkx2-6 Ankzf1 Zbtb32 Oprm1 Chrm1 Obox3 Lrrc61 Cnga4 Bpifa3 Tram2 Spo11 Asb16 Pde4a Panx3 Uvssa Olfr71 Otop2 Arpc5 Nr6a1 Brsk1 Cst13 Plcd4 Padi6 Eif4h Lrig1 Tpo Lpo Lipi 0.0 1.0

GSE40939 [10] GSE10813 [12]

GSE7958 [12] Scale ofaveragePearsoncorrelations GSE13753 [10] GSE42008 [6] GSE23016 [9] GSE8249 [46] GSE11259 [9] GSE5763 [9] 0.2 GSE36378 [20] GSE5891 [6] GSE37301 [20] GSE9975 [36] GSE9338 [42] GSE17112 [8] GSE22140 [13] GSE19079 [6] GSE34863 [8] 0.4 GSE38672 [6] GSE24614 [6] GSE45044 [12] GSE17404 [9] GSE16564 [15] GSE29382 [36] GSE46496 [9] GSE35761 [6] GSE46150 [8] 0.6 GSE16874 [12] GSE24489 [14] GSE43197 [27] GSE6675 [8] GSE8488 [15] GSE18597 [42] GSE9441 [36] GSE11818 [6] GSE10904 [6] 0.8 GSE13148 [10] GSE19925 [6] GSE40087 [15] GSE29082 [6] Score 0.32 0.32 0.33 0.33 0.33 0.33 0.34 0.34 0.35 0.36 0.38 0.38 0.39 0.41 0.41 0.43 0.43 0.43 0.44 0.44 0.44 0.45 0.45 0.45 0.46 0.47 0.47 0.47 0.47 0.47 0.48 0.48 0.49 0.49 0.50 0.51 0.51 0.52 0.53 0.53 0.55 0.55 0.56 0.58 0.59 0.60 0.60 0.60 0.62 0.62 1.0 Notes 4930415O20Rik 1700067K01Rik 1700102P08Rik 1700034E13Rik 4930402F06Rik 2310007L24Rik Symbol Num ofCEMGenes:13.Predicted1063.SelectedDatasets:36.Strength:0.7 CEM 1,Geneset"[G]axonemaldyneincomplex",Page21 BC061194 Krtap31-1 Fam227b Arhgef17 Serpina5 Hsd17b3 Gm1564 Slc34a2 Zswim2 Dusp15 Nccrp1 Pou3f2 Prss21 Vstm2l Epm2a Rwdd3 Tas1r1 Zfp169 Bpifb3 Pfkfb2 Pde6g Asb18 Actl10 Letm2 Fkbp6 Iglon5 Gpr63 Olfr17 Olfr70 Gcnt7 Dgcr6 Gadl1 Nhlh1 Cetn1 Tekt2 Glp1r Klrg2 Srms Aqp7 Evi5l Lcn3 Mzf1 Arr3 C8b 0.0 1.0

GSE40939 [10] GSE10813 [12]

GSE7958 [12] Scale ofaveragePearsoncorrelations GSE13753 [10] GSE42008 [6] GSE23016 [9] GSE8249 [46] GSE11259 [9] GSE5763 [9] 0.2 GSE36378 [20] GSE5891 [6] GSE37301 [20] GSE9975 [36] GSE9338 [42] GSE17112 [8] GSE22140 [13] GSE19079 [6] GSE34863 [8] 0.4 GSE38672 [6] GSE24614 [6] GSE45044 [12] GSE17404 [9] GSE16564 [15] GSE29382 [36] GSE46496 [9] GSE35761 [6] GSE46150 [8] 0.6 GSE16874 [12] GSE24489 [14] GSE43197 [27] GSE6675 [8] GSE8488 [15] GSE18597 [42] GSE9441 [36] GSE11818 [6] GSE10904 [6] 0.8 GSE13148 [10] GSE19925 [6] GSE40087 [15] GSE29082 [6] Score 0.12 0.12 0.13 0.13 0.13 0.14 0.14 0.15 0.15 0.15 0.16 0.16 0.16 0.17 0.17 0.18 0.18 0.18 0.19 0.19 0.19 0.19 0.19 0.19 0.20 0.20 0.21 0.21 0.22 0.23 0.23 0.23 0.24 0.24 0.24 0.25 0.26 0.26 0.27 0.27 0.27 0.27 0.29 0.29 0.29 0.30 0.30 0.31 0.32 0.32 1.0 Notes 4930432K21Rik 4932438H23Rik 1700018B08Rik 1110032A03Rik Symbol Num ofCEMGenes:13.Predicted1063.SelectedDatasets:36.Strength:0.7 CEM 1,Geneset"[G]axonemaldyneincomplex",Page22 Cacna2d2 Ppp1r16a Vmn2r88 Ankrd61 Gm4787 Chrna3 Defb19 Shisa7 Glt6d1 Syce1 Gpat2 Dcst1 Ypel1 Grsf1 Grik5 Nlrp5 Sftpb Ubn2 Wnt1 Evx2 Mc3r Tsx 0.0 1.0

GSE40939 [10] GSE10813 [12]

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40939 Status: Public on Dec 21 2012 Title: Leukemogenesis by CDX2 involves KLF4 repression and deregulated PPARgamma signaling. Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 23202735 Summary & Design: Summary: Aberrant expression of the homeodomain transcription factor CDX2 occurs in most cases of acute myeloid leukemia (AML) and promotes leukemogenesis, making CDX2, in principle, an attractive therapeutic target. Conversely, CDX2 acts as a tumor suppressor in colonic epithelium. The effectors mediating the leukemogenic activity of CDX2 and the mechanism underlying its context-dependent properties are poorly characterized, and strategies for interfering with CDX2 function in AML remain elusive. We report data implicating repression of the transcription factor KLF4 as important for the oncogenic activity of CDX2, and demonstrate that CDX2 differentially regulates KLF4 in AML versus colon cancer cells through a mechanism that involves tissue-specific patterns of promoter binding and epigenetic modifications. Furthermore, we identified deregulation of the PPARÎ³ signaling pathway as a feature of AML expressing CDX2, and observed that PPARÎ³ agonists derepress KLF4 and are preferentially toxic to CDX2-positive leukemic cells. These data delineate transcriptional programs associated with CDX2 expression in hematopoietic cells; provide insight into the antagonistic duality of CDX2 function in AML versus colon cancer; and suggest reactivation of KLF4 expression, through modulation of PPARÎ³ signaling, as a new therapeutic modality in a large proportion of AML patients.

Overall design: Experiment 2 (Samples 7-10): The transcriptional changes induced by Cdx2 were assessed in vivo in Cdx2-initiated murine leukemias and compared with those of leukemias initiated by 5 different MLL fusion oncogenes (previously published data, available at GSE13690). Bone marrow cells isolated from C57BL/6 mice were transduced with pMSCV-Cdx2-IRES-GFP, and 8x10e5 GFP-positive cells were injected into lethally irradiated syngeneic recipient mice after 48 hours, followed by injection of 1x10e6 spleen cells from primary leukemic animals into sublethally irradiated secondary recipients. Spleen cells from secondary leukemic animals were harvested.

Background corr dist: KL-Divergence = 0.0204, L1-Distance = 0.0686, L2-Distance = 0.0061, Normal std = 0.8753

0.456 Kernel fit Pairwise Correlations Normal fit

Density 0.228

0.000 CEM 1

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

Pre-normalization Quantiles

control controlrep1 (0.0673492) controlrep2 (0.053215) murinerep3 (0.085477) murineCdx2 rep1 murineCdx2 (0.0294231) rep2 Cdx2 (0.0568924) inducedrep3Cdx2 (0.0448119) induced leukemia_secondary_rep1Cdx2 induced leukemia_secondary_rep2Cdx2 induced leukemia_primary leukemia_primary (0.114963) rep1 (0.369604) [(0.0906407) minrep2 (0.0876234) ] [ medium ] [ max ] CEM 1 Dnah6 50.2 66.8 207.5 P ( S | Z, I ) = 1.00 Dnali1 47.6 56.6 67.5 Mean Corr = 0.76953 Dnah7a 22.1 29.7 41.9 Dnah2 48.3 58.3 92.6 Dnah1 76.6 108.9 190.3 Dnah8 68.6 84.8 863.2 Dnah5 24.9 38.5 66.6 Dnah9 28.1 38.7 101.5 Dnal4 321.0 356.2 592.2 Dnah11 141.6 191.9 319.2 Dnaic2 53.8 79.0 187.8 Dync2li1 402.0 452.9 796.9 Dnah17 64.3 73.3 133.5 Foxj1 46.1 62.2 101.5 Fank1 68.7 95.7 510.5 Lrguk 23.2 31.9 65.5 Wdr65 69.9 79.7 341.7 1700012B09Rik 169.9 223.7 736.7 CEM 1 + Fsip1 21.9 31.7 98.1 Top 10 Genes Mapk15 69.5 86.9 232.9 B3gnt4 35.1 43.0 217.8 Ccdc19 29.8 36.2 47.4 Maats1 21.5 32.9 53.4

Null module GEO Series "GSE10813" 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=GSE10813 Status: Public on Feb 01 2009 Title: The in vitro expanded CD8+ T cells and its controls Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 18664279 Summary & Design: Summary: CD8+ NKT cells are naturally occurring but rare T cells that express both T cell and natural killer (NK) cell markers. These cells may play key roles in establishing tolerance to self antigens; however, the mechanism of action and the molecular profiles of these cells are poorly characterized due to their extremely low frequencies. We developed a highly efficient in vitro conversion/expansion protocol for such cells and extensively characterized their functional and molecular phenotypes using a variety of genomic and immunological techniques.

We used microarrays to elucidate the molecular mechanisms underlying the suppression function of the converted CD8+ NKT cells.

Keywords: Cell type comparison

Overall design: To identify candidate genes that might be related to the suppressive activity, the CD8+ NKT cells with potent suppressive activity were compared to three different control cells: 1) CD4+ T cells (with very weak suppression) cultured under the same condition as a control for culture condition, 2) naÃ¯ve CD8 T cells as the baseline expression level, and 3) CD8+ T cells activated using conventional activation protocols. The last two cell populations do not possess suppressive activity. This data set allows us to examine a number of different questions

Background corr dist: KL-Divergence = 0.0515, L1-Distance = 0.0980, L2-Distance = 0.0166, Normal std = 0.6629

0.602 Kernel fit Pairwise Correlations Normal fit

Density 0.301

0.000 CEM 1

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

Pre-normalization Quantiles

ExpandedExpanded CD8 ExpandedTcells CD8 with ExpandedTcells CD8 Suppression with ExpandedTcells CD8 Suppression with FreshTcells functionCD4 Suppression CD8 with FreshTcells function rep1 rep1Suppression CD8 withExpanded (0.163289) (0.0177094) function rep2 rep3lessExpanded (0.161366)suppression(0.0241891) functionCD8 rep4 ExpandedTcells (0.0623544) CD4 rep5 withrep1 StimulatedTcells (0.0156193) CD4 Suppression(0.0190954) with StimulatedTcells CD8less with rep1suppression function CD8less (0.0681501) rep2suppression rep2 (0.343064) rep2 (0.012661) (0.0623552) rep3[ min (0.0501475) ] [ medium ] [ max ] CEM 1 Dnah6 195.0 229.8 340.2 P ( S | Z, I ) = 1.00 Dnali1 93.3 112.6 166.4 Mean Corr = 0.75035 Dnah7a 57.2 71.2 107.0 Dnah2 60.1 71.5 96.2 Dnah1 180.5 231.6 294.3 Dnah8 154.4 259.7 697.8 Dnah5 128.8 160.6 249.3 Dnah9 117.6 162.9 270.5 Dnal4 317.8 416.8 636.3 Dnah11 331.2 381.3 596.3 Dnaic2 208.2 270.4 472.8 Dync2li1 141.7 158.5 296.1 Dnah17 165.6 194.9 339.3 Foxj1 82.4 96.4 110.6 Fank1 496.6 720.3 1148.2 Lrguk 51.7 68.2 142.5 Wdr65 66.7 77.5 93.1 1700012B09Rik 116.2 140.9 184.4 CEM 1 + Fsip1 162.0 231.6 380.7 Top 10 Genes Mapk15 206.4 255.8 389.9 B3gnt4 105.7 130.7 182.2 Ccdc19 103.1 112.8 149.4 Maats1 72.4 92.3 108.1

Null module GEO Series "GSE8726" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 7 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE8726 Status: Public on Aug 06 2008 Title: Expression Data from Sod2-/- and Sod2+/+ Mouse Erythroblasts. Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: The mitochondrial superoxide dismutase (SOD2) is a major antioxidant protein which detoxifies superoxide anion radicals generated by mitochondrial respiration (Weisiger and Fridovich, J. Biol. Chem. 1973). We designed a model of oxidative stress-induced anemia caused by SOD2-deficiency (Friedman et al. J. Exp. Med. 2001). Our previous work showed that mice reconstituted with SOD2-deficient hematopoietic stem cells develop an anemia with striking similarity to human sideroblastic anemia (SA) (Friedman et al. Blood 2004; Martin et al. Exp Hematol 2005). Our overall goal was to define early events in the pathogenesis of SOD2-deficiency SA and, in particular, to identify genes involved in the response of erythroid progenitors to oxidative stress. We compared gene expression of sorted TER-119+ CD71+ erythroblasts from SOD2-/- ('KO') versus Sod2+/+ ('WT') hematopoietic stem cell recipients using cDNA microarrays.

Samples used in this study were re-hybridized with GLYCOv2 oligonucleotide arrays. GLYCOv2 oligonucleotide arrays are custom Affymetrix GeneChip arrays (Affymetrix, Santa Clara, CA) designed for the Functional Glycomics Gateway, collaboration between the Consortium for Functional Glycomics (CFG, http://www.functionalglycomics.org/) and Nature Publishing Group. A complete description of the array can be found at http://www.functionalglycomics.org/static/consortium/resources/resourcecoree.shtml . Hybridization results and quality control details can be found at https://www.functionalglycomics.org/glycomics/publicdata/microarray.jsp , by clicking on the Raw Data icon link for microarray experiment Jeff Friedman 1: Sod2 KO anemic mice. Briefly but importantly, one Sod2-/- sample, which was prepared separately, and whose GAPDH 3'/5' ratio was off range, was legitimately removed from the analysis of the GLYCOv2 and 430 2.0 arrays.

Keywords: Genotype comparison, genetic modification

Overall design: We sorted Sod2-/- and Sod2+/+ size-matched mouse erythroblasts based on the expression of two developmental surface markers, CD71 and TER-119. Total RNA from 4 biological replicates per genotype were extracted and hybridized on 8 Affymetrix Mouse Genome 430 2.0 arrays (Affymetrix, Santa Clara, CA). After quality controls (see scan protocol), analysis was performed with GeneSifter (VizX Labs, Seattle, WA) using 4 Sod2+/+ (control samples, WT) and 3 Sod2-/- (KO) replicates.

Background corr dist: KL-Divergence = 0.0320, L1-Distance = 0.0795, L2-Distance = 0.0104, Normal std = 0.7538

0.529 Kernel fit Pairwise Correlations Normal fit

Density 0.265

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

Erythroblast_SOD2+/+_repWT17Erythroblast_SOD2+/+_repWT29Erythroblast_SOD2+/+_repWT33Erythroblast_SOD2+/+_repWT37Erythroblast_SOD2-/-_repKO31 (0.0347827)Erythroblast_SOD2-/-_repKO35 (0.198386)Erythroblast_SOD2-/-_repKO39 (0.053415) (0.274711) (0.0271003) (0.277803)[ (0.133802)min ] [ medium ] [ max ] CEM 1 Dnah6 283.3 319.1 392.5 P ( S | Z, I ) = 1.00 Dnali1 104.5 120.7 130.8 Mean Corr = 0.72926 Dnah7a 86.7 107.1 122.2 Dnah2 95.0 118.2 130.7 Dnah1 135.7 150.3 232.3 Dnah8 173.8 190.3 242.7 Dnah5 107.9 149.3 199.1 Dnah9 97.9 128.9 144.8 Dnal4 309.6 369.0 430.2 Dnah11 444.5 537.9 602.6 Dnaic2 270.5 353.7 429.8 Dync2li1 265.7 307.2 336.6 Dnah17 235.5 344.6 390.1 Foxj1 136.6 149.2 175.4 Fank1 298.6 386.9 498.2 Lrguk 96.8 116.4 132.4 Wdr65 177.6 235.8 285.3 1700012B09Rik 150.5 185.7 223.5 CEM 1 + Fsip1 157.3 188.2 212.9 Top 10 Genes Mapk15 173.9 261.5 340.4 B3gnt4 142.1 168.5 179.2 Ccdc19 161.2 169.5 216.5 Maats1 96.6 119.0 133.3

Null module GEO Series "GSE10192" 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=GSE10192 Status: Public on Jan 15 2009 Title: PPAR Controls Gene Expression in MSC Cells Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 19115254 Summary & Design: Summary: Rosiglitazone (Rosi), a member of the thiazolidinedione class of drugs used to treat type 2 diabetes, activates the adipocyte-specific transcription factor peroxisome proliferator-activated receptor gamma (PPARg). This activation causes bone loss in animals and humans, at least in part due to suppression of osteoblast differentiation from marrow mesenchymal stem cells (MSC). In order to identify mechanisms by which PPARg2 suppresses osteoblastogenesis and promotes adipogenesis in MSC, we have analyzed the PPARg2 transcriptome in response to Rosi. A total of 4,252 transcriptional changes resulted when Rosi (1 uM) was applied to the U-33 marrow stromal cell line, stably transfected with PPARg2 (U-33/g2), as compared to non-induced U-33/g2 cells. Differences between U-33/g2 and U-33 cells stably transfected with empty vector (U-33/c) comprised 7,928 transcriptional changes, independent of Rosi. Cell type-, time- and treatment-specific gene clustering uncovered distinct patterns of PPARg2 transcriptional control of MSC lineage commitment. The earliest changes accompanying Rosi activation of PPARg2 included adjustments in morphogenesis, Wnt signaling, and immune responses, as well as sustained induction of lipid metabolism. Expression signatures influenced by longer exposure to Rosi provided evidence for distinct mechanisms governing the repression of osteogenesis and stimulation of adipogenesis. Our results suggest interactions that could lead to the identification of a master regulatory scheme controlling osteoblast differentiation.

Keywords: rosiglitazone, PPARgamma, microarray, time course, gene expression, stem cells

Overall design: U-33/g2 and U-33/c cells were cultured in the presence or absence of Rosi and gene expression was monitored at three different time points (2, 24, 72h) after exposure to the agonist. Each time point corresponds to a separate stage of Rosi-treated U-33/g2 cell conversion from the osteoblast-like phenotype to the adipocyte-like phenotype and includes induction (2h), intermediate alterations in phenotype progression (24h), and a terminally differentiated adipocytic with completely suppressed osteoblastic phenotype (72h). The experiment is a full factorial design performed in replicate.

Background corr dist: KL-Divergence = 0.0462, L1-Distance = 0.0784, L2-Distance = 0.0103, Normal std = 0.6400

0.623 Kernel fit Pairwise Correlations Normal fit

Density 0.312

0.000 CEM 1

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

Pre-normalization Quantiles

Empty vectorEmpty control,vectorEmpty control, vector24Empty hrs, control, vectorRosiglitazone24Empty hrs, control, vectorNo24Empty hrs,Rosiglitazone control,(ROS_24_1) vectorRosiglitazone24Empty hrs, control, vectorNo72PPARg2 (NONE_24_1) hrs,Rosiglitazone (0.0128576) control,(ROS_24_2) Rosiglitazone72PPARg2 expression hrs, No72Empty expression(0.00951556) (NONE_24_2) hrs,Rosiglitazone (0.0153896) construct, (ROS_72_1)vectorNoEmpty Rosiglitazone construct, control,vectorPPARg2 2(0.0216904) (NONE_72_1) hrs, (0.0111291) control, 2PPARg2Rosiglitazone expression2hrs, (NONE_72_2) hrs, Rosiglitazone 2EmptyNo expression(0.00938599)hrs, Rosiglitazone construct,No vector(ACT_2_1)Empty (0.0107944)Rosiglitazone (ROS_2_1)construct, control,vectorPPARg2 2 (PPAR_2_1)(0.0333556)hrs, control, 2PPARg2Rosiglitazone (NONE_2_1)expression2hrs,(0.0432876) hrs, Rosiglitazone 2PPARg2 No(0.0276495) expressionhrs, Rosiglitazone construct,No (0.0223984)(ACT_2_2)PPARg2 expression Rosiglitazone (ROS_2_2)construct,PPARg2 expression24 (PPAR_2_2)(0.0548908) hrs, construct,PPARg2 (NONE_2_2)expressionRosiglitazone24(0.0447388) hrs, construct,PPARg2 (0.016213) expressionNo24 hrs,Rosiglitazone construct, (0.0336254)PPARg2 (ACT_24_1)expressionRosiglitazone24 hrs, construct,Empty expressionNo72 (PPAR_24_1) hrs,Rosiglitazone (0.0600121)construct, vector (ACT_24_2) Rosiglitazone72 hrs, construct, control, No72 (0.0604991) (PPAR_24_2) hrs,Rosiglitazone (0.0509348) 72 (ACT_72_1) Rosiglitazone72 hrs, hrs, Rosiglitazone[ No min(0.0807058) (PPAR_72_1) Rosiglitazone (0.139638) (ACT_72_2) ] (ROS_72_2) (0.0714414) (PPAR_72_2) (0.0515725)[ (0.0151322) medium (0.103142) ] [ max ] CEM 1 Dnah6 50.5 100.2 245.9 P ( S | Z, I ) = 1.00 Dnali1 64.0 83.5 141.2 Mean Corr = 0.72502 Dnah7a 16.4 25.5 45.9 Dnah2 25.2 40.9 55.6 Dnah1 90.8 119.0 260.8 Dnah8 30.5 55.2 123.6 Dnah5 29.0 46.3 80.7 Dnah9 26.7 40.7 81.2 Dnal4 439.3 540.0 743.0 Dnah11 92.4 152.4 323.5 Dnaic2 57.1 84.2 199.6 Dync2li1 927.9 1868.3 4305.0 Dnah17 65.4 85.6 131.6 Foxj1 44.2 62.2 97.5 Fank1 116.8 174.1 459.0 Lrguk 20.1 32.1 60.5 Wdr65 37.0 56.4 108.7 1700012B09Rik 52.0 62.8 106.4 CEM 1 + Fsip1 72.6 92.5 139.2 Top 10 Genes Mapk15 123.1 197.8 387.6 B3gnt4 85.2 113.3 153.3 Ccdc19 32.9 47.9 71.3 Maats1 32.1 49.6 103.8

Null module GEO Series "GSE50122" 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=GSE50122 Status: Public on Nov 18 2013 Title: Runx3 function in splenic NK cells (IL-2 or IL-15) Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 24236182 Summary & Design: Summary: NK cells are innate immune cells that recognize and kill foreign, virally-infected and tumor cells without the need for prior immunization. NK expansion following viral infection is IL-2 or IL-15-dependent.

Overall design: To identify Runx3 responsive genes, NK cells were isolated from spleen of WT and Runx3-/- mice . Ten samples (5 WT and 5 Runx3-/-) of freshly isolated NK cells were separately obtained from individual mice. Cells were cultured for 7 days with IL-2 or IL-15.

Background corr dist: KL-Divergence = 0.0244, L1-Distance = 0.0693, L2-Distance = 0.0057, Normal std = 0.8495

0.470 Kernel fit Pairwise Correlations Normal fit

Density 0.235

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

NK_IL2_wt1NK_IL2_wt2 (0.265358)NK_IL2_wt3 (0.0215408)NK_IL2_ko1 (0.124287)NK_IL2_ko2 (0.0541459)NK_IL2_ko3 (0.118135)NK_IL15_wt1 (0.0274143)NK_IL15_wt2 (0.0755425)NK_IL15_ko1 (0.171491)NK_IL15_ko2 (0.103094) (0.0389919) [ min ] [ medium ] [ max ] CEM 1 Dnah6 4.4 5.2 6.3 P ( S | Z, I ) = 1.00 Dnali1 4.6 5.1 5.8 Mean Corr = 0.68753 Dnah7a 5.0 5.6 6.2 Dnah2 5.2 5.9 6.8 Dnah1 5.4 6.2 7.5 Dnah8 8.3 14.8 35.8 Dnah5 6.4 7.4 8.3 Dnah9 4.4 4.8 5.4 Dnal4 97.3 130.5 147.9 Dnah11 8.9 10.0 11.6 Dnaic2 5.4 6.0 7.1 Dync2li1 9.5 10.6 11.8 Dnah17 8.1 8.8 10.5 Foxj1 6.4 7.5 8.3 Fank1 6.1 7.7 8.7 Lrguk 4.8 5.4 5.9 Wdr65 4.6 5.1 5.8 1700012B09Rik 7.1 7.9 8.9 CEM 1 + Fsip1 7.7 9.0 10.4 Top 10 Genes Mapk15 2.8 3.1 3.7 B3gnt4 3.7 4.1 4.7 Ccdc19 5.2 5.6 6.7 Maats1 4.6 5.1 5.6

Null module GEO Series "GSE32020" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 26 -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=GSE32020 Status: Public on Jan 22 2013 Title: Expression data from mammary gland during pregnancy and lactation of CBA/CaH, QSi5 and Advanced Intercross Line (AIL; CBA/CaH X QSi5, the 14th generation) Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 23284081 Summary & Design: Summary: Previously we have shown significant differences in lactation performance, mammary gland histology and expression profiles of mammary transcriptome during peak-lactation (lactation day 9; L9) between the ordinary CBA/CaH (CBA) and the superior QSi5 strains of mice. In the present study, we compared mammary gland histology between CBA and QSi5 at mid-pregnancy (pregnancy day 12; P12). We assessed lactation performance during the first 8 days of lactation of the 13th - 14th generation of the Advanced Intercross Line (AIL) (CBA X QSi5) mice.

We utilized an integrative approach to analyzing mammary microarray expression profiles of CBA and QSi5 at P12 and CBA, AIL and QSi5 at L9.

Overall design: The inguinal mammary glands of CBA/CaH and QSi5 during mid-pregnancy (Pregnancy day 12; P12), and the glands of CBA/CaH, AIL and QSi5 during peak lactation (Lactation day 9; L9) were collected and total RNA was extracted for Affymetrix microarray (mouse genome 430 2) assay

Background corr dist: KL-Divergence = 0.0494, L1-Distance = 0.0894, L2-Distance = 0.0125, Normal std = 0.6669

0.598 Kernel fit Pairwise Correlations Normal fit

Density 0.299

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

P12_CBA_repP12_CBA_rep 1P12_CBA_rep (0.0352009) 2P12_CBA_rep (0.0320554) 3P12_CBA_rep (0.0160129) 4P12_QSi5_rep1 (0.0599047) 5P12_QSi5_rep2 (0.0281029)P12_QSi5_rep3 (0.0444446)P12_QSi5_rep4 (0.0590764)P12_QSi5_rep5 (0.0408111)L9_CBA_rep1 (0.0370311)L9_CBA_rep2 (0.0448416) (0.0516335)L9_CBA_rep3 (0.0763733)L9_QSi5_rep1 (0.120111)L9_QSi5_rep2 (0.0951712)L9_QSi5_rep3 (0.0965802)L9_AIL_rep1 (0.0539049)L9_AIL_rep2 (0.00750509)L9_AIL_rep3 (0.00757076)L9_AIL_rep4 (0.00434806)L9_AIL_rep5 (0.018534)L9_AIL_rep6 (0.010245)L9_AIL_rep7 (0.00731193)L9_AIL_rep8 (0.0130202)L9_AIL_rep9 (0.0284087)L9_AIL_rep10 (0.00686826) (0.00493196) [ min ] [ medium ] [ max ] CEM 1 Dnah6 140.5 260.9 576.2 P ( S | Z, I ) = 1.00 Dnali1 106.2 406.8 540.1 Mean Corr = 0.68692 Dnah7a 32.5 58.1 100.2 Dnah2 49.6 73.0 117.9 Dnah1 78.5 134.3 243.8 Dnah8 43.0 75.3 168.8 Dnah5 44.1 63.3 135.8 Dnah9 75.0 125.8 236.4 Dnal4 237.1 595.4 844.5 Dnah11 144.1 289.2 577.5 Dnaic2 72.0 228.9 493.3 Dync2li1 149.7 202.0 254.5 Dnah17 76.7 152.3 210.8 Foxj1 63.5 107.7 169.2 Fank1 241.0 446.7 782.4 Lrguk 39.7 60.1 97.2 Wdr65 45.8 109.4 369.8 1700012B09Rik 39.3 101.7 165.9 CEM 1 + Fsip1 87.7 177.4 297.5 Top 10 Genes Mapk15 78.2 242.3 513.0 B3gnt4 72.0 151.6 266.8 Ccdc19 39.2 68.8 129.6 Maats1 54.2 121.8 276.8

Null module GEO Series "GSE30865" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 68 -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=GSE30865 Status: Public on Jul 22 2011 Title: Gene expression of polyoma middle T antigen induced mammary tumors [NZB x PyMT] Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 22308418 Summary & Design: Summary: Mouse genetic crosses were established between the PyMT model of metastatic breast cancer and NZB strain. Tumors were harvested from the animals for gene expression analysis to identify genes and network modules associated with progression to distant metastatic disease.

Overall design: Gene expression of 68 samples from the NZB crosses were assayed on Affymetrix chips

Background corr dist: KL-Divergence = 0.0881, L1-Distance = 0.0712, L2-Distance = 0.0127, Normal std = 0.4866

0.869 Kernel fit Pairwise Correlations Normal fit

Density 0.435

0.000 CEM 1

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

Pre-normalization Quantiles

NZB BackcrossNZB BackcrossNZB animal BackcrossNZB 2421animal Backcross (0.00586276)NZB 2424animal Backcross (0.00692335)NZB 2426animal Backcross (0.0552442)NZB 2703animal Backcross (0.00501447)NZB 3001animal Backcross (0.00307563)NZB 3004animal Backcross (0.00356261)NZB 3039Ranimal Backcross NZB(0.00643217) 3042animal Backcross (0.011729)NZB 3046animal Backcross (0.00664417)NZB 3053animal Backcross (0.0259236)NZB 3197animal Backcross (0.00148915)NZB 3199animal Backcross (0.00555045)NZB 3289animal Backcross (0.00130923)NZB 3290animal Backcross (0.00552351)NZB 3291animal Backcross (0.0662955)NZB 3295animal Backcross (0.004095)NZB 3296animal Backcross (0.00664742)NZB 3296Ranimal Backcross NZB(0.0655683) 3299Ranimal Backcross NZB(0.00403982) 3351animal Backcross (0.00887793)NZB 3351Ranimal Backcross NZB(0.0628789) 3353animal Backcross (0.00427232)NZB 3355animal Backcross (0.0101015)NZB 3394animal Backcross (0.00283471)NZB 3397animal Backcross (0.0424591)NZB 3546animal Backcross (0.00265928)NZB 3547animal Backcross (0.00333348)NZB 3548animal Backcross (0.0503747)NZB 3550animal Backcross (0.00534409)NZB 3567animal Backcross (0.0348958)NZB 3568animal Backcross (0.00390538)NZB 3569animal Backcross (0.00274997)NZB 3570animal Backcross (0.00328289)NZB 3572animal Backcross (0.00282209)NZB 3738animal Backcross (0.00295154)NZB 3739animal Backcross (0.00382268)NZB 3769animal Backcross (0.00179587)NZB 3824animal Backcross (0.010689)NZB 3825animal Backcross (0.00422712)NZB 3827animal Backcross (0.00286414)NZB 3830Ranimal Backcross NZB(0.00336587) 3852Ranimal Backcross NZB(0.00193005) 3853animal Backcross (0.0151615)NZB 3854Ranimal Backcross NZB(0.01016) 3855animal Backcross (0.00454776)NZB 3864animal Backcross (0.00610266)NZB 3867animal Backcross (0.00443683)NZB 3868animal Backcross (0.00438336)NZB 3890Ranimal Backcross NZB(0.0107863) 3891animal Backcross (0.0478953)NZB 4946animal Backcross (0.0798036)NZB 4950animal Backcross (0.00374367)NZB 4955animal Backcross (0.00545838)NZB 4956animal Backcross (0.0117115)NZB 4957Ranimal Backcross NZB(0.00522075) 4958animal Backcross (0.00339214)NZB 4960animal Backcross (0.00800802)NZB 4963animal Backcross (0.0779911)NZB 4966animal Backcross (0.00916312)NZB 4967animal Backcross (0.00228924)NZB 4971animal Backcross (0.0061572)NZB 4973animal Backcross (0.0728221)NZB 4975animal Backcross (0.013759)NZB 4977animal Backcross (0.0103607)NZB 4978animal Backcross (0.00724126) 4979Ranimal (0.00563493) 4980animal (0.00451366) 5000 (0.00588721)[ min ] [ medium ] [ max ] CEM 1 Dnah6 59.9 81.2 187.3 P ( S | Z, I ) = 1.00 Dnali1 30.1 37.4 82.3 Mean Corr = 0.64787 Dnah7a 23.0 31.3 73.8 Dnah2 23.5 32.0 80.4 Dnah1 70.2 89.7 126.7 Dnah8 32.4 42.9 117.1 Dnah5 21.1 30.8 52.6 Dnah9 37.1 47.5 118.0 Dnal4 332.6 445.2 716.8 Dnah11 123.4 165.3 706.3 Dnaic2 78.3 96.8 359.7 Dync2li1 450.5 625.2 1175.2 Dnah17 32.2 42.2 67.3 Foxj1 53.4 70.8 91.6 Fank1 113.4 137.8 433.4 Lrguk 19.5 24.3 52.5 Wdr65 30.2 38.2 120.5 1700012B09Rik 27.2 35.0 74.6 CEM 1 + Fsip1 31.9 39.9 84.7 Top 10 Genes Mapk15 87.3 113.7 405.3 B3gnt4 47.2 61.5 119.4 Ccdc19 26.7 31.3 94.9 Maats1 24.4 31.0 116.3

Null module GEO Series "GSE15401" 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=GSE15401 Status: Public on Aug 09 2010 Title: Expression data from mouse aorta during and following transient hyperglycaemia Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 20844862 Summary & Design: Summary: Immediate and early effects of transient hyperglycaemia were examined using fully- reversible transgenic diabetic mice. Transient hyperglycaemia altered expression of 769 arterial genes, of which 200 did not reverse following recovery from hyperglycaemia. Many such genes are known to promote atherogenesis, including several implicated in arterial calcification and inflammation. This supports the view that hyperglycaemia causes not only very early deleterious changes in arterial gene expression but that to a large extent these persist for some time after restoration of normal blood glucose levels in vivo. Together, results support the contention that avoiding excess CVD risk in diabetes requires very early correction of hyperglycaemia.

Overall design: As shown previously (Pelengaris et al., 2002 Cell), c-MycERTAM protein is activated in pancreatic beta cells of adult transgenic mice, by daily intraperitoneal (IP) administration of tamoxifen (TAM; Sigma-Aldrich, Dorset, UK) (1 mg/0.2 ml in peanut oil). Inactivation of c-MycERTAM protein was achieved through withdrawal of TAM. Adult female mice, 3-6 months of age, inbred into CBA-C57Bl/6 background and maintained under barrier conditions, were treated with TAM for up to 7 days (Myc ON) and then monitored during recovery for more than 4 months (140 days) (Myc OFF). Experimental timepoints were: Days 2, 4 and 7: c-Myc ON; days 0, 11, 26: c-Myc OFF. Biological replicates: each timepoint included 3 biological replicates (n=3 mice).

Background corr dist: KL-Divergence = 0.0868, L1-Distance = 0.0831, L2-Distance = 0.0144, Normal std = 0.5024

0.794 Kernel fit Pairwise Correlations Normal fit

Density 0.397

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

Aorta_cMycOFF_0days_biologicalAorta_cMycOFF_0days_biologicalAorta_cMycOFF_0days_biologicalAorta_cMycON_2days_biologicalAorta_cMycON_2days_biological rep1Aorta_cMycON_2days_biological (0.0170589) rep2Aorta_cMycON_4days_biological (0.161358) rep3Aorta_cMycON_4days_biological (0.0165457) rep1Aorta_cMycON_4days_biological (0.038396) rep2Aorta_cMycON_7days_biological (0.0831242) rep3Aorta_cMycON_7days_biological (0.0313914) rep1Aorta_cMycON_7days_biological (0.0380933) rep2Aorta_cMycOFF_11days_biological (0.0551287) rep3Aorta_cMycOFF_11days_biological (0.0430876) rep1Aorta_cMycOFF_11days_biological (0.0512638) rep2Aorta_cMycOFF_26days_biological (0.0226844) rep3Aorta_cMycOFF_26days_biological (0.0348142) rep1Aorta_cMycOFF_26days_biological (0.169653) rep2 (0.110568) rep3 (0.0364795) rep1 (0.00725268) rep2[ min (0.0284318) rep3 (0.0546689)] [ medium ] [ max ] CEM 1 Dnah6 117.0 157.2 226.0 P ( S | Z, I ) = 1.00 Dnali1 37.9 44.3 63.1 Mean Corr = 0.63881 Dnah7a 20.4 30.9 47.0 Dnah2 35.6 51.2 62.4 Dnah1 77.8 97.8 138.7 Dnah8 61.9 88.3 153.5 Dnah5 35.0 39.5 56.3 Dnah9 48.1 61.0 85.7 Dnal4 453.8 552.4 707.9 Dnah11 176.4 278.3 440.6 Dnaic2 91.9 134.1 228.1 Dync2li1 193.0 273.1 407.8 Dnah17 93.0 117.1 150.3 Foxj1 57.0 67.2 101.4 Fank1 253.6 347.2 616.8 Lrguk 29.9 35.9 49.1 Wdr65 33.0 42.4 77.0 1700012B09Rik 57.4 70.2 106.1 CEM 1 + Fsip1 149.9 179.2 229.7 Top 10 Genes Mapk15 101.5 131.2 180.3 B3gnt4 88.0 111.5 140.5 Ccdc19 42.5 58.6 98.8 Maats1 24.5 36.1 51.9

Null module GEO Series "GSE39391" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 21 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

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

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

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

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

0.712 Kernel fit Pairwise Correlations Normal fit

Density 0.356

0.000 CEM 1

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

Pre-normalization Quantiles

AH129-5,AH129-5, biologicalAH129-5, biological rep1AH129-N1,biological biological(0.0119709) rep2AH129-N1,biological (0.0173189) rep3AH129-N1,biological (0.0171092) rep1AH129-NC1, (0.00949293) rep2AH129-NC1, (0.0137549) biological rep3AH129-NC1, (0.0133832) biologicalCS1-1, rep1 biological(0.0120426) biologicalCS1-1, rep2 (0.0139871) biologicalCS1-1, rep3 rep1 (0.0221283) biologicalR1,(0.0086351) rep2 biological R1,(0.010718) rep3 biological rep1 R1,(0.0227488) biological(0.0115143) rep2MEF, (0.0466638) biological rep3MEF, (0.0153045) biologicalMEF, rep1 biological(0.0145839)round rep2 (0.0126978)sperm,round rep3 (0.0208177)sperm,biologicalround sperm,biological rep1 biological(0.240489) rep2 (0.235451) rep3 (0.229188)[ min ] [ medium ] [ max ] CEM 1 Dnah6 3.8 8.1 2631.2 P ( S | Z, I ) = 1.00 Dnali1 1.5 4.9 8783.9 Mean Corr = 0.61087 Dnah7a 2.2 19.7 545.8 Dnah2 7.5 74.5 3730.5 Dnah1 1.8 5.1 746.1 Dnah8 2.5 2231.5 27291.2 Dnah5 3.7 27.8 142.1 Dnah9 1.9 5.2 45.3 Dnal4 167.1 241.5 4167.1 Dnah11 8.6 45.6 467.0 Dnaic2 1.5 17.4 55.4 Dync2li1 222.3 527.3 2616.8 Dnah17 3.1 16.6 59.7 Foxj1 1.0 23.7 3981.2 Fank1 2.4 9.6 1678.3 Lrguk 1.0 5.0 2209.3 Wdr65 3.8 28.5 5569.7 1700012B09Rik 2.1 8.2 12474.0 CEM 1 + Fsip1 4.2 30.9 5606.3 Top 10 Genes Mapk15 5.0 25.7 314.7 B3gnt4 2.4 8.0 237.6 Ccdc19 7.4 44.1 6591.0 Maats1 1.9 7.0 289.4

Null module GEO Series "GSE17923" 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=GSE17923 Status: Public on Sep 03 2009 Title: Gene Expression in White Adipose Tissue of KSR2-/- mice compared to wild type mice Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 19883615 Summary & Design: Summary: The goal of this study was to define the gene expression changes that take place in the white adipose tissue of KSR2-/- mice at 6 months of age.

Overall design: Three wild type mice and three KSR2-/- mice were used for total RNA extraction from white adipose tissue. The RNA from each mouse was analyzed on one Affymetrix gene chip and the differences were compared using Gene Set Enrichment Analysis.

Background corr dist: KL-Divergence = 0.0231, L1-Distance = 0.0257, L2-Distance = 0.0009, Normal std = 0.7211

0.553 Kernel fit Pairwise Correlations Normal fit

Density 0.277

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

6114 KSR2-/-6171 Wild Mouse6112 Type KSR2-/-White6169 Mouse AdiposeWild Mouse5796 White Type KSR2-/- WhiteTissue Adipose5720 Mouse AdiposeWild (0.0958884)Mouse WhiteTissue Type WhiteTissue Adipose (0.489895)Mouse Adipose (0.161989) WhiteTissue Tissue Adipose[ (0.0946508) min (0.0646797) Tissue ] (0.0928974)[ medium ] [ max ] CEM 1 Dnah6 49.9 81.2 89.6 P ( S | Z, I ) = 1.00 Dnali1 43.1 51.1 61.4 Mean Corr = 0.62016 Dnah7a 31.7 34.3 47.8 Dnah2 27.5 32.6 40.3 Dnah1 55.2 64.0 75.4 Dnah8 32.3 40.0 57.7 Dnah5 27.6 28.1 33.5 Dnah9 27.0 34.7 44.4 Dnal4 240.5 347.3 408.3 Dnah11 131.1 151.8 184.8 Dnaic2 48.5 64.0 123.2 Dync2li1 507.9 786.7 1016.9 Dnah17 40.3 44.5 65.4 Foxj1 51.5 65.9 72.2 Fank1 118.8 167.6 291.3 Lrguk 17.8 25.9 38.9 Wdr65 28.1 39.1 46.8 1700012B09Rik 19.7 26.0 32.9 CEM 1 + Fsip1 44.8 58.7 67.2 Top 10 Genes Mapk15 51.6 84.1 94.0 B3gnt4 28.0 38.8 43.3 Ccdc19 27.1 32.8 38.4 Maats1 18.8 21.9 27.8

Null module GEO Series "GSE12769" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 20 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12769 Status: Public on Sep 18 2008 Title: Murine postpartum testis developmental time course (0 to 35 day) Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: Murine testis developmental time course created from tissue samples collected from birth through adulthood and hybridized to M430_2 chips in duplicate.

Keywords: time-course

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

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

0.590 Kernel fit Pairwise Correlations Normal fit

Density 0.295

0.000 CEM 1

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

Pre-normalization Quantiles

mtestis_D0pp_rep1mtestis_D0pp_rep2mtestis_D3pp_rep1 (0.034615)mtestis_D3pp_rep2 (0.0391993)mtestis_D6pp_rep1 (0.0300943)mtestis_D6pp_rep2 (0.0236268)mtestis_D8pp_rep1 (0.0422467)mtestis_D8pp_rep2 (0.031391)mtestis_D10pp_rep1 (0.0280845)mtestis_D10pp_rep2 (0.0350728)mtestis_D14pp_rep1 (0.0323286)mtestis_D14pp_rep2 (0.0418649)mtestis_D18pp_rep1 (0.0335503)mtestis_D18pp_rep2 (0.0228124)mtestis_D20pp_rep1 (0.0863917)mtestis_D20pp_rep2 (0.0381218)mtestis_D30pp_rep1 (0.0694881)mtestis_D30pp_rep2 (0.0675944)mtestis_D35pp_rep1 (0.0609491)mtestis_D35pp_rep2 (0.0795624) (0.0668629) (0.136143)[ min ] [ medium ] [ max ] CEM 1 Dnah6 7.4 56.1 1155.7 P ( S | Z, I ) = 1.00 Dnali1 4.0 173.3 4279.1 Mean Corr = 0.58147 Dnah7a 7.3 423.2 1594.6 Dnah2 52.0 230.2 3150.4 Dnah1 19.4 77.5 531.1 Dnah8 152.4 3437.8 15602.1 Dnah5 4.0 68.4 245.8 Dnah9 4.0 50.3 279.8 Dnal4 285.9 440.4 1930.6 Dnah11 6.5 64.0 196.9 Dnaic2 6.5 43.9 83.0 Dync2li1 552.8 1138.2 1904.3 Dnah17 5.0 30.6 95.3 Foxj1 28.9 73.3 1090.2 Fank1 12.8 342.5 1903.8 Lrguk 16.5 173.0 739.2 Wdr65 7.3 323.1 2546.8 1700012B09Rik 4.0 655.6 6842.8 CEM 1 + Fsip1 52.8 163.2 2159.5 Top 10 Genes Mapk15 23.1 149.1 905.4 B3gnt4 7.1 21.0 310.5 Ccdc19 13.2 116.3 3599.7 Maats1 4.0 61.2 270.1

Null module GEO Series "GSE31972" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 6 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE31972 Status: Public on Dec 07 2011 Title: Transcriptional profiling of ICAM-positive and -negative cells from the mouse olfactory epithelium Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: We used trasncriptional profiling of fluorescent activated cell sorting (FACS) purified ICAM1-positive and negative cells from the olfactory epithelium (OE) of three-week old mice to identify genes enriched in the horizontal basal cells.

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

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

0.490 Kernel fit Pairwise Correlations Normal fit

Density 0.245

0.000 CEM 1

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

Pre-normalization Quantiles

Mm OE MmICAM1-negative-1 OE MmICAM1-positive-1 OE MmICAM1-negative-2 (0.141302)OE MmICAM1-positive-2 (0.177573) OE MmICAM1-negative-3 (0.261086)OE ICAM1-positive-3 (0.144056) (0.164583) (0.111399)[ min ] [ medium ] [ max ] CEM 1 Dnah6 7.5 15.0 68.8 P ( S | Z, I ) = 1.00 Dnali1 5.5 9.5 17.5 Mean Corr = 0.57667 Dnah7a 18.4 170.8 355.4 Dnah2 30.0 59.9 72.8 Dnah1 3.4 22.8 24.8 Dnah8 1.3 15.1 30.9 Dnah5 26.6 53.9 76.1 Dnah9 7.3 162.9 183.7 Dnal4 368.8 723.7 1330.5 Dnah11 29.1 626.5 783.5 Dnaic2 27.7 94.0 122.2 Dync2li1 1212.8 1989.3 2755.2 Dnah17 3.5 7.7 44.6 Foxj1 43.0 217.6 565.4 Fank1 43.4 577.4 791.8 Lrguk 3.3 32.3 46.5 Wdr65 34.3 246.2 344.3 1700012B09Rik 47.0 1030.4 2167.5 CEM 1 + Fsip1 32.0 181.7 193.0 Top 10 Genes Mapk15 72.6 948.5 1039.7 B3gnt4 3.2 62.2 113.9 Ccdc19 73.0 110.7 133.1 Maats1 5.0 151.0 261.0

Null module GEO Series "GSE7831" 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=GSE7831 Status: Public on Dec 13 2007 Title: Expression data from immature pDC and pDC activated with CpG 1826 and influenza virus PR8 Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 18029397 Summary & Design: Summary: CpG 1826 binds to Toll-like receptor (TLR)9, whereas influenza virus PR8 activates pDC via TLR7. Differential stimulation of pDCs is expected to result in unique activation mechanism(s) leading to a different phenotypically and functionally matured pDC

We used microarrays to detail the global programme of gene expression underlying the maturation process of pDC activated with CpG 1826 and influenza virus PR8. We identified a distinct expression profile of upregulated immunomediators.

Keywords: time course

Overall design: Sorted pDCs were cultured for 1h and 4hs in medium control or with 5 ´g/ml CpG 1826 or 300 HAU/ml purified influenza A/PR/8 virus. The first experiment (e1) included pDC in media and stimulated with CpG for 4h. In two other independent experimental batches (e2 and e3), we obtained samples of sorted pDC cultured in medium alone (med), and with CpG or PR8 (flu) for 1h and 4h. RNA extraction was performed using the RNeasy Kit (Qiagen) and hybridization on Affymetrix microarrays was performed using standard protocols. We sought to obtain homogeneous populations of pDCs at different time points under defined activation conditions in order to decipher the temporal resolution of expression profiles during the process of their maturation.

Background corr dist: KL-Divergence = 0.0526, L1-Distance = 0.0887, L2-Distance = 0.0101, Normal std = 0.7226

0.552 Kernel fit Pairwise Correlations Normal fit

Density 0.276

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 mediumpDC medium 1h,pDC biological CpG 1h,pDC biological1h, CpGrep1 biologicalpDC 1h,(0.0471762) flurep2 biologicalpDC 1h, rep1 (0.0762435) biological flu (0.0508293)pDC 1h, rep2 biological medium (0.205321)rep1pDC (0.00968062)medium 4h, rep2pDC biological (0.0359785)medium 4h,pDC biological CpGrep1 4h,pDC biological4h,(0.0602873) CpGrep2 biologicalpDC 4h,(0.00713691) CpGrep3 biologicalpDC rep1 4h,(0.040732) flu biological(0.0855969)pDC 4h, rep2 biological flu (0.142076) 4h, rep3 biological (0.184099)rep1 (0.0317487) rep2 (0.0230935)[ min ] [ medium ] [ max ] CEM 1 Dnah6 25.5 30.0 36.5 P ( S | Z, I ) = 1.00 Dnali1 16.4 20.9 24.8 Mean Corr = 0.56574 Dnah7a 30.8 37.4 45.6 Dnah2 19.0 22.9 26.3 Dnah1 10.6 12.8 14.1 Dnah8 18.8 22.4 26.1 Dnah5 26.0 30.5 41.4 Dnah9 12.3 17.0 20.2 Dnal4 56.3 118.6 143.0 Dnah11 34.8 42.3 54.3 Dnaic2 28.3 33.4 39.8 Dync2li1 152.1 199.4 250.1 Dnah17 19.8 25.9 32.5 Foxj1 46.3 52.1 69.5 Fank1 32.8 39.9 50.7 Lrguk 14.9 19.8 23.7 Wdr65 14.7 17.2 19.1 1700012B09Rik 19.8 26.8 32.1 CEM 1 + Fsip1 23.4 28.1 34.8 Top 10 Genes Mapk15 12.6 15.1 19.2 B3gnt4 9.9 11.8 13.7 Ccdc19 16.0 18.5 20.5 Maats1 16.4 19.4 21.2

Null module GEO Series "GSE23908" 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=GSE23908 Status: Public on Dec 20 2010 Title: Expression analysis of Wv/Wv fetal gonads Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21148109 Summary & Design: Summary: Following sex determination, XY and XX gonads develop into a testis and an ovary, respectively. Depending on the sex of the gonad, resident germ cells will subsequently be committed to either spermatogenesis or oogenesis. In this study we took advantage of the Wv/Wv mouse genetic model, in which gonads are almost devoided of germ cells, to uncover gene expression underlying fetal germ cell development.

Overall design: Male and Female gonads were collected at 12, 14 and 16 days post coitum (dpc) from wild-type and Wv/Wv mouse embryos. Total RNAs were extracted and hybridized on Affymetrix microarrays. Expression signals from male and female gonads or from wild-type and mutant gonads were compared to identify sexually dimorphic genes as well as genes expressed in germ cell during fetal gonad development.

Background corr dist: KL-Divergence = 0.0515, L1-Distance = 0.0758, L2-Distance = 0.0094, Normal std = 0.6178

0.653 Kernel fit Pairwise Correlations Normal fit

Density 0.326

0.000 CEM 1

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

Pre-normalization Quantiles

Wild-typeWild-type Ovary,Wild-type 16dpc,Ovary,Mutant biol16dpc,Ovary, rep MutantOvary, biol 16dpc,1 (0.0573809) rep 16dpc,MutantOvary, biol 2 (0.00757238) rep biol16dpc,Wild-typeOvary, 3 rep (0.0327652) biol 16dpc,Wild-type1 (0.0135279)Ovary, rep biol Wild-type2 (0.0371643)14dpc,Ovary, rep Mutant3 (0.00812857)biol14dpc,Ovary, rep MutantOvary, biol 14dpc,1 (0.00544033) rep 14dpc,MutantOvary, biol 2 (0.0125964) rep biol14dpc,Wild-typeOvary, 3 rep (0.0141471) biol 14dpc,Wild-type1 (0.0153479)Ovary, rep biol Mutant2 (0.0379129)12dpc,Ovary, rep MutantOvary,3 (0.0785473)biol12dpc, rep 12dpc,Wild-typeOvary, biol 1 (0.0098307) repbiol12dpc,Wild-type Testis,2 rep (0.0124128) biol Wild-type1 (0.0146405)16dpc,Testis, rep Mutant2 (0.00933665)biol16dpc,Testis, rep MutantTestis, biol 16dpc,1 (0.359738) rep 16dpc,MutantTestis, biol 2 (0.00771094) rep biol16dpc,Wild-typeTestis, 3 rep (0.0207899) biol 16dpc,Wild-type1 (0.0597447)Testis, rep biol Wild-type2 (0.0205049)14dpc,Testis, rep Mutant3 (0.0140041)biol14dpc,Testis, rep MutantTestis, biol 14dpc,1 (0.0208639) rep 14dpc,Wild-typeTestis, biol 2 (0.00965808) repbiol14dpc,Mutant Testis,3 rep (0.0137361) biol MutantTestis,1 (0.020084)12dpc, rep 12dpc,MutantTestis,2 (0.0260465)biol rep biol12dpc,Testis, 1 rep (0.0153012) biol 12dpc,1 (0.0143219) rep biol 2 (0.0138171) rep [3 (0.0169272)min ] [ medium ] [ max ] CEM 1 Dnah6 59.5 77.3 219.4 P ( S | Z, I ) = 1.00 Dnali1 18.5 29.0 87.2 Mean Corr = 0.59623 Dnah7a 33.4 43.2 86.3 Dnah2 44.7 72.7 235.8 Dnah1 60.2 71.8 153.3 Dnah8 35.2 42.9 198.0 Dnah5 24.5 31.1 71.8 Dnah9 34.0 39.2 201.2 Dnal4 426.5 528.5 833.7 Dnah11 113.1 137.0 913.0 Dnaic2 59.1 75.0 381.3 Dync2li1 572.4 1295.2 1838.1 Dnah17 55.6 66.6 111.4 Foxj1 50.7 57.7 151.8 Fank1 86.7 114.9 859.4 Lrguk 23.3 28.5 78.9 Wdr65 40.4 50.4 282.0 1700012B09Rik 21.8 26.7 170.0 CEM 1 + Fsip1 52.2 69.0 246.4 Top 10 Genes Mapk15 68.0 96.9 1187.5 B3gnt4 26.6 32.4 77.3 Ccdc19 43.4 62.1 127.7 Maats1 26.1 33.8 155.7

Null module GEO Series "GSE9038" 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=GSE9038 Status: Public on Aug 23 2011 Title: Gene expression profiles of striatum and cerebellum from knock-in mouse model of Huntington's disease Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21840924 Summary & Design: Summary: Huntingtons disease (HD) involves marked early neurodegeneration in the striatum whereas the cerebellum is relatively spared despite the ubiquitous expression of full-length mutant huntingtin, implying that inherent tissue-specific differences determine susceptibility to the HD CAG mutation. To understand this tissue specificity, we compared early mutant huntingtin-induced gene expression changes in striatum to those in cerebellum in young Hdh CAG knock-in mice, prior to onset of evident pathological alterations. Endogenous levels of full-length mutant huntingtin caused qualitatively similar, but quantitatively different gene expression changes in the two brain regions. Importantly, the quantitatively different responses in striatum and cerebellum in mutant mice were well accounted for by the intrinsic molecular differences in gene expression between striatum and cerebellum in wild-type animals. Tissue-specific gene expression changes in response to the HD mutation, therefore, appear to reflect the different inherent capacities of these tissues to buffer qualitatively similar effects of mutant huntingtin. These findings highlight a role for intrinsic quantitative tissue differences in contributing to HD pathogenesis, and likely to other neurodegenerative disorders exhibiting tissue-specificity, thereby guiding the search for effective therapeutic interventions.

Overall design: Total RNA was isolated from striatum and cerebellum of Hdh CAG knock-in mice (HdhQ111/HdhQ111) and wild-type mice (Hdh+/Hdh+, 3~10 weeks) for gene expression profiling using Affymetrix MG430 2.0 arrays.

Background corr dist: KL-Divergence = 0.0382, L1-Distance = 0.0736, L2-Distance = 0.0076, Normal std = 0.7672

0.545 Kernel fit Pairwise Correlations Normal fit

Density 0.272

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

Hdh+/Hdh+Hdh+/Hdh+ striatumHdh+/Hdh+ striatum atHdhQ111/HdhQ111 3~10 striatum atweeksHdhQ111/HdhQ111 3~10 biologicalatweeksHdhQ111/HdhQ111 3~10 striatum biologicalweeksHdh+/Hdh+ rep striatum1 biological at(0.0164066)Hdh+/Hdh+ rep3~10 striatumstriatum2 atweeks(0.0235872)Hdh+/Hdh+ rep3~10 striatum 3 at biologicalatweeks(0.0313254)HdhQ111/HdhQ111 3~103~10 striatum at biologicalweeksweeksHdhQ111/HdhQ111 3~10 rep 1 biologicalatbiologicalweeks (0.0848543)HdhQ111/HdhQ111 3~10 rep striatum 2 biologicalweeks (0.026769)Hdh+/Hdh+ reprep striatum 43biological at (0.0222467)(0.00977494)Hdh+/Hdh+ rep3~10 cerebellumstriatum5 atweeks(0.0163352)Hdh+/Hdh+ rep3~10 cerebellum 6 biologicalatweeks(0.0461884)HdhQ111/HdhQ111 at3~10 3~10 cerebellum biologicalweeksHdhQ111/HdhQ111 atweeksrep 3~10 4 biological (0.0276246)HdhQ111/HdhQ111 biologicalatweeksrep 3~10 cerebellum 5 (0.0151528)Hdh+/Hdh+ biologicalweeksrep rep cerebellum 6 (0.0937147) Hdh+/Hdh+1 biological at(0.0840529) rep3~10 cerebellumcerebellum Hdh+/Hdh+2 atweeks(0.0138249) rep3~10cerebellum HdhQ111/HdhQ1113 at biologicalatweeks(0.0891949) 3~10 3~10cerebellumHdhQ111/HdhQ111 at biologicalweeksweeks 3~10 repHdhQ111/HdhQ111 1 biologicalatbiologicalweeks (0.0104218) 3~10 repcerebellum 2 biologicalweeks (0.0704965) rep repcerebellum 43biological at (0.0542166)(0.0208225) rep3~10 cerebellum 5 atweeks(0.00889344) rep3~10 [6 biologicalat weeks(0.0701798)min 3~10 biologicalweeks rep] 4 biological (0.018553) rep 5 (0.0554385)[ rep medium 6 (0.0899251) ] [ max ] CEM 1 Dnah6 14.1 16.3 19.3 P ( S | Z, I ) = 1.00 Dnali1 19.5 21.2 23.3 Mean Corr = 0.55558 Dnah7a 13.8 15.2 16.2 Dnah2 16.9 18.0 18.9 Dnah1 11.7 12.4 13.2 Dnah8 13.0 13.9 14.7 Dnah5 13.4 14.2 15.4 Dnah9 13.0 13.9 14.7 Dnal4 152.8 407.7 563.9 Dnah11 14.3 20.4 26.8 Dnaic2 19.9 22.8 26.3 Dync2li1 135.0 245.2 423.2 Dnah17 20.5 23.7 26.2 Foxj1 46.8 81.2 169.7 Fank1 13.7 14.9 16.1 Lrguk 13.5 14.7 15.6 Wdr65 16.2 17.3 18.2 1700012B09Rik 21.6 24.0 26.5 CEM 1 + Fsip1 22.3 24.6 26.6 Top 10 Genes Mapk15 8.7 9.3 9.8 B3gnt4 10.8 11.8 12.6 Ccdc19 17.4 18.5 19.6 Maats1 10.3 10.9 11.6

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

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

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

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

0.430 Kernel fit Pairwise Correlations Normal fit

Density 0.215

0.000 CEM 1

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

Pre-normalization Quantiles

Wild-typeMutant testes Wild-typetestes at P21, atMutant P21,biological testes biological Wild-typetestes at P21,rep1 atMutant P21,biological rep1(0.123055)testes biological(0.150272)testes at P21,rep2 at P21,biologicalrep2(0.129832) biological(0.14453) rep3[ rep3(0.226252)min (0.226058) ] [ medium ] [ max ] CEM 1 Dnah6 6.2 858.6 1357.1 P ( S | Z, I ) = 1.00 Dnali1 43.6 2055.8 2603.1 Mean Corr = 0.52357 Dnah7a 360.0 878.8 1249.6 Dnah2 194.5 2344.0 3057.9 Dnah1 68.6 281.0 340.9 Dnah8 1092.7 11060.7 12737.8 Dnah5 11.9 44.5 69.3 Dnah9 30.5 48.0 50.9 Dnal4 449.0 1413.2 1753.1 Dnah11 9.2 44.8 113.5 Dnaic2 18.8 43.1 53.9 Dync2li1 1453.1 1981.1 2110.1 Dnah17 6.1 31.8 41.7 Foxj1 49.6 206.3 240.3 Fank1 345.6 1613.6 2057.9 Lrguk 178.1 844.5 1119.7 Wdr65 218.0 2930.4 3640.0 1700012B09Rik 225.6 2843.5 3266.9 CEM 1 + Fsip1 195.3 461.6 635.3 Top 10 Genes Mapk15 89.9 738.7 756.8 B3gnt4 8.7 97.6 258.6 Ccdc19 102.1 1552.5 2124.3 Maats1 40.2 337.0 399.5

Null module GEO Series "GSE9977" 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=GSE9977 Status: Public on Sep 30 2009 Title: Expression data from NIH-3T3 cells treated with mock, 100 U/ml IFN alpha or 100 U/ml gamma for 1or 3h Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 18658122 Summary & Design: Summary: Differential gene expression caused by 1h and 3h of IFN alpha or gamma treatment was analyzed in total cellular RNA of NIH-3T3 cells compared to mock

We used microarrays to analyze the effects of 1 and 3h of IFNalpha and gamma treatment in total cellular RNA

Keywords: time course in total cellular RNA (tc-RNA)

Overall design: NIH-3T3 cells ( 5th to 15th passage after thawing) were split from confluent plates 24h before start of the experiment. At the begin of the experiment about 80% confluency was reached. The experiment was started by applying fresh, prewarmed, CO2-equilibrated medium containing either mock, 100U/ml IFN alpha or 100 U/ml IFN gamma. Labeling was either started together with addition of IFN for 60 minutes or for 30 minutes starting 150 minutes after begin of treatment.

Background corr dist: KL-Divergence = 0.0343, L1-Distance = 0.0629, L2-Distance = 0.0042, Normal std = 0.7786

0.512 Kernel fit Pairwise Correlations Normal fit

Density 0.256

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

1h mock1h tc-RNA mock1h tc-RNARep.1 mock1h (0.00587874) tc-RNARep.2 mock1h (0.0221689) 200´MRep.3 mock1h (0.0411951) 4sU200´M mock tc-RNA1h 4sU200´M mock tc-RNARep.11h 4sU200´M 100U/ml (0.00986834) tc-RNARep.21h 4sU 100U/ml IFNalpha (0.107859) tc-RNARep.31h 100U/ml IFNalpha (0.0382095) Rep.4+1h 200´M 100U/ml IFNalpha (0.0201697) + 1h 4sU200´M 100U/ml IFNalphatc-RNA + 1h 4sU200´M 100U/ml IFN tc-RNARep.1 200´M 1h 4sUgamma 100U/ml (0.00967892) IFN tc-RNARep.2 4sU1h gamma+ tc-RNA100U/ml200´M (0.0842324)IFN Rep.33h gamma+ 4sUmock,200´MRep.4 (0.00789529)IFN tc-RNA3h gamma,+ (0.0157342) 150-180 4sUmock,200´M tc-RNA3hRep.1 200´M 150-180 4sUmock,min (0.0117962) tc-RNA3h500´MRep.2 4sU 150-180 100U/mlmin tc-RNA(0.268152) 4sU3h500´MRep.3 100U/mlmin tc-RNAIFNalpha, Rep.4(0.106974) 4sU3h500´M 100U/ml tc-RNAIFNalpha,Rep.1 (0.0407305) 150-1804sU3h 100U/ml(0.0140909) tc-RNAIFNalpha,Rep.2 150-180 3hmin 100U/ml(0.0218787) IFNgamma,Rep.3500´M 150-180 3hmin 100U/ml(0.0432902) IFNgamma,4sU500´M min 150-180tc-RNA IFNgamma,4sU500´M 150-180tc-RNA Rep.1min 4sU 500´M (0.0117099) 150-180tc-RNA Rep.2min 4sU500´M [(0.0101765) Rep.3min mintc-RNA 4sU500´M (0.0208491) tc-RNA Rep.1] 4sU (0.0278792) tc-RNARep.2 (0.0358521) [Rep.3 medium (0.0237295) ] [ max ] CEM 1 Dnah6 20.7 21.4 24.4 P ( S | Z, I ) = 1.00 Dnali1 24.2 25.1 28.6 Mean Corr = 0.46512 Dnah7a 20.4 21.0 28.6 Dnah2 23.2 24.5 29.4 Dnah1 19.6 20.2 22.4 Dnah8 20.2 20.9 24.1 Dnah5 21.0 21.7 28.4 Dnah9 20.7 21.4 26.7 Dnal4 32.3 136.9 200.8 Dnah11 47.4 50.8 83.6 Dnaic2 25.7 26.9 31.4 Dync2li1 289.6 547.9 799.5 Dnah17 28.8 32.1 37.5 Foxj1 29.0 31.5 41.1 Fank1 17.0 17.6 19.1 Lrguk 21.4 22.0 24.4 Wdr65 23.3 24.1 27.3 1700012B09Rik 27.3 29.0 33.7 CEM 1 + Fsip1 28.5 30.2 38.1 Top 10 Genes Mapk15 14.5 14.9 18.4 B3gnt4 19.2 20.1 23.3 Ccdc19 24.3 25.2 28.2 Maats1 18.2 18.7 20.8

Null module GEO Series "GSE56236" 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=GSE56236 Status: Public on Jul 14 2014 Title: Glomerular transcriptomic analysis of the influence of Genetic background effect during anti-GBM glomerulonephritis in mice Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: We analyzed the impact of the genetic background during experimental passive non-accelerated anti-glomerular basement membrane glomerulonephritis (anti-GBM-GN) (an equivalent to nephrotoxic nephritis) in two different mouse genetic backgrounds (C57BL6/J vs 129S2svPAS/crl).

Glomerular extracts have been made at an early time point (e.g day 4 of the induction of the glomerulonephritis). RNA have been extracted following standard procedures.

Overall design: 3 mice per group have been compared. 3 Control mice from each background. And 3 anti-GBM-GN challenged mice from each Genetic background, corresponding to 12 samples in total.

Background corr dist: KL-Divergence = 0.0993, L1-Distance = 0.0856, L2-Distance = 0.0127, Normal std = 0.5345

0.830 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

Day_4_anti_GBM_GN_C57BL6JDay_4_anti_GBM_GN_C57BL6JDay_4_anti_GBM_GN_C57BL6JControlControl animal rep1 Control(0.00673679)C57BL6Janimal rep2 Day_4_anti_GBM_GN_129S2SvPAs(0.0503429)C57BL6Janimal rep3rep1 Day_4_anti_GBM_GN_129S2SvPAs(0.0874689)(0.106065)C57BL6J rep2 Day_4_anti_GBM_GN_129S2SvPAs(0.140317) rep3 Control(0.046345)Control animal rep1 Control129S2SvPASanimal (0.287679) rep2 129S2SvPASanimal (0.035142) rep3rep1 129S2SvPAS (0.0221043)(0.0532762) rep2 (0.0502667) rep3[ min (0.114256) ] [ medium ] [ max ] CEM 1 Dnah6 20.9 21.4 22.2 P ( S | Z, I ) = 1.00 Dnali1 26.2 27.1 29.7 Mean Corr = 0.43964 Dnah7a 23.3 23.9 24.8 Dnah2 24.2 25.2 26.1 Dnah1 17.3 17.8 19.6 Dnah8 20.6 21.3 21.9 Dnah5 20.9 21.6 22.2 Dnah9 19.6 20.1 20.7 Dnal4 241.3 339.1 497.9 Dnah11 20.2 20.8 23.0 Dnaic2 26.4 27.9 28.9 Dync2li1 846.1 1308.9 1845.0 Dnah17 30.3 32.7 33.7 Foxj1 30.0 31.2 32.0 Fank1 20.9 22.1 22.7 Lrguk 24.2 24.8 25.7 Wdr65 23.5 24.1 25.0 1700012B09Rik 33.2 35.3 36.4 CEM 1 + Fsip1 30.4 31.6 32.3 Top 10 Genes Mapk15 13.9 14.3 16.1 B3gnt4 19.1 19.7 20.3 Ccdc19 24.5 25.1 26.1 Maats1 18.1 18.5 19.1

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 (0.359311)VehVeh3 (0.0574712)VehLPS1 (0.023417)VehLPS2 (0.0312001)VehLPS (0.0738634)SimvaVeh1 (0.0662871)SimvaVeh2 (0.0303163)SimvaVeh3 (0.050227)SimvaLPS1 (0.0380226)SimvaLPS2 (0.0466473)SimvaLPS3 (0.125002) (0.098235) [ min ] [ medium ] [ max ] CEM 1 Dnah6 453.5 1231.4 2322.9 P ( S | Z, I ) = 1.00 Dnali1 26.7 544.1 1310.5 Mean Corr = 0.43516 Dnah7a 116.6 184.1 311.4 Dnah2 180.7 309.6 977.0 Dnah1 19.4 28.7 113.9 Dnah8 9.4 237.2 409.1 Dnah5 138.0 420.4 798.2 Dnah9 7.0 18.4 39.1 Dnal4 357.7 457.5 534.6 Dnah11 174.0 453.0 974.0 Dnaic2 19.4 55.4 147.7 Dync2li1 391.0 892.2 1781.9 Dnah17 11.0 39.7 66.8 Foxj1 1087.9 2087.8 3528.1 Fank1 318.3 450.8 842.7 Lrguk 140.4 377.5 914.5 Wdr65 59.5 290.2 576.7 1700012B09Rik 22.4 189.4 412.7 CEM 1 + Fsip1 149.3 268.5 431.0 Top 10 Genes Mapk15 356.7 903.3 2664.7 B3gnt4 5.3 14.7 92.2 Ccdc19 187.4 295.3 711.4 Maats1 173.7 251.8 433.0

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 (0.188961) [biological atwildtype min replicate miceE13,from 2 (0.162775) biologicalatwildtype replicate miceE13, ]3 (0.067782) biologicalat mice E13, replicate4 (0.130302) biologicalat[ E13, replicatemedium 1 (0.0648087) biological replicate 2 (0.0585778) replicate 3 (0.178564)] 4 (0.148229)[ max ] CEM 1 Dnah6 853.0 1204.0 1434.5 P ( S | Z, I ) = 1.00 Dnali1 206.4 550.4 606.4 Mean Corr = 0.42795 Dnah7a 305.3 499.9 680.6 Dnah2 260.0 485.6 539.0 Dnah1 213.2 382.9 507.6 Dnah8 113.7 136.7 154.9 Dnah5 54.4 81.0 87.1 Dnah9 60.4 66.8 88.2 Dnal4 785.7 1096.5 1203.3 Dnah11 269.1 441.5 555.7 Dnaic2 102.4 136.1 193.9 Dync2li1 2768.3 3799.3 4263.2 Dnah17 44.6 46.3 49.2 Foxj1 1775.4 4143.8 5104.7 Fank1 193.2 291.3 360.8 Lrguk 228.2 290.6 353.6 Wdr65 394.3 622.1 767.4 1700012B09Rik 1139.7 1810.2 2205.3 CEM 1 + Fsip1 164.4 227.6 279.9 Top 10 Genes Mapk15 181.9 221.9 255.4 B3gnt4 76.9 132.6 156.7 Ccdc19 423.0 817.4 1022.7 Maats1 49.1 85.0 101.6

Null module GEO Series "GSE9743" 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=GSE9743 Status: Public on May 30 2008 Title: The in vivo effect of actin cytoskeletal abnormalities on gene expression Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 18381839 Summary & Design: Summary: Remodeling of the actin cytoskeleton through actin dynamics (assembly and disassembly of filamentous actin) is known to be essential for numerous basic biological processes. In addition, recent in vitro studies provided evidence that actin dynamics participate in the control of gene expression. A spontaneous mouse mutant, corneal disease 1 (corn1), is deficient for a regulator of actin dynamics, destrin (DSTN; also known as actin depolymerizing factor or ADF), and develops epithelial hyperproliferation and neovascularization in the cornea. Dstncorn1 mice exhibit the actin dynamics defect in the corneal epithelial cells as evidenced by increased filamentous actin, offering an in vivo model to investigate the physiological significance of the transcriptional regulation by actin dynamics. To examine the effect of the Dstncorn1 mutation on gene expression, we performed a microarray analysis using the cornea from Dstncorn1 and wild-type control mice. A dramatic alteration of gene expression was observed in the Dstncorn1 cornea, with 1,226 annotated genes differentially expressed. Functional annotation of these genes revealed that most significantly enriched functional categories are associated with actin and/or cytoskeleton. Among genes that belong to these categories, a considerable number of serum response factor (SRF) target genes were found, indicating the existence of the actin-SRF pathway of transcriptional regulation in vivo. A comparative study using an allelic mutant strain, Dstncorn1-2J, with milder corneal phenotypes also suggested that the severity of the actin dynamics defect correlates with the level of gene expression changes. Our study provides evidence that actin dynamics have a strong impact on gene expression in vivo.

Keywords: Comparative gene expression

Overall design: Microarray analysis was performed in triplicate with RNA from each genotype, A. BY H2bc H2-T18f/SnJ (A. BY wild-type), A. BY H2bc H2-T18f/SnJ-Dstncorn1/J (Dstncorn1), C57BL/6J (B6 wild-type), C57BL/6JSmn-Dstncorn1-2J/J (Dstncorn1-2J), and C.129S2(B6)-Il8rbtm1Mwm/J (Il8rb-/-), hybridized to three Affymetrix MG 430 2.0 arrays.

Background corr dist: KL-Divergence = 0.0655, L1-Distance = 0.0932, L2-Distance = 0.0099, Normal std = 0.8050

0.563 Kernel fit Pairwise Correlations Normal fit

Density 0.282

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

A.BY WT_Rep1A.BY WT_Rep2A.BY (0.0720693) WT_Rep3Dstncorn1_Rep1 (0.0669883)Dstncorn1_Rep2 (0.112378)Dstncorn1_Rep3 (0.079471)Dstncorn1-2J_Rep1 (0.0800695)Dstncorn1-2J_Rep2 (0.0930082)Dstncorn1-2J_Rep3 (0.0512746)B6 WT_Rep1 (0.0980347)B6 WT_Rep2 (0.105592)(0.0445747)B6 WT_Rep3 (0.0617071) (0.134833) [ min ] [ medium ] [ max ] CEM 1 Dnah6 7.8 9.5 10.0 P ( S | Z, I ) = 1.00 Dnali1 10.8 12.3 12.9 Mean Corr = 0.41871 Dnah7a 7.7 8.9 9.3 Dnah2 9.8 11.3 12.0 Dnah1 7.2 8.5 8.8 Dnah8 7.9 11.5 16.5 Dnah5 7.9 10.8 11.4 Dnah9 7.7 9.0 9.4 Dnal4 113.0 155.9 326.6 Dnah11 14.5 17.0 18.3 Dnaic2 9.4 11.5 12.3 Dync2li1 321.6 718.6 901.1 Dnah17 13.2 14.4 15.6 Foxj1 14.3 17.7 23.3 Fank1 6.9 8.4 8.9 Lrguk 8.1 9.4 9.9 Wdr65 9.4 10.8 11.3 1700012B09Rik 11.4 13.4 14.3 CEM 1 + Fsip1 13.0 14.3 15.2 Top 10 Genes Mapk15 5.7 6.7 7.0 B3gnt4 6.9 8.3 8.7 Ccdc19 9.6 11.3 12.0 Maats1 6.6 7.6 8.0

Null module GEO Series "GSE18534" 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=GSE18534 Status: Public on Jun 01 2010 Title: Mouse small cell lung cancer model Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 20406986 Summary & Design: Summary: A mouse model for human small cell lung carcinoma (SCLC) has been developed based on evidence in human tumors that the tumor suppressor functions of RB and p53 are defective in more than 90% of SCLC cases. We also developed another mouse model also combines loss of p130 (Rbl2), an RB-related gene, with deletion of RB and p53. These two mouse tumors were shown to closely resemble human SCLC.

Overall design: The goal of this array experiment is to assess genome-wide gene expression of those mouse tumors and determine the similarity of the mouse models to human SCLC. Gene expression from Mouse Rb/p53 ( n=10 ) and Rb/p53/p130 primary tumors ( n=3 ) as well as tumor-free adult mouse lungs ( n=2 ) was measured using the Affymetrix GeneChip Mouse Genome 430-2.0 arrays.

Background corr dist: KL-Divergence = 0.0991, L1-Distance = 0.0337, L2-Distance = 0.0022, Normal std = 0.4651

0.881 Kernel fit Pairwise Correlations Normal fit

Density 0.440

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

double doubleknockout doubleknockout lung doubleknockoutcancer lung doubleknockout-cancer 1 lung(0.0229146) doubleknockout-cancer 2 lung(0.0484271) doubleknockout-cancer 3 lung(0.0576509) doubleknockout-cancer 4 lung(0.0414767) doubleknockout-cancer 5 lung(0.0424836) doubleknockout-cancer 6 lung(0.0190582) normalknockout-cancer 7 lung(0.0279216) normal-cancerlung 8 lung(0.0657093) - 1 triple-cancerlung (0.382818)9 (0.025671) -knockout 2 triple- (0.127182)10 (0.0508252) knockouttriple lung knockoutcancer lung -cancer 11 lung (0.0218368) -cancer 12 (0.033566) - 13[ (0.0324589)min ] [ medium ] [ max ] CEM 1 Dnah6 81.4 99.2 1617.6 P ( S | Z, I ) = 1.00 Dnali1 39.6 54.8 613.8 Mean Corr = 0.40327 Dnah7a 156.2 221.5 322.3 Dnah2 42.9 53.8 541.8 Dnah1 47.9 57.8 107.8 Dnah8 85.2 126.7 426.7 Dnah5 58.6 68.9 337.5 Dnah9 31.1 36.0 42.0 Dnal4 445.1 535.5 754.7 Dnah11 106.8 120.0 438.9 Dnaic2 40.8 52.1 75.8 Dync2li1 779.9 1138.2 1914.1 Dnah17 52.9 60.3 70.6 Foxj1 112.3 153.7 1884.3 Fank1 92.3 107.9 241.1 Lrguk 33.9 47.9 587.0 Wdr65 22.7 30.3 216.8 1700012B09Rik 27.3 32.8 462.5 CEM 1 + Fsip1 45.3 54.9 217.2 Top 10 Genes Mapk15 60.7 76.3 305.6 B3gnt4 45.0 59.1 141.2 Ccdc19 39.4 53.8 385.1 Maats1 17.7 28.6 38.5

Null module GEO Series "GSE31013" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 12 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

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

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

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

0.871 Kernel fit Pairwise Correlations Normal fit

Density 0.436

0.000 CEM 1

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

Pre-normalization Quantiles

Lung_normal_1Lung_normal_2Lung_normal_3 (0.103567)Lung_normal_4 (0.0844388)Lung_normal_5 (0.139681)Lung_normal_6 (0.0446557)Spontaneous_lung_tumor_1 (0.0624105)Spontaneous_lung_tumor_2 (0.0762106)Spontaneous_lung_tumor_3Spontaneous_lung_tumor_4 (0.0683389)Spontaneous_lung_tumor_5 (0.0950511)Spontaneous_lung_tumor_6 (0.0872628) (0.0253407) (0.114988) (0.0980547)[ min ] [ medium ] [ max ] CEM 1 Dnah6 13.3 887.1 1245.9 P ( S | Z, I ) = 1.00 Dnali1 3.5 356.1 640.7 Mean Corr = 0.40021 Dnah7a 3.8 110.4 218.1 Dnah2 11.8 208.1 373.0 Dnah1 5.8 26.2 76.7 Dnah8 11.7 273.8 347.0 Dnah5 29.6 285.2 441.7 Dnah9 2.6 10.3 50.0 Dnal4 302.5 408.4 559.3 Dnah11 12.5 313.6 600.3 Dnaic2 2.7 20.8 66.8 Dync2li1 519.3 1519.4 2005.5 Dnah17 8.4 21.5 115.9 Foxj1 14.5 477.4 947.7 Fank1 13.1 198.0 239.7 Lrguk 7.4 207.1 298.4 Wdr65 4.3 242.1 293.6 1700012B09Rik 4.0 93.9 204.9 CEM 1 + Fsip1 47.0 106.8 190.5 Top 10 Genes Mapk15 43.3 408.8 493.4 B3gnt4 9.2 16.0 31.6 Ccdc19 23.6 263.1 354.2 Maats1 2.5 228.5 295.7

Null module GEO Series "GSE27568" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 16 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

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

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

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

0.679 Kernel fit Pairwise Correlations Normal fit

Density 0.340

0.000 CEM 1

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

Pre-normalization Quantiles

ubb_d7_ko_1ubb_d7_ko_2 (0.0395035)ubb_d7_wt_1 (0.0339127)ubb_d7_wt_2 (0.0318281)ubb_d14_ko_1 (0.0451119)ubb_d14_ko_2 ubb_d14_wt_1(0.0380749) ubb_d14_wt_2(0.0534389) ubb_d21_ko_1(0.0279136) ubb_d21_ko_2(0.0279168) ubb_d21_wt_1(0.0777305) ubb_d21_wt_2(0.0256141) ubb_d28_ko_1(0.112963) ubb_d28_ko_2(0.0675943) ubb_d28_wt_1(0.0187058) ubb_d28_wt_2(0.0453896) (0.225565) (0.128738) [ min ] [ medium ] [ max ] CEM 1 Dnah6 8.8 71.4 1341.8 P ( S | Z, I ) = 1.00 Dnali1 4.0 12.0 3338.5 Mean Corr = 0.39101 Dnah7a 9.6 357.0 1442.7 Dnah2 85.8 233.4 2171.9 Dnah1 18.5 90.2 359.7 Dnah8 50.1 594.4 10543.7 Dnah5 4.4 53.3 128.7 Dnah9 4.0 12.1 43.7 Dnal4 151.2 371.8 1513.5 Dnah11 10.8 70.6 318.5 Dnaic2 4.0 35.7 85.4 Dync2li1 662.5 1728.3 2937.1 Dnah17 6.8 32.1 68.2 Foxj1 20.9 57.4 998.9 Fank1 19.7 174.5 1664.2 Lrguk 50.9 97.9 1373.1 Wdr65 8.4 56.1 3931.6 1700012B09Rik 5.6 328.9 5557.4 CEM 1 + Fsip1 69.4 158.1 2356.4 Top 10 Genes Mapk15 13.2 79.4 748.4 B3gnt4 4.0 15.6 271.1 Ccdc19 10.8 53.8 3745.9 Maats1 19.3 65.4 440.3

Null module GEO Series "GSE29081" 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=GSE29081 Status: Public on Sep 13 2011 Title: Cerebellar gene expression analysis of Gb5-deficient mice Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21883221 Summary & Design: Summary: Gb5 is a divergent, evolutionarily-conserved, member of the heterotrimeric G protein b subunit family that is expressed principally in brain and neuronal tissue. Among Gb isoforms, Gb5 is unique in its ability to heterodimerize with members of the R7 subfamily of the regulator of G protein signaling (RGS) proteins that contain G protein-g like (GGL) domains. Previous studies employing Gb5 knockout mice have shown that Gb5 is an essential stabilizer of GGL domain-containing RGS proteins and regulates the deactivation of retinal phototransduction and the proper functioning of retinal bipolar cells. The purpose of this study is to better understand the functions of Gb5 in the brain outside the visual system by employing molecular biology, immunohistochemistry and confocal imaging technologies. We show here that mice lacking Gb5 have a markedly abnormal neurologic phenotype that includes neurobehavioral developmental delay, wide-based gait, motor learning and coordination deficiencies, and hyperactivity. Using immunohistochemical analysis and a green fluorescent reporter of Purkinje cell maturation we show that the phenotype of Gb5-deficient mice includes, in part, delayed development of the cerebellar cortex, an abnormality that likely contributes to the neurobehavioral phenotype. Multiple neuronally-expressed genes are dysregulated in cerebellum of Gb5 KO mice.

Overall design: Brain tissues from WT and KO with three biological replications of mice were collected, frozen in liquid nitrogen, and stored at -70 ´C

Background corr dist: KL-Divergence = 0.0327, L1-Distance = 0.0161, L2-Distance = 0.0003, Normal std = 0.6500

0.619 Kernel fit Pairwise Correlations Normal fit

Density 0.309

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

1-WT (0.229682)2-WT (0.0440001)3-WT (0.0669442)4-KO (0.173022)5-KO (0.370177)6-KO (0.116175) [ min ] [ medium ] [ max ] CEM 1 Dnah6 128.2 144.3 182.7 P ( S | Z, I ) = 1.00 Dnali1 50.4 78.5 91.2 Mean Corr = 0.51731 Dnah7a 109.3 130.4 170.9 Dnah2 40.1 65.6 81.9 Dnah1 10.3 11.4 13.3 Dnah8 82.3 105.6 122.7 Dnah5 7.5 8.7 10.1 Dnah9 45.7 60.3 75.9 Dnal4 83.4 86.9 109.4 Dnah11 264.7 278.3 347.2 Dnaic2 29.6 43.3 46.3 Dync2li1 386.0 425.8 487.2 Dnah17 11.5 13.0 15.7 Foxj1 19.8 25.6 34.1 Fank1 25.4 37.1 49.1 Lrguk 30.8 36.1 43.8 Wdr65 18.4 23.5 33.0 1700012B09Rik 26.3 28.0 32.2 CEM 1 + Fsip1 13.5 18.2 22.6 Top 10 Genes Mapk15 51.0 56.3 57.9 B3gnt4 61.9 64.0 71.6 Ccdc19 38.7 41.0 46.4 Maats1 8.3 8.6 8.8

Null module GEO Series "GSE9954" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 70 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE9954 Status: Public on Dec 20 2007 Title: Large-scale analysis of the mouse transcriptome Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 18365009 Summary & Design: Summary: We used microarrays to compare gene expression across different murine tissues.

Keywords: Other

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

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

1.449 Kernel fit Pairwise Correlations Normal fit

Density 0.724

0.000 CEM 1

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

Pre-normalization Quantiles

Mouse diaphragm,Mouse diaphragm,Mouse biological diaphragm,Mouse biological spleen,replicateMouse biological spleen,replicateMousebiological 1 (0.00279332) spleen,replicateMousebiological 2 replicate(0.0042522) muscle,Mousebiological 3 replicate(0.00314566) 1 (0.00280396)muscle,Mouse biological replicate 2 (0.00435334)muscle,Mouse biological replicate 3 (0.00353121)muscle,Mouse biological replicate 1 liver,(0.00350196)Mouse biological replicate biological2 liver,(0.00390361)Mouse replicate biological3 liver,(0.0036431)Mouse replicate biological4 brain,(0.00225766)Mouse replicate 1 (0.00277859) biological brain,Mouse replicate 2 (0.00404459) biological brain,Mouse replicate 3 (0.0111049) biological lung,Mouse replicate 1 (0.00493939)biological lung,Mouse replicate 2 (0.00304734)biological lung,Mouse replicate 3 (0.0029682)biological kidney,Mouse replicate 1 (0.015487) kidney,Mousebiological replicate 2 (0.022054) kidney,Mousebiological 3replicate (0.028934) adrenalMousebiological replicate 1 (0.00380737)adrenal Mousegland, replicate 2 (0.00325422)biologicaladrenal Mousegland, 3 (0.00418442)biologicalbone Mousegland, replicate marrow, biologicalboneMouse replicate 1 marrow, (0.00291344) biologicalboneMouse replicate 2 marrow, (0.00386416) biologicalboneMouse replicate 3 marrow, (0.00353002) biologicaladiposeMouse replicate 1 (0.0137011) biologicaladiposeMouse tissue, replicate 2 (0.011238) adiposeMouse biologicaltissue, replicate 3 (0.00917567) pituitaryMouse biologicaltissue, replicate4 (0.00716188) pituitaryMouse biologicalgland, replicate 1 (0.00193762)pituitaryMouse biological gland, replicate 2 (0.00289321)pituitaryMouse biological gland, replicate 3 (0.00487905)pituitaryMouse biological gland, replicate 1 (0.00628975)salivaryMouse biological gland, replicate 2 (0.00567885)salivaryMouse biologicalgland, replicate 3 (0.00296838)salivaryMousebiological gland, replicate 4 (0.00532017)seminalMousebiological gland, replicate 5 (0.00398547)seminalMousebiological vesicle, replicate 1 (0.0154529) seminalMouse vesicle, biological replicate 2 (0.00722188) thymus,Mouse vesicle, biological replicate3 (0.0247056) thymus,Mouse biologicalbiological replicate 1 thymus,Mouse (0.002153)biological replicatereplicate 2 testis,Mouse (0.00290089)biological replicate 13biological testis,Mouse (0.00288228)(0.00740697) replicate 2 biological testis,Mouse(0.00639388) replicate 3 biological heart,Mouse(0.00240351) replicate 1 (0.126196)biological heart,Mouse replicate 2 (0.148446)biological heart,Mouse replicate 3 (0.179182)biological smallMouse replicate 1 (0.0164983)intestine, smallMouse replicate 2 (0.0242917)intestine, smallMouse biological 3 (0.0213452)intestine, eye,Mouse biological replicate biological eye,Mouse biological replicate biological 1 (0.00812477)eye,Mousereplicate replicate biological 2 (0.00872361)ESMousereplicate 1 cells,(0.00417201) 3 (0.00822728)ESMousereplicate biological2 cells,(0.00243361) ESMouse biological3 cells,(0.00321066) replicate placenta,Mouse biological replicate 1 placenta,Mouse (0.00507775) biological replicate 2 placenta,Mouse (0.0047846) biological replicate 3 ovary,Mouse (0.00741586) biological replicate biological 1ovary,Mouse (0.00840253) replicate biological 2ovary,Mouse (0.0134298) replicate biological 3fetus,Mouse (0.00866407) replicate 1 (0.0137877)biological fetus,Mouse replicate 2 (0.0144251)biological fetus, replicate 3 (0.0295186)biological replicate 1 (0.0153239) replicate 2 (0.0119059)[ min3 (0.0185649) ] [ medium ] [ max ] CEM 1 Dnah6 187.4 294.0 714.3 P ( S | Z, I ) = 1.00 Dnali1 169.5 233.5 3336.0 Mean Corr = 0.34855 Dnah7a 138.8 197.0 705.8 Dnah2 167.9 213.2 992.5 Dnah1 175.5 252.9 936.1 Dnah8 177.8 231.7 6506.8 Dnah5 160.8 223.7 392.7 Dnah9 144.3 203.2 305.4 Dnal4 364.2 499.0 1642.8 Dnah11 218.1 300.4 436.2 Dnaic2 185.4 283.8 436.2 Dync2li1 250.3 526.0 1775.9 Dnah17 184.8 244.8 374.8 Foxj1 186.1 239.6 741.3 Fank1 190.3 353.9 1548.2 Lrguk 139.5 188.6 857.8 Wdr65 174.8 222.4 1608.6 1700012B09Rik 152.1 215.0 2656.8 CEM 1 + Fsip1 167.7 247.3 1334.2 Top 10 Genes Mapk15 199.2 311.3 581.3 B3gnt4 178.3 243.6 614.2 Ccdc19 175.3 230.6 2185.3 Maats1 151.3 204.9 651.0

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

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

Background corr dist: KL-Divergence = 0.5414, L1-Distance = 0.1198, L2-Distance = 0.0520, Normal std = 0.2635 GEO Series "GSE24207" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 73 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE24207 Status: Public on Nov 18 2010 Title: mRNA analysis in different mouse tissues Organism: Mus musculus Experiment type: Third-party reanalysis Platform: GPL1261 Pubmed ID: 21088282 Summary & Design: Summary: The functioning of a specific tissue depends on the expression pattern of the different genes. We used microarrays to compare gene expression across different murine tissues, to get a better understanding in the expression pattern and functioning of the different tissues. With this analysis, we were not only able to identify genes that were specifically expressed in a spicific tissue but, as important, we also identified genes that were specifically repressed in a tissue, compared to al the other analysed tissues.

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

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

1.542 Kernel fit Pairwise Correlations Normal fit

Density 0.771

0.000 CEM 1

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

Pre-normalization Quantiles

Mouse diaphragm,Mouse diaphragm,Mouse biological diaphragm,Mouse biological spleen,replicateMouse biological spleen,replicateMousebiological 1 (0.00621481) spleen,replicateMousebiological 2 replicate(0.00422198) muscle,Mousebiological 3 replicate(0.00413759) 1 (0.00362218)muscle,Mouse biological replicate 2 (0.00311405)muscle,Mouse biological replicate 3 (0.00593722)muscle,Mouse biological replicate 1 liver,(0.0053752)Mouse biological replicate biological2 liver,(0.00431556)Mouse replicate biological3 liver,(0.00510194)Mouse replicate biological4 brain,(0.00367763)Mouse replicate 1 (0.00451807) biological brain,Mouse replicate 2 (0.00547033) biological brain,Mouse replicate 3 (0.00441718) biological lung,Mouse replicate 1 (0.00386795)biological lung,Mouse replicate 2 (0.00265093)biological lung,Mouse replicate 3 (0.00387304)biological kidney,Mouse replicate 1 (0.0118326) kidney,Mousebiological replicate 2 (0.0213508) kidney,Mousebiological 3replicate (0.0435011) adrenalMousebiological replicate 1 (0.0034534)adrenal Mousegland, replicate 2 (0.00577387)biologicaladrenal Mousegland, 3 (0.00396064)biologicalbone Mousegland, replicate marrow, biologicalboneMouse replicate 1 marrow, (0.00402801) biologicalboneMouse replicate 2 marrow, (0.00384789) biologicalboneMouse replicate 3 marrow, (0.00344145) biologicaladiposeMouse replicate 1 (0.0135623) biologicaladiposeMouse tissue, replicate 2 (0.00331737) adiposeMouse biologicaltissue, replicate 3 (0.00476871) pituitaryMouse biologicaltissue, replicate4 (0.0040708) pituitaryMouse biologicalgland, replicate 1 (0.00338614)pituitaryMouse biological gland, replicate 2 (0.00420477)pituitaryMouse biological gland, replicate 3 (0.00459995)pituitaryMouse biological gland, replicate 1 (0.00636487)salivaryMouse biological gland, replicate 2 (0.00652199)salivaryMouse biologicalgland, replicate 3 (0.00568423)salivaryMousebiological gland, replicate 4 (0.00432633)seminalMousebiological gland, replicate 5 (0.00397547)seminalMousebiological vesicle, replicate 1 (0.00231173) seminalMouse vesicle, biological replicate 2 (0.0023178) thymus,Mouse vesicle, biological replicate3 (0.00763753) thymus,Mouse biologicalbiological replicate 1 thymus,Mouse (0.00514258)biological replicatereplicate 2 testis,Mouse (0.0106566)biological replicate 13biological testis,Mouse (0.00277937)(0.00439441) replicate 2 biological testis,Mouse(0.00391934) replicate 3 biological heart,Mouse(0.00313968) replicate 1 (0.104054)biological heart,Mouse replicate 2 (0.137867)biological heart,Mouse replicate 3 (0.197936)biological smallMouse replicate 1 (0.00816235)intestine, smallMouse replicate 2 (0.017285)intestine, smallMouse biological 3 (0.00303414)intestine, eye,Mouse biological replicate biological eye,Mouse biological replicate biological 1 (0.00733251)eye,Mousereplicate replicate biological 2 (0.00746634)placenta,Mousereplicate 1 (0.0156774) 3 (0.00609905)placenta,Mousereplicate 2biological (0.00434708) placenta,Mouse 3biological (0.00357242) replicate ovary,Mouse biological replicate biological 1ovary,Mouse (0.00412823) replicate biological 2ovary,Mouse (0.00271488) replicate biological 3pancreaticMouse (0.00510103) replicate 1 (0.00941198) pancreaticMouse replicate acini,2 (0.0124615) pancreaticMouse biological acini,3 (0.0204986) pancreaticMouse biological acini, replicate pancreaticMouse biological islets, replicate 1pancreaticCell-line, (0.0243475) biological islets, replicate 2Cell-line, (0.0552107) MIN6, biological islets, replicate 3Cell-line, biological(0.030012) MIN6, biological replicate 1 biological (0.00545691)MIN6, replicate replicate 2 biological (0.00891806) replicate 1 (0.00444242)3 (0.0140665) replicate 2 (0.00553636)[ min 3 (0.00607236) ] [ medium ] [ max ] CEM 1 Dnah6 6.7 21.4 779.6 P ( S | Z, I ) = 1.00 Dnali1 3.3 10.0 4349.9 Mean Corr = 0.31163 Dnah7a 3.3 56.8 920.2 Dnah2 3.3 43.6 1291.6 Dnah1 3.3 40.2 512.3 Dnah8 3.3 60.3 7117.0 Dnah5 13.4 80.4 381.0 Dnah9 3.3 26.7 170.7 Dnal4 167.4 408.5 2062.1 Dnah11 10.0 50.2 361.0 Dnaic2 6.7 40.2 267.9 Dync2li1 90.5 541.7 2434.4 Dnah17 6.7 26.8 418.7 Foxj1 3.4 63.6 1113.0 Fank1 16.7 130.4 2161.5 Lrguk 3.3 30.2 1218.0 Wdr65 3.3 46.9 2509.5 1700012B09Rik 3.3 16.8 4286.3 CEM 1 + Fsip1 10.0 93.8 2062.7 Top 10 Genes Mapk15 26.8 160.6 1066.6 B3gnt4 6.7 13.4 364.9 Ccdc19 3.3 67.0 2499.5 Maats1 3.3 63.6 749.5

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 (0.0595857)mus-6dpp-50ng_activin-rep1 (0.093767)mus-6dpp-50ng_activin-rep2 (0.0762936)mus-15dpp-0ng_activin-rep1 (0.0491668)mus-15dpp-0ng_activin-rep2 (0.0462805)mus-15dpp-5ng_activin-rep1 (0.123695)mus-15dpp-5ng_activin-rep2 (0.226006) (0.116512) (0.145593) (0.063099)[ min ] [ medium ] [ max ] CEM 1 Dnah6 7.2 20.3 146.8 P ( S | Z, I ) = 1.00 Dnali1 4.0 12.3 263.9 Mean Corr = 0.29316 Dnah7a 27.1 64.7 999.1 Dnah2 38.8 105.5 386.6 Dnah1 6.7 76.4 192.4 Dnah8 69.4 111.3 3661.2 Dnah5 11.5 62.0 84.1 Dnah9 4.0 19.5 62.2 Dnal4 277.2 379.0 607.4 Dnah11 12.7 45.5 69.3 Dnaic2 4.0 17.1 101.7 Dync2li1 956.5 1114.8 1545.7 Dnah17 6.3 19.7 63.2 Foxj1 12.7 39.0 62.6 Fank1 14.5 160.4 479.8 Lrguk 9.8 49.6 254.7 Wdr65 5.9 41.9 546.2 1700012B09Rik 5.2 58.7 595.4 CEM 1 + Fsip1 16.0 111.3 257.3 Top 10 Genes Mapk15 23.2 73.0 244.0 B3gnt4 7.9 14.2 95.2 Ccdc19 27.0 71.5 273.3 Maats1 4.8 56.3 97.5

Null module GEO Series "GSE3100" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 23 -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=GSE3100 Status: Public on Mar 01 2006 Title: Cystic Fibrosis Mouse Lung Profiles Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 16614460 Summary & Design: Summary: Gene expression profiling with microarrays was used to identify genes differentially expressed in the lungs of B6 and BALB CF mice compared to non-CF littermates

Keywords: disease state analysis

Overall design: BALB/c and C57BL/6 mice (male and female) were examined in CF-/- and CF+/+ genotypes. 3 arrays of each combination of strain sex and CF status were analyzed (except for B6 male CF, which only had two replicates)

Background corr dist: KL-Divergence = 0.2285, L1-Distance = 0.0493, L2-Distance = 0.0056, Normal std = 0.3145

1.268 Kernel fit Pairwise Correlations Normal fit

Density 0.634

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

B6_Male_CF_rep1B6_Female_Control_rep1B6_Male_Control_rep1 (0.0381493)B6_Female_Control_rep2B6_Female_Control_rep3 (0.0505939)B6_Male_Control_rep2 (0.0190858)B6_Male_Control_rep3 (0.0916095)B6_Female_CF_rep1 (0.0475933)B6_Female_CF_rep2 (0.0464081)B6_Female_CF_rep3 (0.0277529) (0.0264201)B6_Male_CF_rep2 (0.0172704)BALB_Male_CF_rep1 (0.0410526)BALB_Male_Control_rep1 (0.06856)BALB_Male_Control_rep2 (0.0260723)BALB_Male_Control_rep3BALB_Female_CF_rep1 (0.0386098)BALB_Female_CF_rep2 (0.0309683)BALB_Female_CF_rep3 (0.0567632)BALB_Female_Control_rep1 (0.121899)BALB_Female_Control_rep2 (0.0591898)BALB_Female_Control_rep3 (0.0491567)BALB_Male_CF_rep2 (0.0322365)BALB_Male_CF_rep3 (0.0282912) (0.0219408)(0.0291298) (0.0312466)[ min ] [ medium ] [ max ] CEM 1 Dnah6 381.5 691.8 998.8 P ( S | Z, I ) = 1.00 Dnali1 370.8 529.7 816.1 Mean Corr = 0.21541 Dnah7a 61.7 81.3 151.1 Dnah2 135.6 206.0 334.2 Dnah1 106.3 135.9 197.4 Dnah8 169.1 284.2 471.9 Dnah5 184.2 256.0 414.2 Dnah9 64.0 77.2 99.1 Dnal4 621.1 692.5 773.6 Dnah11 339.9 422.3 631.8 Dnaic2 79.9 109.4 147.8 Dync2li1 631.1 831.0 1208.2 Dnah17 103.8 125.9 163.1 Foxj1 311.8 708.9 1034.6 Fank1 147.9 188.6 241.9 Lrguk 80.0 117.3 229.1 Wdr65 167.0 264.6 369.2 1700012B09Rik 119.4 164.2 271.4 CEM 1 + Fsip1 90.2 109.3 158.1 Top 10 Genes Mapk15 345.8 474.3 721.0 B3gnt4 122.1 140.5 192.3 Ccdc19 179.0 245.4 323.4 Maats1 82.2 144.2 258.9

Null module GEO Series "GSE17097" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 20 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

GEO Link: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17097 Status: Public on Dec 09 2011 Title: mRNA composition of IRP2 mRNPs in mouse tissues Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21940823 Summary & Design: Summary: Affymetrix microarrays were used to determine the mRNA composition of mRNPs obtained by immunoprecipitation with IRP2 (iron regulatory protein 2).

Overall design: All the microarray procedures were conducted at the EMBL Genomics Core Facility using standard Affymetrix protocols. In brief, approximately 120ng of immunoprecipitated RNA was used as input to a two-step amplification procedure to generate biotin-labeled RNA fragments for hybridization to the Affymetrix GeneChip Mouse Genome 430 2.0 array (Eukaryotic Sample and Array Processing manual 701024 Rev.3). Intensity values for the hybridizations were obtained either using RMA, calculations done in bioconductor (www.bioconductor.org) or MAS5, calculated using Affymetrix GCOS package. MAS5 calculated intensities were further quantile normalized using bioconductor.

Background corr dist: KL-Divergence = 0.0612, L1-Distance = 0.0894, L2-Distance = 0.0146, Normal std = 0.5980

0.686 Kernel fit Pairwise Correlations Normal fit

Density 0.343

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

IRP2 immunoprecipitationIRP2 controlIRP2 immunoprecipitationimmunoprecipitationIRP2 duodenum controlIRP2 immunoprecipitationimmunoprecipitationIRP2 replica duodenumduodenum controlIRP2 1 (0.016875) immunoprecipitationimmunoprecipitationIRP2 replicareplica liverduodenum controlIRP2 21 replica (0.0245622)(0.0616186) immunoprecipitationimmunoprecipitationIRP2 replica 1 (0.0457002) liverliver controlIRP2 2 replicareplica (0.012177) immunoprecipitationimmunoprecipitationIRP2 21 (0.0332544) (0.0170172) spleenliver controlIRP2 replica replica immunoprecipitationimmunoprecipitationIRP2 2 (0.00976464) 1spleenspleen control(0.0773305)IRP2 replicareplica immunoprecipitationimmunoprecipitationIRP2 2bone1spleen control (0.0608746)(0.063791)IRP2 marrow replica immunoprecipitationimmunoprecipitationIRP2 replica bone2bone control (0.075401)IRP2 marrow marrow1 (0.0747598) immunoprecipitationimmunoprecipitationIRP2 replicareplica brainbone control replicamarrow 21 (0.092012) (0.0246729)immunoprecipitation 1 replica (0.0216863)brainbrain replica replica2 (0.128285)[ 21min (0.0564863)(0.00966794)brain replica ] 2 (0.0940639)[ medium ] [ max ] CEM 1 Dnah6 86.5 188.0 308.1 P ( S | Z, I ) = 0.99 Dnali1 17.3 35.7 65.8 Mean Corr = 0.52621 Dnah7a 22.1 60.3 93.4 Dnah2 54.0 93.6 170.8 Dnah1 40.2 82.0 154.6 Dnah8 68.2 204.3 843.1 Dnah5 34.8 51.8 71.3 Dnah9 36.3 75.5 123.6 Dnal4 251.1 456.0 601.6 Dnah11 118.8 254.0 596.5 Dnaic2 117.0 407.5 587.1 Dync2li1 129.1 188.5 532.9 Dnah17 58.1 113.0 192.0 Foxj1 49.7 94.1 165.7 Fank1 295.9 692.6 1732.2 Lrguk 28.6 48.9 119.0 Wdr65 50.1 190.2 421.3 1700012B09Rik 31.7 61.1 154.3 CEM 1 + Fsip1 64.3 99.4 156.7 Top 10 Genes Mapk15 102.6 238.1 419.0 B3gnt4 32.3 89.4 152.8 Ccdc19 40.2 53.8 114.3 Maats1 17.5 63.7 115.0

Null module GEO Series "GSE1983" 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=GSE1983 Status: Public on Jul 01 2005 Title: Transcriptional Profiling of the Metanephric Kidney Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 15917337 Summary & Design: Summary: In this study we identify molecules with highly restricted expression patterns during the initial stages of metanephric development, when the ureteric bud has entered the metanephric mesenchyme and initiated branching morphogenesis. Using the Affymetrix Mouse Genome 430 2.0 Array, we compare gene expression patterns in ureteric bud tips, stalks and metanephric mesenchymes from mouse E12.5 embryos. To identify conserved molecular pathways, we also analyze transcriptional profiles in rat E13.5 ureteric buds and metanephric mesenchymes using the Affymetrix Rat Genome U34 Set. Taken together, these data sets help to identify conserved and highly localized transcripts in the metanephric kidney.

Keywords = Mus musculus

Keywords = Rattus norvegicus

Keywords = metanephric mesenchyme

Keywords = ureteric bud

Keywords = ureteric bud tips

Keywords = ureteric bud stalks

Keywords = molecular screen for spatially restricted transcripts

Keywords: other

Overall design:

Background corr dist: KL-Divergence = 0.0190, L1-Distance = 0.0266, L2-Distance = 0.0009, Normal std = 0.7646

0.528 Kernel fit Pairwise Correlations Normal fit

Density 0.264

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

UB tip 1UB (0.141941) tip 2UB (0.360006) stalkUB 1 (0.164684)stalkmetanephric 2 (0.0543435)metanephric mesenchyme mesenchyme 1 (0.118077) 2 (0.160948)[ min ] [ medium ] [ max ] CEM 1 Dnah6 106.2 129.1 171.7 P ( S | Z, I ) = 0.98 Dnali1 32.4 38.5 57.0 Mean Corr = 0.58798 Dnah7a 44.0 66.8 85.5 Dnah2 31.1 37.0 40.1 Dnah1 79.6 91.2 144.3 Dnah8 53.7 72.1 89.2 Dnah5 49.8 70.7 81.1 Dnah9 32.9 43.0 62.3 Dnal4 415.1 488.6 500.0 Dnah11 118.9 141.5 185.5 Dnaic2 123.3 144.5 182.1 Dync2li1 1315.3 1532.7 1581.2 Dnah17 64.7 70.5 84.5 Foxj1 60.4 82.5 97.7 Fank1 167.1 199.7 261.2 Lrguk 23.3 27.4 37.3 Wdr65 40.7 53.5 58.4 1700012B09Rik 36.5 41.5 48.3 CEM 1 + Fsip1 66.9 82.6 89.2 Top 10 Genes Mapk15 149.8 234.5 373.8 B3gnt4 51.8 60.2 71.8 Ccdc19 35.2 42.2 58.6 Maats1 38.1 51.2 64.0

Null module GEO Series "GSE8498" 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=GSE8498 Status: Public on Aug 04 2007 Title: The MicroRNA miR-124 Promotes Neuronal Differentiation by Triggering Brain-Specific Alternative Pre-mRNA Splicing Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 17679093 Summary & Design: Summary: Both microRNAs and alternative pre-mRNA splicing have been implicated in the development of the nervous system (NS), but functional interactions between these two pathways are poorly understood. We demonstrate that the neuron-specific microRNA miR-124a directly targets PTBP1/PTB/hnRNPI mRNA, which encodes a global repressor of alternative pre-mRNA splicing in non-neuronal cells. Among the targets of PTBP1 is a critical cassette exon in the pre-mRNA of PTBP2/nPTB/brPTB, an NS-enriched PTBP1 homolog. When this exon is skipped, PTBP2 mRNA is subject to nonsense-mediated decay. During neuronal differentiation, miR-124a reduces PTBP1 levels leading to the accumulation of correctly spliced PTBP2 mRNA and a dramatic increase in PTBP2 protein. These events culminate in the transition from non-NS to NS-specific alternative splicing patterns. We also present evidence that miR-124a plays a key role in the differentiation of progenitor cells to mature neurons. Thus, miR-124a promotes NS development at least in part by regulating an intricate network of NS-specific alternative splicing.

We used microarrays to detail the global programme of gene expression of CAD cells over-expressing miR-124a-2.

Keywords: treatment versus control

Overall design: Expression data from CAD cells transfected with plasmid expressing miR-124a-2.

Background corr dist: KL-Divergence = 0.0253, L1-Distance = 0.0120, L2-Distance = 0.0002, Normal std = 0.6906

0.578 Kernel fit Pairwise Correlations Normal fit

Density 0.289

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

CAD_C1CAD_C2 (0.231106)CAD_C3 (0.0977128)CAD_T1 (0.196863)CAD_T2 (0.199891)CAD_T3 (0.127246) (0.147182) [ min ] [ medium ] [ max ] CEM 1 Dnah6 70.7 84.5 99.0 P ( S | Z, I ) = 0.96 Dnali1 81.9 92.9 97.2 Mean Corr = 0.62108 Dnah7a 36.8 42.3 46.4 Dnah2 66.2 74.3 81.4 Dnah1 97.5 116.8 163.4 Dnah8 52.1 68.0 77.5 Dnah5 42.2 53.5 57.6 Dnah9 42.1 43.3 48.6 Dnal4 634.9 732.0 793.6 Dnah11 120.4 129.8 137.9 Dnaic2 86.0 105.1 116.6 Dync2li1 539.5 577.5 680.2 Dnah17 83.5 101.3 121.9 Foxj1 92.3 108.0 127.1 Fank1 240.7 305.3 348.8 Lrguk 34.3 45.7 48.7 Wdr65 46.3 57.0 84.0 1700012B09Rik 105.5 127.1 156.1 CEM 1 + Fsip1 82.3 89.0 127.5 Top 10 Genes Mapk15 179.7 253.1 282.8 B3gnt4 103.1 155.6 182.0 Ccdc19 128.3 150.9 183.6 Maats1 43.5 53.5 62.4

Null module GEO Series "GSE17373" 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=GSE17373 Status: Public on Dec 01 2009 Title: Expression data from EGFR mutant transgenic mice Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 19759520 Summary & Design: Summary: We performed mRNA expression profiling of lung tumors from C/L858R, C/T790M, and C/L+T mice and from corresponding normal lung tissue.

Overall design: mRNA was extracted from pulverized lung samples using Trizol (Invitrogen) and then hybridized to MOE 430 2.0 chips (Affymetrix) using standard hybridization techniques.

Background corr dist: KL-Divergence = 0.1056, L1-Distance = 0.0255, L2-Distance = 0.0009, Normal std = 0.4309

0.926 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

control control1 (0.0569229) control2 (0.0317113) control3 (0.0332627) control4 (0.0507475) L858R5 (0.0435168) 1L858R (0.101291) 2L858R (0.0366173) 3L858R (0.0426428) 4L858R+T790M (0.0434585)L858R+T790M 1L858R+T790M (0.0285775) 2L858R+T790M (0.0195196) 3L858R+T790M (0.0356822) 4Normal (0.0316797) 5 Normal1 (0.0646805) (0.0231386) Normal2 (0.0734198) Normal3 (0.0370497) Normal4 (0.0812575) T790M5 (0.0285527) 1T790M (0.0174122) 2T790M (0.0330663) 3T790M (0.025374) 4T790M (0.0465704) 5 (0.0138482) [ min ] [ medium ] [ max ] CEM 1 Dnah6 198.2 327.8 616.2 P ( S | Z, I ) = 0.94 Dnali1 69.6 113.5 283.1 Mean Corr = 0.23733 Dnah7a 39.8 69.6 153.7 Dnah2 56.4 108.2 192.0 Dnah1 108.3 138.8 155.5 Dnah8 156.0 268.1 951.9 Dnah5 90.5 152.9 297.0 Dnah9 65.6 83.0 112.1 Dnal4 373.6 472.3 544.5 Dnah11 166.6 245.3 392.1 Dnaic2 94.3 130.7 154.0 Dync2li1 503.3 673.0 1003.4 Dnah17 84.4 103.8 118.6 Foxj1 96.5 196.5 524.0 Fank1 193.8 250.8 352.3 Lrguk 29.7 56.4 112.6 Wdr65 44.9 93.5 141.7 1700012B09Rik 45.8 62.8 100.8 CEM 1 + Fsip1 53.9 66.5 91.2 Top 10 Genes Mapk15 179.9 277.6 492.8 B3gnt4 84.5 102.2 133.5 Ccdc19 41.3 63.4 104.9 Maats1 110.2 161.8 248.1

Null module GEO Series "GSE10849" 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=GSE10849 Status: Public on Mar 04 2009 Title: Caveolin-1 Knockout Hearts Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 18719368 Summary & Design: Summary: Hearts Lacking Caveolin-1 Develop Hypertrophy with Normal Cardiac Substrate Metabolism

Keywords: gene knockout

Overall design: 3 wild types, 3 knockouts

Background corr dist: KL-Divergence = 0.0216, L1-Distance = 0.0174, L2-Distance = 0.0003, Normal std = 0.7235

0.551 Kernel fit Pairwise Correlations Normal fit

Density 0.276

0.000 CEM 1

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

Pre-normalization Quantiles

WT 1 1508WT (0.484514)2 1509WT (0.118315)3 1782Cav1KO (0.107516)Cav1KO 1758 (0.0902778)Cav1KO 1761 (0.110208) 1762 (0.0891698) [ min ] [ medium ] [ max ] CEM 1 Dnah6 135.3 154.5 178.9 P ( S | Z, I ) = 0.65 Dnali1 34.4 36.7 46.7 Mean Corr = 0.55546 Dnah7a 24.3 27.2 44.0 Dnah2 35.6 44.9 54.5 Dnah1 83.6 99.2 130.9 Dnah8 35.7 40.9 53.4 Dnah5 43.5 51.8 63.6 Dnah9 31.7 40.5 50.3 Dnal4 506.0 584.2 591.1 Dnah11 141.4 164.6 198.9 Dnaic2 68.4 76.5 112.6 Dync2li1 228.6 231.5 240.5 Dnah17 74.9 81.7 99.9 Foxj1 57.3 65.8 100.5 Fank1 221.3 242.4 314.6 Lrguk 23.4 27.4 28.2 Wdr65 40.8 44.9 63.1 1700012B09Rik 38.6 42.9 48.1 CEM 1 + Fsip1 79.0 84.6 95.8 Top 10 Genes Mapk15 121.7 140.6 165.0 B3gnt4 53.5 61.7 70.9 Ccdc19 47.2 49.0 58.4 Maats1 39.0 44.0 47.5

Null module GEO Series "GSE45487" 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=GSE45487 Status: Public on Mar 26 2013 Title: Identification of genes responsive to low-intensity pulsed ultrasound (LIPUS) in MC3T3-E1 preosteoblast cells Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 24252911 Summary & Design: Summary: Although LIPUS has been shown to enhance fracture healing, the underlying mechanism of LIPUS remains to be fully elucidated. Here, to understand the molecular mechanism underlying cellular responses to LIPUS, we investigated gene expression profiles in mouse MC3T3-E1 preosteoblast cells using a GeneChipÂ® system.

Overall design: The mouse preosteoblast MC3T3-E1cells were treated with LIPUS (30 mW/cm2) for 20 min followed by culturing for 6 and 24 h at 37C. Mock-treated cells were served as control. Total RNA samples were prepared from the cells, and quality of the RNA was analyzed using a Bioanalyzer 2100. Gene expression was monitored by an Affymetrix GeneChip system with a Mouse Genome 430 2.0 array. Sample preparation for array hybridization was carried out as described in the manufacturer's instructions.

Background corr dist: KL-Divergence = 0.0154, L1-Distance = 0.0176, L2-Distance = 0.0004, Normal std = 0.7802

0.511 Kernel fit Pairwise Correlations Normal fit

Density 0.256

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

MC3T3-E1MC3T3-E1 (control-1)MC3T3-E1 (control-2) (0.12056)MC3T3-E1 (control-3) (0.0730463)MC3T3-E1 LIPUS-24 (0.202988)MC3T3-E1 LIPUS-24 h MC3T3-E11 (0.078005) LIPUS-24 h MC3T3-E12 (0.0578206) LIPUS-6 h MC3T3-E13 (0.12071) LIPUS-6 h 1 (0.138016) LIPUS-6 h 2 (0.0728377) h 3 (0.136016)[ min ] [ medium ] [ max ] CEM 1 Dnah6 50.4 52.6 69.9 P ( S | Z, I ) = 0.51 Dnali1 31.8 40.1 46.1 Mean Corr = 0.57941 Dnah7a 12.1 16.1 19.1 Dnah2 14.0 20.5 23.3 Dnah1 47.4 51.6 65.8 Dnah8 15.9 24.0 39.2 Dnah5 25.2 31.0 75.4 Dnah9 15.0 19.3 51.1 Dnal4 263.6 344.9 369.1 Dnah11 65.0 91.3 97.5 Dnaic2 46.0 54.5 75.4 Dync2li1 1534.4 1602.6 1813.1 Dnah17 16.3 54.1 69.0 Foxj1 28.6 35.1 41.9 Fank1 65.2 78.8 206.7 Lrguk 11.8 14.3 18.4 Wdr65 18.9 21.9 31.6 1700012B09Rik 17.3 34.5 43.6 CEM 1 + Fsip1 19.7 31.0 40.2 Top 10 Genes Mapk15 80.9 89.8 128.3 B3gnt4 27.3 29.2 32.3 Ccdc19 25.0 28.9 44.7 Maats1 14.5 17.8 32.6

Null module GEO Series "GSE28664" 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=GSE28664 Status: Public on Sep 04 2011 Title: Akt1 is critical in Maintaining the Blood-Testis Barrier Following Exposure to the Neonatal Goitrogen, 6-N-Propylthiouracil (PTU) Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: Akt1 plays a protective role in the postnatal C57BL6 mouse testis following lactational exposure to the neonatal goitrogen, propylthiouracil (PTU). To elucidate the transcriptional profile mediating this phenotypic effect, we monitored changes in testicular gene expression at postnatal days (PNDs) 15 and 25 in Akt1+/+, Akt1+/-, and Akt1-/- testes following exposure to 0.01% PTU allowing us to determine changes in gene expression due to 1.) genotype effects; 2.) exposure effects; and 3.) genotype-by-exposure interactions. Early PTU-dependent gene changes included genes involved in lipid metabolism, spermatid differentiation, meiosis and adhesion. Early Akt1-dependent effects were associated with germ cell development, spermatid development and differentiation, and sperm motility. By PND25, the Akt1 gene-environment interaction had pronounced effects on genes associated with Sertoli cell (SC) differentiation and claudin-associated junctional formation suggesting delayed formation of the blood-testis barrier (BTB). To confirm these observations, biotin tracer experiments demonstrated a permeable blood-testis barrier in PTU-exposed PKBalpha/Akt1-/- tubules as late as PND25 compared to PTU-exposed Akt1+/+ seminiferous tubules. Transmission electron microscopy demonstrated altered SC morphology, aberrant SC localization, and disorganized actin bundle formation. Taken together, loss of Akt1 coupled with postnatal exposure to the neonatal goitrogen, PTU, in the testis contributes to a transcriptional profile associated with impaired integrity of the blood-testis barrier. In summary, the Akt1-/- mouse represents a potentially important model to study BTB formation and reassembly in response to male reproductive toxicants and the various signaling networks which mediate these responses.

Overall design: The microarray analysis employed a balanced factorial design, with one chip created for each of three mice under each experimental condition: mouse genotype (Akt1+/+, Akt1+/-, and Akt1-/-), exposure (PTU and Control), and age (sacrificed at PND15 and 25), with a total of 36 mice and 36 chips. MoGene 1.0 st v1 arrays were used for the samples from PND 15 and Mouse Genome 430 2.0 arrays were used for the samples from PND 25. One chip, PTU-exposed, Akt1-/-, PND25, was determined to not be of high quality and was not included in the analysis or provided here.

Background corr dist: KL-Divergence = 0.0331, L1-Distance = 0.0207, L2-Distance = 0.0005, Normal std = 0.6440

0.619 Kernel fit Pairwise Correlations Normal fit

Density 0.310

0.000 CEM 1

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

Pre-normalization Quantiles

testis genetestis expression genetestis expression genetestis data expression fromgenetestis data Akt1expression fromgenetestis dataheterozygous Akt1expression fromgenetestis dataheterozygous Akt1expression fromgenetestis mice dataheterozygous Akt1expression fromgeneattestis mice datapostnatalheterozygous, Akt1expression fromgeneattestis mice datapostnatalheterozygous, dayAkt1expression fromgeneat testis 25, datapostnatalPTU-exposedheterozygous, dayAkt1sampleexpression fromgene testis 25, dataPTU-exposedhomozygous dayAkt1 sampleexpression1 fromgene(0.0403422) testis 25,mice dataPTU-exposedhomozygous Akt1 sampleexpression2 fromatgene(0.0753022) testismice mice postnataldatahomozygous Akt1 expression3 at fromatgene(0.0268132) testismice postnatalmice postnataldatahomozygous, day Akt1expression at fromatgene testismice25, postnatal postnataldatahomozygous, day day Akt1sampleexpression at fromgene 25, testis 25, postnatalPTU-exposed datawildtype day sampleday Akt1sample1expression (0.0233406)fromgene 25, 25, PTU-exposed datawildtype miceday sample 1Akt1sample2expression (0.0869579)(0.0250338)from 25,mice atdatawildtype mice samplepostnatal 2Akt13 at (0.0305929)(0.0192792)from micepostnatal atdatawildtype, mice postnatal3Akt1 at (0.0423834)dayfrom [postnatal atwildtype, 25,day min postnatalPTU-exposedAkt1 daysample 25, wildtype, 25,day sample PTU-exposed] day sample 125, (0.0151005) 25,mice sample1PTU-exposed (0.187136) sample2 at(0.0199678) mice [postnatal2 (0.290919)medium 3 at(0.0152373) micepostnatal day at 25, postnatal daysample ] 25, day sample1 (0.0189108) 25, sample2[ (0.0482356) max 3 (0.0344469) ] CEM 1 Dnah6 117.2 1053.7 1537.4 P ( S | Z, I ) = 0.28 Dnali1 246.3 2754.0 4387.8 Mean Corr = 0.55032 Dnah7a 582.0 1273.0 1569.3 Dnah2 658.6 2622.1 3747.4 Dnah1 254.2 443.2 572.1 Dnah8 3297.9 11090.8 16034.2 Dnah5 44.6 53.8 66.0 Dnah9 22.6 31.2 36.1 Dnal4 732.2 2074.2 2696.2 Dnah11 68.6 104.9 124.7 Dnaic2 39.8 68.5 88.8 Dync2li1 1460.8 2341.7 3069.3 Dnah17 19.8 23.5 27.5 Foxj1 60.9 798.8 1119.3 Fank1 409.4 1902.3 2297.6 Lrguk 316.6 878.9 1040.1 Wdr65 609.9 3278.8 3756.8 1700012B09Rik 885.7 3863.6 4929.5 CEM 1 + Fsip1 204.6 1082.0 1778.7 Top 10 Genes Mapk15 359.9 1000.5 1270.1 B3gnt4 183.2 428.4 544.5 Ccdc19 276.8 2749.4 3761.5 Maats1 44.9 420.5 632.0

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 (0.0919939) TTrep Hflu ME2 (0.0962169) controlrep ME1 (0.0660702) controlrep ME3 (0.0839643) TTrep Hflu ME4 (0.0289451) controlrep ME2 (0.0497725) controlrep ME5 (0.037799) controlrep ME6 (0.0486682) TTrep Hflu ME7 (0.0877916) TTrep Hflu ME3 (0.0589361) TTrep Hflu ME4 (0.0793685) controlrep ME5 (0.0444083) TTrep Hflu ME8 (0.0441639) TTrep Hflu ME6 (0.0123887) TTrep Hflu ME7 (0.0372928) TTrep Hflu 8 (0.0850106) rep 9 (0.0472094) [ min ] [ medium ] [ max ] CEM 1 Dnah6 297.0 402.9 645.7 P ( S | Z, I ) = 0.04 Dnali1 180.4 327.1 605.0 Mean Corr = 0.36168 Dnah7a 21.0 39.0 64.0 Dnah2 142.6 202.0 322.5 Dnah1 27.5 33.1 49.0 Dnah8 176.2 310.3 635.7 Dnah5 24.6 36.7 51.0 Dnah9 8.0 10.5 13.7 Dnal4 369.2 498.8 618.2 Dnah11 799.3 1005.2 1295.6 Dnaic2 17.3 26.4 33.9 Dync2li1 391.6 517.6 823.6 Dnah17 14.2 20.2 23.6 Foxj1 159.9 198.8 352.7 Fank1 70.4 83.9 150.6 Lrguk 38.9 61.4 84.1 Wdr65 100.1 188.1 279.8 1700012B09Rik 22.0 27.9 48.0 CEM 1 + Fsip1 67.2 108.8 161.2 Top 10 Genes Mapk15 54.2 75.0 106.3 B3gnt4 45.1 64.0 102.9 Ccdc19 157.1 258.3 307.7 Maats1 4.6 6.9 10.1

Null module GEO Series "GSE18765" 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=GSE18765 Status: Public on Nov 19 2010 Title: The transcriptome of prospectively isolated adult neural stem cells Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21112568 Summary & Design: Summary: Since the discovery of adult neural stem cells, their exact identity is still under discussion. Moreover, the lack of a reproducible procedure to purify neural stem cells prospectively rather than by growing them in vitro has so far precluded their study at the transcriptome level. Here we demonstrate a novel procedure to prospectively isolate neural stem cells from the adult mouse subependymal zone on the basis of their GFAP- and prominin1-expression by fluorescence-activated cell sorting. All self-renewing, multipotent stem cells are contained in this fraction at 70% purity. The stem cell identity of these double-positive cells is further demonstrated in vivo, by using a novel split-Cre-technology for fate mapping.

Comparison of the transcriptome of these prospectively isolated neural stem cells to the transcriptomes of other astrocytes or ependymal cells revealed a distinct clustering of the stem cells, highlighting their unique features, as well as profound similarities to the astrocyte as well as ependyma transcriptome.

Overall design: FACS-sorting was used to isolate prospective neural stem, astrocytes and ependymal cells from brain regions of hGFAP eGFP expressing mice. Total RNA from these cells was hybridised on Affymetrix MOE430 2.0 arrays and expression patterns were analysed.

Background corr dist: KL-Divergence = 0.1676, L1-Distance = 0.0466, L2-Distance = 0.0051, Normal std = 0.3611

1.105 Kernel fit Pairwise Correlations Normal fit

Density 0.552

0.000 CEM 1

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

Pre-normalization Quantiles

DIEC_GFP,DIEC_GFP, biologicalDIEC_GFP, biological replicateDIEC_GFP, biological replicateSEZ_CD24, 1 (0.0324941) biological replicateSEZ_CD24, 2 (0.0484142) biological replicateSEZ_GFP, 3 (0.0115891) biological replicateSEZ_GFP, 4 biological(0.0305874) replicateSEZ_GFPprom, 1 biological(0.0464025) replicateSEZ_GFPprom, 2 (0.0342858) replicateSEZ_GFPprom, 1biological (0.0677634)SEZ_GFPprom, 2biological (0.0503893) replicateSEZ_Prom, biological replicate 1 SEZ_Prom,(0.178413) biological replicatebiological 2 (0.129682) replicatebiological 3 replicate(0.0825454) 4 replicate(0.135429) 1 (0.0735784)[ 2 min(0.0784261) ] [ medium ] [ max ] CEM 1 Dnah6 278.8 2909.1 8181.5 P ( S | Z, I ) = 0.04 Dnali1 143.2 434.5 3105.8 Mean Corr = 0.28508 Dnah7a 60.2 130.1 563.8 Dnah2 78.7 900.8 3609.6 Dnah1 97.0 143.6 481.0 Dnah8 37.0 55.6 101.7 Dnah5 41.8 55.5 101.8 Dnah9 41.6 50.8 60.3 Dnal4 361.1 471.5 720.3 Dnah11 189.6 356.0 1581.7 Dnaic2 116.0 152.6 212.4 Dync2li1 529.7 1212.8 2484.4 Dnah17 46.5 60.1 83.2 Foxj1 222.3 799.8 5022.7 Fank1 194.0 254.2 318.8 Lrguk 23.2 50.9 290.9 Wdr65 32.4 171.1 943.5 1700012B09Rik 50.9 259.0 2839.7 CEM 1 + Fsip1 37.0 88.0 379.0 Top 10 Genes Mapk15 106.9 457.9 1327.4 B3gnt4 41.7 115.6 291.0 Ccdc19 60.1 1242.2 2518.8 Maats1 37.0 46.2 55.8

Null module GEO Series "GSE34765" 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=GSE34765 Status: Public on Sep 30 2012 Title: Transcriptomic analysis of the cerebellum of daDREAM mice Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 22563308 Summary & Design: Summary: DREAM (downstream regulatory element antagonist modulator) is a Ca2+-binding protein that binds DNA and represses transcription in a Ca2+-dependent manner. Previous studies have shown a role for DREAM in cerebellar function regulating the expression of the sodium/calcium exchanger3 (NCX3) in cerebellar granules to control Ca2+ homeostasis and survival of these neurons. To achieve a more global view of the genes regulated by DREAM in the cerebellum, we performed a genome-wide analysis in transgenic cerebellum expressing a Ca2+-insensitive/CREB-independent dominant active mutant DREAM (daDREAM). Our results indicate that DREAM is a major transcription factor in the cerebellum that regulates genes important for cerebellar development.

Overall design: We used Affymetrix microarrays (GeneChip Mouse Genome 430 2.0) to compare global gene expression in wild type (WT) versus transgenic cerebellum cells. For ech type of sample three hybridizations were carried-out (independent biological replicates).

Background corr dist: KL-Divergence = 0.0144, L1-Distance = 0.0300, L2-Distance = 0.0013, Normal std = 0.8079

0.494 Kernel fit Pairwise Correlations Normal fit

Density 0.247

0.000 CEM 1

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

Pre-normalization Quantiles

Cerebellum_WildType_REP1Cerebellum_WildType_REP2Cerebellum_WildType_REP3Cerebellum_Transgenic_REP1 (0.0961878)Cerebellum_Transgenic_REP2 (0.0990297)Cerebellum_Transgenic_REP3 (0.0675277) (0.31345) (0.111571)[ (0.312234) min ] [ medium ] [ max ] CEM 1 Dnah6 103.2 151.9 184.9 P ( S | Z, I ) = 0.03 Dnali1 77.8 95.5 102.8 Mean Corr = 0.61683 Dnah7a 37.5 45.3 63.9 Dnah2 42.2 57.0 70.8 Dnah1 63.6 87.2 111.9 Dnah8 48.2 61.1 68.0 Dnah5 44.0 58.6 62.7 Dnah9 43.4 55.7 80.8 Dnal4 537.3 652.9 683.4 Dnah11 348.1 465.3 532.5 Dnaic2 106.1 154.0 225.5 Dync2li1 298.3 380.6 510.8 Dnah17 92.4 131.9 132.6 Foxj1 104.7 126.8 185.7 Fank1 179.7 280.8 327.8 Lrguk 37.8 48.1 54.1 Wdr65 37.6 48.3 60.0 1700012B09Rik 76.2 99.5 111.2 CEM 1 + Fsip1 106.3 117.2 146.7 Top 10 Genes Mapk15 116.9 202.7 266.3 B3gnt4 96.3 120.8 176.9 Ccdc19 65.0 69.7 104.5 Maats1 47.2 66.6 69.9

Null module GEO Series "GSE7275" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 8 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

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

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

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

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

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

0.458 Kernel fit Pairwise Correlations Normal fit

Density 0.229

0.000 CEM 1

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

Pre-normalization Quantiles

ExosomalExosomal RNA,Exosomal biological RNA,Exosomal biological RNA, rep1Mast biological(0.152412) RNA, rep2 cellsMast biological(0.144464) RNA, rep3 cellsMast biological(0.131801) RNA, rep4 cellsMast biological(0.214266) RNA, rep1 cells biological(0.0896927) RNA, rep2 biological(0.102716) rep3 (0.0798543) rep4[ (0.0847939)min ] [ medium ] [ max ] CEM 1 Dnah6 5.9 78.2 121.8 P ( S | Z, I ) = 0.02 Dnali1 5.0 60.3 186.4 Mean Corr = 0.57137 Dnah7a 5.0 547.7 1313.7 Dnah2 5.0 240.2 604.8 Dnah1 5.0 54.6 348.5 Dnah8 5.0 340.8 443.5 Dnah5 30.3 338.5 766.5 Dnah9 5.0 568.6 1609.9 Dnal4 132.0 321.0 1485.0 Dnah11 12.3 129.3 194.0 Dnaic2 23.7 68.7 969.9 Dync2li1 32.6 114.8 1108.6 Dnah17 5.0 102.9 1218.3 Foxj1 5.0 276.4 959.3 Fank1 10.3 78.9 279.1 Lrguk 5.0 84.7 989.0 Wdr65 11.4 33.7 509.2 1700012B09Rik 5.0 39.8 83.6 CEM 1 + Fsip1 20.0 203.2 806.4 Top 10 Genes Mapk15 18.4 91.3 1221.1 B3gnt4 5.0 33.9 224.7 Ccdc19 31.1 144.6 492.0 Maats1 5.0 51.5 552.2

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 (0.0601102)WAT2-ct (0.0959574)WAT8-ko (0.221332)WAT3-ctr (0.169733)WAT9-ko (0.183553)WAT4-ct (0.110213)WAT10-ko (0.0836809) (0.0754198) [ min ] [ medium ] [ max ] CEM 1 Dnah6 104.7 452.9 548.8 P ( S | Z, I ) = 0.02 Dnali1 116.2 296.6 353.0 Mean Corr = 0.34852 Dnah7a 33.5 43.6 50.4 Dnah2 31.1 114.2 171.5 Dnah1 69.3 80.2 86.3 Dnah8 53.2 72.9 150.3 Dnah5 95.0 224.1 301.2 Dnah9 30.2 34.7 43.3 Dnal4 343.5 391.2 416.8 Dnah11 265.2 657.2 752.4 Dnaic2 65.7 70.3 89.2 Dync2li1 527.5 838.2 947.9 Dnah17 25.6 31.7 34.9 Foxj1 46.8 736.2 930.6 Fank1 139.0 155.2 208.5 Lrguk 34.9 155.1 185.0 Wdr65 73.6 105.0 121.6 1700012B09Rik 44.7 192.9 250.0 CEM 1 + Fsip1 47.9 60.6 63.5 Top 10 Genes Mapk15 120.9 265.5 321.5 B3gnt4 34.3 41.5 51.0 Ccdc19 57.0 119.9 150.9 Maats1 51.4 165.8 214.7

Null module GEO Series "GSE32330" 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=GSE32330 Status: Public on Nov 30 2011 Title: Expression data from C/EBP alpha induced transdifferentiation of pre-B cells into macrophages Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 21969581 Summary & Design: Summary: Earlier work has shown that pre-B cells can be converted into macrophages by the transcription factor C/EBP? at very high frequencies. Using this system we have now performed a systematic analysis of the question whether during transdifferentiation the cells transiently reactivate progenitor restricted genes or even retrodifferentiate. A transcriptome analysis of transdifferentiating cells showed that most genes are continuously up or downregulated, acquiring a macrophage phenotype within 5 days. In addition, we observed the transient reactivation of a subset of immature myeloid markers, as well as low levels of the progenitor markers Kit and Flt3 and a few lineage inappropriate genes. However, we were unable to observe the re-expression of cell surface marker combinations that characterize hematopoietic stem and progenitor cells (HSPCs), including c-Kit and Flt3. This was the case even when C/EBPalpha was activated in pre-B cells under culture conditions that favor HSPC growth or when the transcription factor was activated in a time limited fashion. Together, our findings are consistent with the notion that the conversion from pre-B cells to macrophages is mostly direct and does not involve overt retrodifferentiation.

Our microarray data indicate that most expression changes are direct, and that transdifferentiation does not involve retrodifferentiation. Our data also show that there is a low level transient activation of selected progenitor genes, as well as myeloid precursor genes.

Overall design: Primary mouse pre-B cells were infected with an inducible form of C/EBPa and cells induced to transdifferentiate with beta Estradiol (b-Est) harvested at different time points to analyze expression profiles, using Affymetrix 430.2 arrays.

Background corr dist: KL-Divergence = 0.0510, L1-Distance = 0.0769, L2-Distance = 0.0119, Normal std = 0.6064

0.660 Kernel fit Pairwise Correlations Normal fit

Density 0.330

0.000 CEM 1

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

Pre-normalization Quantiles

pre-B_3h_EtOH_rep1pre-B_3h_EtOH_rep2pre-B_3h_b-Est_rep1 (0.0210141)pre-B_3h_b-Est_rep2 (0.0999784)pre-B_12h_b-Est_rep1 (0.0198942)pre-B_12h_b-Est_rep2 (0.0218008)pre-B_48h_b-Est_rep1pre-B_48h_b-Est_rep2 (0.166654)pre-B_120h_b-Est_rep1 (0.389882)pre-B_120h_b-Est_rep2 (0.0230773)Macrophages_rep1 (0.0373181)Macrophages_rep2 (0.0390161) (0.0559339) (0.0326691) (0.0927616)[ min ] [ medium ] [ max ] CEM 1 Dnah6 49.7 70.1 91.2 P ( S | Z, I ) = 0.01 Dnali1 54.3 70.5 90.1 Mean Corr = 0.67192 Dnah7a 29.6 33.5 40.0 Dnah2 42.5 51.3 60.3 Dnah1 63.1 87.7 135.9 Dnah8 146.8 322.6 846.2 Dnah5 36.0 44.7 49.5 Dnah9 41.0 47.2 88.1 Dnal4 174.0 243.7 445.4 Dnah11 103.0 119.0 234.1 Dnaic2 101.7 138.7 172.4 Dync2li1 83.7 95.6 140.2 Dnah17 73.2 88.9 124.6 Foxj1 53.0 65.8 113.0 Fank1 112.2 156.9 297.9 Lrguk 35.9 42.3 55.2 Wdr65 44.9 65.9 108.8 1700012B09Rik 49.3 71.1 84.6 CEM 1 + Fsip1 103.0 115.6 144.8 Top 10 Genes Mapk15 92.3 146.1 228.1 B3gnt4 68.1 86.7 108.2 Ccdc19 37.6 56.9 81.3 Maats1 29.6 39.9 88.9

Null module GEO Series "GSE35435" 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=GSE35435 Status: Public on Sep 29 2012 Title: Genome-wide analysis of mouse macrophages stimulated with IL-4 (bone marrow macrophages) (Affymetrix) Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 23293084 Summary & Design: Summary: Analysis of alternative activation of macrophages at gene expression level. The study forms part of a wider study where we compare the effects of IL-4 in different human and mouse macrophages. Our results support the notion that in vitro culture conditions greatly affect the macrophage response to IL-4.

Total RNA obtained from bone marrow derived macrophages upon exposure to 20 ng/ml of IL-4 for 18 hours.

Overall design: Bone marrow derived macrophages were stimulated with the Th2 cytokine IL-4, for RNA extraction and hybridization on Affymetrix microarrays.

Background corr dist: KL-Divergence = 0.0170, L1-Distance = 0.0428, L2-Distance = 0.0029, Normal std = 0.8007

0.498 Kernel fit Pairwise Correlations Normal fit

Density 0.249

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

RestingResting MacrophagesResting Macrophages IL-4M0 Macrophages BMMF-1 treated IL-4M0 BMMF-2 treated macrophages(0.16239) IL-4M0 BMMF-3 treated macrophages(0.0637086) M2 macrophages(0.170133) BMMF-1 M2 BMMF-2 (0.209047) M2 BMMF-3[ (0.107574) min (0.287147) ] [ medium ] [ max ] CEM 1 Dnah6 189.1 225.3 241.7 P ( S | Z, I ) = 0.01 Dnali1 100.0 116.3 143.0 Mean Corr = 0.61997 Dnah7a 49.0 53.8 60.2 Dnah2 62.4 73.7 89.2 Dnah1 141.5 173.5 182.1 Dnah8 73.1 76.9 93.0 Dnah5 69.8 80.8 88.5 Dnah9 143.8 158.8 201.6 Dnal4 541.1 656.1 732.2 Dnah11 266.2 312.8 349.8 Dnaic2 253.7 285.1 311.7 Dync2li1 141.4 174.8 187.4 Dnah17 163.9 209.6 223.9 Foxj1 40.8 58.5 69.8 Fank1 630.7 767.1 889.0 Lrguk 71.6 79.7 96.8 Wdr65 91.8 98.2 124.2 1700012B09Rik 48.8 61.1 74.6 CEM 1 + Fsip1 132.4 152.2 180.6 Top 10 Genes Mapk15 213.5 243.6 291.1 B3gnt4 82.6 100.4 109.3 Ccdc19 52.3 56.8 62.5 Maats1 79.8 100.4 131.3

Null module GEO Series "GSE35436" 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=GSE35436 Status: Public on Sep 29 2012 Title: Genome-wide analysis of mouse macrophages stimulated with IL-4 (Biogel and thioglycollate macrophages) (Affymetrix) Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 23293084 Summary & Design: Summary: Analysis of alternative activation of macrophages at gene expression level. The study forms part of a wider study where we compare the effects of IL-4 in different human and mouse macrophages. Our results support the notion that in vitro culture conditions greatly affect the macrophage response to IL-4.

Total RNA obtained from Thioglycollate and Biogel elicited peritoneal macrophages exposed to 20 ng/ml of IL-4 for 18 hours.

Overall design: Biogel and thioglycollate elicited macrophages were stimulated with the Th2 cytokine IL-4, for RNA extraction and hybridization on Affymetrix microarrays.

Background corr dist: KL-Divergence = 0.0230, L1-Distance = 0.0244, L2-Distance = 0.0009, Normal std = 0.7147

0.558 Kernel fit Pairwise Correlations Normal fit

Density 0.279

0.000 CEM 1

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

Pre-normalization Quantiles

Thio permanoxThio permanoxThio M0 (0.0627103) TCPThio M2 M0 (0.102469) TCP (0.197784)Biogel M2 (0.0875634) M0Biogel (0.112869) M2 (0.436604) [ min ] [ medium ] [ max ] CEM 1 Dnah6 183.7 243.4 259.7 P ( S | Z, I ) = 0.01 Dnali1 102.1 130.8 141.3 Mean Corr = 0.52430 Dnah7a 45.8 56.3 60.4 Dnah2 72.3 78.5 105.8 Dnah1 152.9 194.0 220.8 Dnah8 79.5 91.5 110.2 Dnah5 63.2 82.0 88.5 Dnah9 157.3 192.7 193.4 Dnal4 503.4 639.2 664.7 Dnah11 236.2 352.9 384.5 Dnaic2 245.2 335.7 350.0 Dync2li1 100.9 161.9 180.6 Dnah17 144.9 218.6 227.0 Foxj1 54.5 63.9 66.3 Fank1 690.6 818.0 933.4 Lrguk 76.9 92.3 96.4 Wdr65 90.1 100.7 111.3 1700012B09Rik 47.3 62.6 70.5 CEM 1 + Fsip1 137.5 162.6 164.0 Top 10 Genes Mapk15 229.6 278.3 321.4 B3gnt4 71.2 99.6 112.1 Ccdc19 51.5 61.0 62.7 Maats1 94.9 126.7 137.3

Null module GEO Series "GSE33770" 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=GSE33770 Status: Public on Nov 12 2013 Title: Microarray Studies on the STAT5A MUTANT. Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: Stat5+/- mice were bred into the C57BL/6 background. Stat5+/- mice were intercrossed and mouse embryonic fibroblasts (MEFs) were isolated from 12.5-13.5-day WT or Stat5-/- fetuses. The retroviral-expression vector carrying a DNA binding domain mutant Stat5A (E437/E438?AA) or tyrosine-phosphorylated Stat5A Y694F mutation based on an MSCV-IRES-GFP backbone (gift from Richard Moriggl, Ludwig-Boltzmann Institute, Vienna, Austria) was infected into Stat5-/- MEFs. FACS was used to select GFP+ cells. After 5 hours starvation in serum free medium with 0.1% of BSA, MEFs were treated with growth hormone for 2 hours. Total cellular RNA from each group of the MEFs was extracted with TRIzol reagent (Invitrogen) according to the manufacturer's instructions. Microarray analyses were performed using Affymetrix Mouse Genome 430 2.0 GeneChips (Affymetrix, Santa Clara, CA) (four groups, biological replicates for each group). Expression values were determined with GeneChip Operating Software (GCOS) v1.1.1 software. RMA signals were summarized using GeneSpring GX 10.0.1 (Agilent) and normalized by quantile normalization. All data analysis was performed with GeneSpring software GX 10.01.

Overall design: Total 4 groups (EA, EA_GH, YF, YF_GH), biological duplicate replication for each group

Background corr dist: KL-Divergence = 0.0380, L1-Distance = 0.0916, L2-Distance = 0.0110, Normal std = 0.7913

0.534 Kernel fit Pairwise Correlations Normal fit

Density 0.267

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

EA-2 (0.0874546)EA-gh1 EA-gh2(0.0714245) YF1(0.267128) (0.0806124)YF2 (0.0373951)YF-gh1 YF-gh2(0.323672) EA1(0.0535765) (0.0787375) [ min ] [ medium ] [ max ] CEM 1 Dnah6 2.6 2.7 2.9 P ( S | Z, I ) = 0.00 Dnali1 3.1 3.1 3.2 Mean Corr = 0.36246 Dnah7a 2.9 3.1 3.3 Dnah2 2.3 2.5 2.5 Dnah1 1.9 2.0 2.1 Dnah8 2.6 2.8 3.0 Dnah5 2.7 2.8 3.0 Dnah9 3.2 3.4 3.5 Dnal4 88.4 119.1 165.1 Dnah11 476.1 643.9 785.4 Dnaic2 2.6 2.8 2.9 Dync2li1 517.3 679.1 929.7 Dnah17 2.2 2.3 2.4 Foxj1 2.2 2.3 2.5 Fank1 2.7 2.9 3.0 Lrguk 3.4 3.7 4.6 Wdr65 2.2 2.3 2.4 1700012B09Rik 2.5 2.6 2.8 CEM 1 + Fsip1 2.5 2.6 2.6 Top 10 Genes Mapk15 2.1 2.2 2.2 B3gnt4 3.4 3.8 4.3 Ccdc19 1.8 1.8 1.9 Maats1 3.1 3.3 3.6

Null module GEO Series "GSE6837" Expression Profiles Scale of expression profile Z-scores Num of samples in this series: 8 -3.0 -2.0 -1.0 0.0 1.0 2.0 3.0

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

Keywords: comparative study

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

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

0.536 Kernel fit Pairwise Correlations Normal fit

Density 0.268

0.000 CEM 1

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

Pre-normalization Quantiles

unstimulatedunstimulated embryonicstimulated embryonicstimulated fibroblasts embryonicstimulated fibroblasts embryonic WT, stimulatedfibroblasts biologicalembryonic KO, stimulatedfibroblasts biologicalembryonicWT, rep1 stimulatedfibroblasts biological embryonicWT,(0.0603561) rep1 fibroblasts biological embryonicrep1WT,(0.0917957) fibroblasts biological(0.0332089) rep2KO, fibroblasts biological (0.0660291) rep3KO,[ biological (0.0864337) min rep1KO, biological(0.184103) rep2] (0.0869217) rep3 (0.391152)[ medium ] [ max ] CEM 1 Dnah6 6.7 23.2 452.9 P ( S | Z, I ) = 0.00 Dnali1 2.7 8.7 483.5 Mean Corr = 0.39250 Dnah7a 2.2 31.2 162.5 Dnah2 6.8 14.9 200.9 Dnah1 4.9 27.1 67.7 Dnah8 2.7 24.0 249.5 Dnah5 3.7 67.0 188.4 Dnah9 1.5 11.9 26.1 Dnal4 283.5 389.7 493.0 Dnah11 7.6 57.8 288.1 Dnaic2 6.5 29.1 58.9 Dync2li1 212.4 335.0 850.7 Dnah17 4.6 37.6 71.4 Foxj1 7.2 66.4 1285.6 Fank1 10.9 65.0 185.2 Lrguk 2.4 24.8 184.6 Wdr65 5.6 41.7 254.4 1700012B09Rik 6.1 17.2 153.4 CEM 1 + Fsip1 50.9 74.7 104.1 Top 10 Genes Mapk15 6.6 87.0 420.1 B3gnt4 6.4 16.3 19.4 Ccdc19 17.7 65.0 293.6 Maats1 4.0 38.6 107.3

Null module GEO Series "GSE14481" 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=GSE14481 Status: Public on Dec 31 2009 Title: identification of TGCT genes involved in initiation and maintenance of transformed germ cells. Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: Summary & Design: Summary: Initially, we had compared gene expression differences in the embryonic gonads (E13.5) of the 129 and M19 strains by performing microarray analysis. These studies allowed us to identify downregulation of expression of the D19Bwg1357e, Zfp162 and Cox15 genes in the M19 strain.

We next decided to examine gene expression profile changes in the embryonic gonads of 129 and M19 at additional stages so as to identify other TGCT genes from M19 that are also involved in initiation and maintenance of transformed germ cells. For this we isolated E13.5, E15.5 and E17.5 genital ridges from male embryos.

Overall design: After data process and quality assessment, 38069 out of 45101 probe sets proceeded for further analysis to identify differentially expressed genes. Hierarchical cluster analysis shows that samples of two strains from the same stage were grouped together and separated from the other stages (Fig.8). The initial analysis indicates a number of trends in gene expression patterns. Moreover, downregulation of expression of D19Bwg1357e, Zfp162 and Cox15 genes in M19 was also verified in this analysis. These data are currently being analyzed with the help of Dr. Y. Ji and L. Xiao from the Department of Bioinformatics and Computational Biology and Department of Biostatistics at M.D. Anderson Cancer Center. The results are unpublished.

Background corr dist: KL-Divergence = 0.0538, L1-Distance = 0.0246, L2-Distance = 0.0009, Normal std = 0.5415

0.737 Kernel fit Pairwise Correlations Normal fit

Density 0.368

0.000 CEM 1

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

Pre-normalization Quantiles

E13.5 MouseE13.5 testis_129/Sv_1MouseE13.5 testis_129/Sv_2MouseE13.5 testis_M19_1Mouse (0.137944)E15.5 testis_M19_2Mouse (0.117114)E15.5 (0.0499301) testis_129/Sv_1MouseE15.5 (0.090782) testis_129/Sv_2MouseE15.5 testis_M19_1Mouse (0.0310162)E17.5 testis_M19_2Mouse (0.0925033)E17.5 (0.106528) testis_129/Sv_1MouseE17.5 (0.0391724) testis_129/Sv_2MouseE17.5 testis_M19_1Mouse (0.0897374) testis_M19_2 (0.0460828) (0.152895) (0.0462948)[ min ] [ medium ] [ max ] CEM 1 Dnah6 175.8 201.9 221.3 P ( S | Z, I ) = 0.00 Dnali1 47.6 60.2 76.4 Mean Corr = 0.55152 Dnah7a 66.8 81.3 91.0 Dnah2 60.8 106.4 137.4 Dnah1 115.7 129.8 157.2 Dnah8 496.1 643.3 754.2 Dnah5 193.5 233.1 274.3 Dnah9 47.8 58.9 71.0 Dnal4 698.4 840.6 961.0 Dnah11 490.4 676.3 805.8 Dnaic2 136.5 177.1 213.0 Dync2li1 899.5 1016.1 1343.1 Dnah17 231.9 323.9 385.1 Foxj1 52.3 68.4 113.9 Fank1 428.4 490.5 682.2 Lrguk 69.5 92.0 100.8 Wdr65 75.9 94.1 180.5 1700012B09Rik 31.4 40.1 51.4 CEM 1 + Fsip1 187.4 227.9 251.8 Top 10 Genes Mapk15 120.2 137.0 172.9 B3gnt4 96.5 106.0 128.5 Ccdc19 64.5 74.4 87.4 Maats1 134.0 179.8 247.1

Null module GEO Series "GSE5128" 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=GSE5128 Status: Public on Sep 01 2006 Title: Gene Expression Biomarkers for Predicting Liver Tumors in Two-Year Rodent Bioassays Organism: Mus musculus Experiment type: Expression profiling by array Platform: GPL1261 Pubmed ID: 17114358 Summary & Design: Summary: Two-year rodent bioassays play a central role in evaluating both the carcinogenic potential of a chemical and generating quantitative information on the dose-response behavior for chemical risk assessments. The bioassays involved are expensive and time-consuming, requiring nearly lifetime exposures (two years) in mice and rats and costing $2 to $4 million per chemical. Since there are approximately 80,000 chemicals registered for commercial use in the United States and 2,000 more are added each year, applying animal bioassays to all chemicals of concern is clearly impossible. To efficiently and economically identify carcinogens prior to widespread use and human exposure, alternatives to the two-year rodent bioassay must be developed. In this study, animals were exposed for 13 weeks to two chemicals that were positive for liver tumors in the two-year rodent bioassay, two chemicals that were negative for liver tumors, and two vehicle controls. Gene expression analysis was performed on the livers of the animals to assess the potential for identifying gene expression biomarkers that can predict tumor formation in a two-year bioassay following a 13 week exposure.

Keywords: toxicology, chemical carcinogenesis, liver

Overall design: Five week old female B6C3F1 mice were exposed for 13 weeks to the following treatments: 1) 1,5-Naphthalenediamine, CAS No. 2243-62-1, feed, 2000 ppm, positive liver carcinogen; 2) 2,3-Benzofuran, CAS No. 271-89-6, gavage, 240 mg/kg, positive liver carcinogen; 3) N-(1-naphthyl)ethylenediamine dihydrochloride, CAS No. 1465-25-4, feed, 2000 ppm, negative liver carcinogen; 4) Pentachloronitrobenzene, CAS No. 82-68-8, feed, 8187 ppm, negative liver carcinogen; 5) Feed control; 6) Corn oil gavage control. Feed animals were exposed 7 days/week and gavage animals were exposed 5 days/week (5 ml/kg). Microarray analysis was performed on the livers of three mice per treatment group.

Background corr dist: KL-Divergence = 0.0940, L1-Distance = 0.0565, L2-Distance = 0.0073, Normal std = 0.4505

0.886 Kernel fit Pairwise Correlations Normal fit

Density 0.443

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

LiverTissue_GavageTreatment_2,3-Benzofuran_Animal10LiverTissue_FeedTreatment_N-(1-naphthyl)ethylenediamineDihydrochloride_Animal12LiverTissue_FeedTreatment_N-(1-naphthyl)ethylenediamineDihydrochloride_Animal14LiverTissue_FeedTreatment_N-(1-naphthyl)ethylenediamineDihydrochloride_Animal15LiverTissue_FeedTreatment_Pentachloronitrobenzene_Animal16LiverTissue_FeedTreatment_Pentachloronitrobenzene_Animal18LiverTissue_FeedTreatment_Pentachloronitrobenzene_Animal20LiverTissue_GavageTreatment_CornOil_Control_Animal22 (0.0598468)LiverTissue_GavageTreatment_CornOil_Control_Animal24LiverTissue_GavageTreatment_CornOil_Control_Animal25LiverTissue_FeedTreatment_RodentLiverTissue_FeedTreatment_RodentLiverTissue_FeedTreatment_Rodent (0.0272125) (0.031113)LiverTissue_FeedTreatment_1,5-Naphthalenediamine_Animal2 (0.0372186) (0.0230534)LiverTissue_FeedTreatment_1,5-Naphthalenediamine_Animal4 (0.0273937) (0.0197371) Chow_Control_Animal27(0.0197794)LiverTissue_FeedTreatment_1,5-Naphthalenediamine_Animal5 Chow_Control_Animal28(0.0261081)LiverTissue_GavageTreatment_2,3-Benzofuran_Animal6 Chow_Control_Animal29(0.0546867)LiverTissue_GavageTreatment_2,3-Benzofuran_Animal8 (0.0538356) (0.0301485) (0.39662)[ min (0.0402645) (0.0331123)] (0.0340308) (0.0320798)[ (0.0537595)medium ] [ max ] CEM 1 Dnah6 61.1 78.9 115.0 P ( S | Z, I ) = 0.00 Dnali1 106.1 130.2 186.8 Mean Corr = 0.59900 Dnah7a 38.0 41.8 57.9 Dnah2 44.5 51.8 56.7 Dnah1 69.1 83.8 125.4 Dnah8 43.5 57.3 72.3 Dnah5 43.2 59.9 76.3 Dnah9 45.6 50.3 91.1 Dnal4 217.4 247.9 343.1 Dnah11 86.2 108.2 155.7 Dnaic2 79.4 99.0 185.6 Dync2li1 123.4 145.1 197.3 Dnah17 79.9 103.2 158.6 Foxj1 46.5 57.3 70.2 Fank1 174.9 200.0 331.8 Lrguk 30.5 40.0 50.4 Wdr65 57.9 68.9 118.3 1700012B09Rik 71.3 90.4 126.3 CEM 1 + Fsip1 96.2 123.5 168.9 Top 10 Genes Mapk15 172.7 284.1 393.3 B3gnt4 65.9 82.3 99.7 Ccdc19 47.0 56.0 80.5 Maats1 42.7 50.2 66.1

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_ (0.015794) 12w_rep1lung_9V/null_ (0.0124925) 12w_rep2lung_9V/null_ (0.0144664) 18w_rep1lung_9V/null_ (0.00761222) 18w_rep2lung_9V/null_ (0.0366828) 28w_rep1liver_9V/null_ (0.0194246) 28w_rep2liver_9V/null_ (0.00457567) 4w_rep1liver_9V/null_ (0.00874867) 4w_rep2liver_9V/null_ (0.0204029) 12w_rep1liver_9V/null_ (0.0252239) 12w_rep2liver_9V/null_ (0.0205229) 18w_rep1liver_9V/null_ (0.01974) 18w_rep2liver_9V/null_ (0.0254767) 28w_rep1lung_4L_ (0.0210903) 28w_rep2lung_4L_ (0.0319124)4w_rep1lung_4L_ (0.0263277)4w_rep2 (0.0148959)lung_4L_ 12w_rep1 (0.029202)lung_4L_ 12w_rep2 (0.0361586)lung_4L_ 18w_rep1 (0.0468663)lung_4L_ 18w_rep2 (0.0510314)lung_4L_ 28w_rep1 (0.0370742)liver_4L_ 28w_rep2 (0.0739548)liver_4L_ 4w_rep1 (0.0496546)liver_4L_ 4w_rep2 (0.0209022)liver_4L_ 12w_rep1 (0.018835)liver_4L_ 12w_rep2 (0.0199675)liver_4L_ 18w_rep1 (0.0248387)liver_4L_ 18w_rep2 (0.0218985)liver_4L_ 28w_rep1 (0.0188754)lung_WT_ 28w_rep2 (0.0485431)lung_WT_ 28w_rep1 (0.0565043)lung_WT_ 28w_rep2 (0.0207436)lung_WT_ 28w_rep3 (0.01143)liver_WT_ 28w_rep4 (0.00828742)liver_WT_ 28w_rep1 (0.0244381)liver_WT_ 28w_rep2 (0.0208096) 28w_rep3 (0.0178327) (0.0167624)[ min ] [ medium ] [ max ] CEM 1 Dnah6 9.2 286.8 731.6 P ( S | Z, I ) = 0.00 Dnali1 6.3 178.2 1081.8 Mean Corr = 0.37593 Dnah7a 1.6 51.3 265.0 Dnah2 2.2 68.3 211.0 Dnah1 13.0 46.2 183.7 Dnah8 2.9 263.1 942.6 Dnah5 9.1 100.0 310.5 Dnah9 1.5 19.5 93.8 Dnal4 141.1 353.8 754.2 Dnah11 11.4 140.9 323.6 Dnaic2 5.3 42.8 114.6 Dync2li1 86.9 951.7 2471.7 Dnah17 2.0 18.5 111.8 Foxj1 3.6 581.9 1914.6 Fank1 18.3 128.6 256.5 Lrguk 2.0 97.3 425.7 Wdr65 1.5 137.6 510.5 1700012B09Rik 4.7 56.5 276.2 CEM 1 + Fsip1 17.9 87.0 271.8 Top 10 Genes Mapk15 126.3 258.6 403.1 B3gnt4 4.8 15.4 59.3 Ccdc19 4.2 131.2 388.5 Maats1 13.6 91.1 234.3

Null module