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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,

Latest revision as of 10:54, 17 September 2013


Full id: C196_testicular_iPS_H9_teratocarcinoma_HES3GFP_choriocarcinoma_endometrial



Phase1 CAGE Peaks

Hg19::chr10:126138597..126138612,-p1@NKX1-2
Hg19::chr10:17421411..17421428,-p@chr10:17421411..17421428
-
Hg19::chr10:88715938..88715944,+p@chr10:88715938..88715944
+
Hg19::chr11:571738..571745,+p@chr11:571738..571745
+
Hg19::chr11:68458387..68458424,+p3@GAL
Hg19::chr12:122018746..122018755,+p10@ENST00000541574
Hg19::chr12:4128088..4128115,+p@chr12:4128088..4128115
+
Hg19::chr13:113679015..113679022,+p48@MCF2L
Hg19::chr13:113679026..113679032,+p51@MCF2L
Hg19::chr14:20777397..20777403,+p@chr14:20777397..20777403
+
Hg19::chr14:23019467..23019489,+p@chr14:23019467..23019489
+
Hg19::chr14:23676550..23676564,-p@chr14:23676550..23676564
-
Hg19::chr14:65443907..65443910,-p@chr14:65443907..65443910
-
Hg19::chr14:67958000..67958046,-p@chr14:67958000..67958046
-
Hg19::chr15:89090517..89090532,-p@chr15:89090517..89090532
-
Hg19::chr15:97421623..97421630,+p@chr15:97421623..97421630
+
Hg19::chr16:56703691..56703702,+p4@MT1H
Hg19::chr16:60118628..60118633,-p@chr16:60118628..60118633
-
Hg19::chr17:17495344..17495361,-p18@PEMT
Hg19::chr17:17495366..17495387,-p10@PEMT
Hg19::chr17:77923773..77923782,-p@chr17:77923773..77923782
-
Hg19::chr17:80713164..80713169,+p@chr17:80713164..80713169
+
Hg19::chr19:1584912..1584913,-p6@M77818
Hg19::chr19:20334742..20334750,-p@chr19:20334742..20334750
-
Hg19::chr19:20349204..20349207,-p@chr19:20349204..20349207
-
Hg19::chr19:20349209..20349221,-p@chr19:20349209..20349221
-
Hg19::chr19:20406681..20406707,+p@chr19:20406681..20406707
+
Hg19::chr19:22041202..22041205,+p@chr19:22041202..22041205
+
Hg19::chr19:22041270..22041282,+p@chr19:22041270..22041282
+
Hg19::chr19:282788..282832,-p@chr19:282788..282832
-
Hg19::chr19:40431284..40431296,-p@chr19:40431284..40431296
-
Hg19::chr19:52932435..52932443,+p3@ZNF534
Hg19::chr19:55405124..55405130,+p@chr19:55405124..55405130
+
Hg19::chr1:160160001..160160019,+p9@CASQ1
Hg19::chr1:161392010..161392029,+p@chr1:161392010..161392029
+
Hg19::chr1:27385778..27385789,+p@chr1:27385778..27385789
+
Hg19::chr1:27386571..27386581,+p@chr1:27386571..27386581
+
Hg19::chr1:29513362..29513370,-p@chr1:29513362..29513370
-
Hg19::chr1:36906474..36906481,-p6@OSCP1
Hg19::chr1:52902618..52902666,-p11@ZCCHC11
Hg19::chr1:70833635..70833640,+p@chr1:70833635..70833640
+
Hg19::chr20:18304432..18304433,-p@chr20:18304432..18304433
-
Hg19::chr21:44199834..44199841,+p@chr21:44199834..44199841
+
Hg19::chr22:38716047..38716051,-p@chr22:38716047..38716051
-
Hg19::chr22:44547044..44547092,+p@chr22:44547044..44547092
+
Hg19::chr2:15359103..15359113,-p@chr2:15359103..15359113
-
Hg19::chr2:188430478..188430496,-p16@TFPI
Hg19::chr2:202004516..202004536,+p68@CFLAR
Hg19::chr3:121286771..121286805,+p1@ARGFX
Hg19::chr3:12200340..12200366,-p2@TIMP4
Hg19::chr3:123033372..123033391,-p12@ADCY5
Hg19::chr3:123033401..123033424,-p10@ADCY5
Hg19::chr3:47155553..47155568,-p@chr3:47155553..47155568
-
Hg19::chr4:151970682..151970693,-p@chr4:151970682..151970693
-
Hg19::chr4:165953174..165953189,+p1@TRIM60
Hg19::chr4:24509678..24509683,+p@chr4:24509678..24509683
+
Hg19::chr4:4049981..4049985,-p@chr4:4049981..4049985
-
Hg19::chr5:133984068..133984080,+p14@SEC24A
Hg19::chr5:134260439..134260448,-p@chr5:134260439..134260448
-
Hg19::chr5:23238053..23238064,-p@chr5:23238053..23238064
-
Hg19::chr5:75493822..75493845,-p@chr5:75493822..75493845
-
Hg19::chr5:81277144..81277166,+p@chr5:81277144..81277166
+
Hg19::chr6:15022142..15022148,-p@chr6:15022142..15022148
-
Hg19::chr6:161304316..161304322,+p@chr6:161304316..161304322
+
Hg19::chr6:43392420..43392440,+p@chr6:43392420..43392440
+
Hg19::chr6:6032547..6032560,-p@chr6:6032547..6032560
-
Hg19::chr6:73933968..73933992,-p@chr6:73933968..73933992
-
Hg19::chr6:73934008..73934023,-p@chr6:73934008..73934023
-
Hg19::chr6:73935069..73935097,-p6@KHDC1L
Hg19::chr6:73935132..73935142,-p7@KHDC1L
Hg19::chr6:73935150..73935162,-p3@KHDC1L
Hg19::chr6:73935163..73935172,-p4@KHDC1L
Hg19::chr6:73935193..73935256,-p1@KHDC1L
Hg19::chr6:74072375..74072388,+p1@C6orf221
Hg19::chr7:152251017..152251036,+p@chr7:152251017..152251036
+
Hg19::chr7:30956234..30956256,-p@chr7:30956234..30956256
-
Hg19::chr7:57509877..57509895,+p1@ZNF716
Hg19::chr7:57509910..57509917,+p2@ZNF716
Hg19::chr8:129629467..129629494,-p@chr8:129629467..129629494
-
Hg19::chr8:145700990..145701000,-p4@FOXH1
Hg19::chr8:145701030..145701041,-p3@FOXH1
Hg19::chr8:27834637..27834645,-p@chr8:27834637..27834645
-
Hg19::chr8:37685815..37685822,+p@chr8:37685815..37685822
+
Hg19::chr8:37685860..37685864,+p@chr8:37685860..37685864
+
Hg19::chr9:134782494..134782517,+p@chr9:134782494..134782517
+
Hg19::chr9:85470564..85470567,-p@chr9:85470564..85470567
-


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>

Cell Type
Ontology termp-valuen
germ line cell1.79e-757
germ cell1.79e-757
embryonic stem cell4.63e-275
melanocyte4.24e-1410
melanoblast4.24e-1410
pigment cell2.29e-1014
neurecto-epithelial cell1.52e-0720
Uber Anatomy
Ontology termp-valuen
testis3.66e-668
male reproductive organ2.24e-4811
gonad9.82e-2621
indifferent external genitalia9.82e-2621
indifferent gonad9.82e-2621
gonad primordium9.82e-2621
external genitalia1.34e-2422
male organism1.34e-2422
male reproductive system1.34e-2422
body cavity4.14e-1246
reproductive organ1.25e-1148
body cavity or lining2.10e-1149
body cavity precursor2.12e-1054
reproductive structure1.45e-0959
reproductive system1.45e-0959
anatomical cavity2.88e-0961
Disease
Ontology termp-valuen
germ cell and embryonal cancer1.34e-2422
germ cell cancer1.34e-2422


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.10.00151321
MA0004.10.494764
MA0006.10.0269763
MA0007.10.654581
MA0009.11.287
MA0014.10.00352657
MA0017.10.189254
MA0019.10.224316
MA0024.10.96824
MA0025.10.579751
MA0027.11.5069
MA0028.10.147366
MA0029.10.293026
MA0030.10.0821763
MA0031.10.465879
MA0038.10.851473
MA0040.11.04229
MA0041.10.348421
MA0042.11.97381
MA0043.10.396497
MA0046.10.382264
MA0048.10.00180444
MA0050.10.151181
MA0051.10.164761
MA0052.10.090859
MA0055.10.000484486
MA0056.10
MA0057.10.152522
MA0058.10.136122
MA0059.10.134313
MA0060.10.254572
MA0061.10.062832
MA0063.10
MA0066.10.337377
MA0067.10.324756
MA0068.13.37304
MA0069.10.758385
MA0070.10.36347
MA0071.10.265944
MA0072.10.357927
MA0073.10.000362314
MA0074.10.327044
MA0076.10.0790138
MA0077.10.348502
MA0078.10.858824
MA0081.10.380261
MA0083.10.806966
MA0084.10.471517
MA0087.10.354926
MA0088.10.638836
MA0089.10
MA0090.10.694577
MA0091.10.171206
MA0092.10.123763
MA0093.10.336511
MA0095.10
MA0098.10
MA0100.10.0713489
MA0101.10.131511
MA0103.10.809095
MA0105.10.0278241
MA0106.10.0870718
MA0107.10.0199419
MA0108.22.24768
MA0109.10
MA0111.10.105889
MA0113.10.022441
MA0114.10.788186
MA0115.10.27019
MA0116.11.31037
MA0117.10.445283
MA0119.10.20475
MA0122.10.15907
MA0124.10.242119
MA0125.10.189092
MA0130.10
MA0131.10.13704
MA0132.10
MA0133.10
MA0135.10.141175
MA0136.10.177531
MA0139.10.00491258
MA0140.10.698472
MA0141.10.374387
MA0142.13.92657
MA0143.12.97133
MA0144.10.0131145
MA0145.10.0583352
MA0146.10.833116
MA0147.10.0502534
MA0148.10.0318793
MA0149.10.245143
MA0062.20.0557498
MA0035.21.72404
MA0039.20.835202
MA0138.20.124147
MA0002.20.212713
MA0137.20.0380256
MA0104.20.0149793
MA0047.20.394685
MA0112.20.836335
MA0065.22.11367
MA0150.10.463285
MA0151.10
MA0152.11.02586
MA0153.10.179116
MA0154.10.79525
MA0155.10.1121
MA0156.10.039287
MA0157.10.364034
MA0158.10
MA0159.10.254944
MA0160.10.900442
MA0161.10
MA0162.10.000417684
MA0163.10.270556
MA0164.10.105624
MA0080.20.126507
MA0018.20.423108
MA0099.20.470736
MA0079.20.118677
MA0102.20.502475
MA0258.10.468968
MA0259.10.108147
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

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