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Coexpression cluster:C89

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Full id: C89_small_retinoblastoma_medulloblastoma_iPS_acantholytic_eye_bronchogenic



Phase1 CAGE Peaks

Hg19::chr10:113190125..113190134,+p@chr10:113190125..113190134
+
Hg19::chr10:129346546..129346561,+p@chr10:129346546..129346561
+
Hg19::chr10:61515407..61515414,-p@chr10:61515407..61515414
-
Hg19::chr10:72370054..72370064,+p1@ENST00000500803
Hg19::chr10:74714458..74714477,-p3@PLA2G12B
Hg19::chr10:74714487..74714498,-p4@PLA2G12B
Hg19::chr11:111364948..111364961,-p@chr11:111364948..111364961
-
Hg19::chr11:20538015..20538023,-p@chr11:20538015..20538023
-
Hg19::chr11:73475071..73475076,-p@chr11:73475071..73475076
-
Hg19::chr11:95994394..95994403,+p@chr11:95994394..95994403
+
Hg19::chr11:98528704..98528712,+p@chr11:98528704..98528712
+
Hg19::chr12:133040060..133040064,+p@chr12:133040060..133040064
+
Hg19::chr12:22421536..22421552,-p4@ST8SIA1
Hg19::chr12:54431666..54431676,+p16@HOXC4
Hg19::chr12:54431694..54431704,+p17@HOXC4
Hg19::chr12:54431720..54431732,+p13@HOXC4
Hg19::chr12:54567359..54567401,-p@chr12:54567359..54567401
-
Hg19::chr13:21477124..21477144,-p3@XPO4
Hg19::chr13:26155734..26155742,+p@chr13:26155734..26155742
+
Hg19::chr13:76481510..76481517,+p@chr13:76481510..76481517
+
Hg19::chr13:76515062..76515068,+p@chr13:76515062..76515068
+
Hg19::chr13:76549637..76549662,+p@chr13:76549637..76549662
+
Hg19::chr13:76554315..76554319,+p@chr13:76554315..76554319
+
Hg19::chr13:76563913..76563916,+p@chr13:76563913..76563916
+
Hg19::chr13:76688920..76688924,+p@chr13:76688920..76688924
+
Hg19::chr13:76694533..76694542,+p@chr13:76694533..76694542
+
Hg19::chr13:76755731..76755739,+p@chr13:76755731..76755739
+
Hg19::chr13:93957776..93957797,+p@chr13:93957776..93957797
+
Hg19::chr13:95133267..95133279,-p@chr13:95133267..95133279
-
Hg19::chr13:95133382..95133389,-p@chr13:95133382..95133389
-
Hg19::chr14:23835464..23835478,-p@chr14:23835464..23835478
-
Hg19::chr14:32684998..32685005,+p@chr14:32684998..32685005
+
Hg19::chr14:32685029..32685039,+p@chr14:32685029..32685039
+
Hg19::chr14:32685046..32685057,+p@chr14:32685046..32685057
+
Hg19::chr14:56584414..56584464,+p18@PELI2
Hg19::chr14:57273996..57274007,-p@chr14:57273996..57274007
-
Hg19::chr14:57274753..57274759,-p@chr14:57274753..57274759
-
Hg19::chr14:57277357..57277384,-p5@OTX2
Hg19::chr14:57283471..57283510,-p@chr14:57283471..57283510
-
Hg19::chr14:58045730..58045732,-p@chr14:58045730..58045732
-
Hg19::chr14:58045800..58045814,-p@chr14:58045800..58045814
-
Hg19::chr14:58264837..58264840,-p@chr14:58264837..58264840
-
Hg19::chr14:58331575..58331582,-p@chr14:58331575..58331582
-
Hg19::chr14:58331678..58331725,-p@chr14:58331678..58331725
-
Hg19::chr14:58332762..58332773,-p5@SLC35F4
Hg19::chr14:58332774..58332786,-p4@SLC35F4
Hg19::chr14:58332793..58332817,-p1@SLC35F4
Hg19::chr14:58415850..58415853,-p@chr14:58415850..58415853
-
Hg19::chr14:58439259..58439262,-p@chr14:58439259..58439262
-
Hg19::chr14:58448696..58448733,-p9@SLC35F4
Hg19::chr14:58449672..58449684,-p@chr14:58449672..58449684
-
Hg19::chr14:58449882..58449909,-p@chr14:58449882..58449909
-
Hg19::chr14:59113338..59113345,+p@chr14:59113338..59113345
+
Hg19::chr14:59113347..59113360,+p@chr14:59113347..59113360
+
Hg19::chr14:59132994..59133018,+p@chr14:59132994..59133018
+
Hg19::chr14:60194043..60194066,-p18@RTN1
Hg19::chr14:60194070..60194083,-p25@RTN1
Hg19::chr14:60194267..60194275,-p20@RTN1
Hg19::chr14:60194285..60194311,-p10@RTN1
Hg19::chr14:60194318..60194325,-p22@RTN1
Hg19::chr14:60194331..60194336,-p36@RTN1
Hg19::chr14:60194347..60194365,-p17@RTN1
Hg19::chr14:60194368..60194387,-p11@RTN1
Hg19::chr14:60194446..60194457,-p16@RTN1
Hg19::chr14:60194459..60194462,-p43@RTN1
Hg19::chr14:60958049..60958051,-p@chr14:60958049..60958051
-
Hg19::chr14:73807668..73807689,+p@chr14:73807668..73807689
+
Hg19::chr14:83609315..83609322,-p@chr14:83609315..83609322
-
Hg19::chr15:48312676..48312679,+p@chr15:48312676..48312679
+
Hg19::chr15:63578231..63578240,+p@chr15:63578231..63578240
+
Hg19::chr15:66386837..66386846,-p@chr15:66386837..66386846
-
Hg19::chr15:85564362..85564385,+p@chr15:85564362..85564385
+
Hg19::chr16:13010455..13010466,+p@chr16:13010455..13010466
+
Hg19::chr16:13010527..13010543,+p@chr16:13010527..13010543
+
Hg19::chr16:13010548..13010555,+p@chr16:13010548..13010555
+
Hg19::chr16:13010571..13010578,+p@chr16:13010571..13010578
+
Hg19::chr16:13010590..13010593,+p@chr16:13010590..13010593
+
Hg19::chr16:72029085..72029092,-p@chr16:72029085..72029092
-
Hg19::chr16:7411388..7411391,+p@chr16:7411388..7411391
+
Hg19::chr17:1944790..1944809,+p4@OVCA2
Hg19::chr17:20771531..20771548,-p1@CCDC144NL
Hg19::chr17:20771796..20771807,+p2@ENST00000439794
Hg19::chr17:20771833..20771846,+p1@ENST00000439794
Hg19::chr17:20807198..20807204,+p@chr17:20807198..20807204
+
Hg19::chr17:70939741..70939790,-p@chr17:70939741..70939790
-
Hg19::chr17:70940275..70940283,+p@chr17:70940275..70940283
+
Hg19::chr17:7111644..7111669,-p@chr17:7111644..7111669
-
Hg19::chr17:9725394..9725400,-p1@ENST00000399363
Hg19::chr18:22212559..22212569,+p@chr18:22212559..22212569
+
Hg19::chr18:55780205..55780223,+p@chr18:55780205..55780223
+
Hg19::chr18:6928495..6928520,-p2@LOC400643
Hg19::chr19:42600094..42600110,-p11@POU2F2
Hg19::chr19:44057957..44057961,-p@chr19:44057957..44057961
-
Hg19::chr19:50323482..50323485,-p@chr19:50323482..50323485
-
Hg19::chr19:7834829..7834834,+p@chr19:7834829..7834834
+
Hg19::chr1:100110807..100110818,+p@chr1:100110807..100110818
+
Hg19::chr1:100110851..100110860,+p@chr1:100110851..100110860
+
Hg19::chr1:11640241..11640246,-p@chr1:11640241..11640246
-
Hg19::chr1:179139285..179139296,-p@chr1:179139285..179139296
-
Hg19::chr1:186430270..186430273,-p2@PDC
Hg19::chr1:211660689..211660695,+p@chr1:211660689..211660695
+
Hg19::chr1:223670577..223670594,+p@chr1:223670577..223670594
+
Hg19::chr1:234816066..234816079,+p@chr1:234816066..234816079
+
Hg19::chr1:33705218..33705225,-p@chr1:33705218..33705225
-
Hg19::chr1:50570200..50570209,+p@chr1:50570200..50570209
+
Hg19::chr20:13085064..13085070,+p@chr20:13085064..13085070
+
Hg19::chr20:33293061..33293072,+p@chr20:33293061..33293072
+
Hg19::chr20:33293077..33293086,+p@chr20:33293077..33293086
+
Hg19::chr20:43324746..43324769,-p1@ENST00000415889
Hg19::chr20:45418126..45418131,-p@chr20:45418126..45418131
-
Hg19::chr20:45434137..45434157,-p@chr20:45434137..45434157
-
Hg19::chr20:54085022..54085026,+p@chr20:54085022..54085026
+
Hg19::chr20:54101133..54101144,+p@chr20:54101133..54101144
+
Hg19::chr21:45682336..45682380,-p5@DNMT3L
Hg19::chr2:138685510..138685520,-p@chr2:138685510..138685520
-
Hg19::chr2:171217277..171217289,+p@chr2:171217277..171217289
+
Hg19::chr2:171217290..171217297,+p@chr2:171217290..171217297
+
Hg19::chr2:194837773..194837784,-p@chr2:194837773..194837784
-
Hg19::chr2:202413051..202413061,-p@chr2:202413051..202413061
-
Hg19::chr2:211532710..211532719,+p@chr2:211532710..211532719
+
Hg19::chr2:215345586..215345590,-p@chr2:215345586..215345590
-
Hg19::chr2:238760492..238760502,+p@chr2:238760492..238760502
+
Hg19::chr2:45168589..45168601,-p2@ENST00000456467
Hg19::chr2:45168633..45168642,-p3@ENST00000456467
Hg19::chr2:48274495..48274509,+p@chr2:48274495..48274509
+
Hg19::chr2:51255337..51255346,+p@chr2:51255337..51255346
+
Hg19::chr2:51255348..51255351,+p@chr2:51255348..51255351
+
Hg19::chr2:55932549..55932580,+p@chr2:55932549..55932580
+
Hg19::chr2:56179262..56179285,+p1@uc002rzk.2
Hg19::chr2:68113370..68113379,-p@chr2:68113370..68113379
-
Hg19::chr2:74740360..74740369,-p@chr2:74740360..74740369
-
Hg19::chr2:8803669..8803680,-p@chr2:8803669..8803680
-
Hg19::chr3:1991867..1991875,-p@chr3:1991867..1991875
-
Hg19::chr3:24206925..24206928,-p29@THRB
Hg19::chr3:24206971..24206999,-p8@THRB
Hg19::chr3:24207018..24207024,-p22@THRB
Hg19::chr3:24207029..24207032,-p37@THRB
Hg19::chr3:24207039..24207050,-p16@THRB
Hg19::chr3:24207220..24207235,-p18@THRB
Hg19::chr3:77129779..77129782,+p@chr3:77129779..77129782
+
Hg19::chr4:169849979..169849990,-p@chr4:169849979..169849990
-
Hg19::chr4:178653531..178653568,+p@chr4:178653531..178653568
+
Hg19::chr4:41749788..41749795,-p10@PHOX2B
Hg19::chr4:41750020..41750029,-p9@PHOX2B
Hg19::chr5:133179082..133179101,-p@chr5:133179082..133179101
-
Hg19::chr5:133191186..133191195,-p6@FSTL4
Hg19::chr5:151338426..151338430,+p1@ENST00000524034
Hg19::chr5:57935348..57935354,-p@chr5:57935348..57935354
-
Hg19::chr5:6961030..6961034,+p@chr5:6961030..6961034
+
Hg19::chr6:125378873..125378876,+p@chr6:125378873..125378876
+
Hg19::chr6:125378908..125378919,+p@chr6:125378908..125378919
+
Hg19::chr6:14592435..14592475,+p@chr6:14592435..14592475
+
Hg19::chr6:17845348..17845358,-p@chr6:17845348..17845358
-
Hg19::chr6:24539757..24539763,-p@chr6:24539757..24539763
-
Hg19::chr6:24539768..24539782,-p@chr6:24539768..24539782
-
Hg19::chr6:44681761..44681769,-p@chr6:44681761..44681769
-
Hg19::chr6:5555405..5555407,+p@chr6:5555405..5555407
+
Hg19::chr7:107369031..107369037,-p@chr7:107369031..107369037
-
Hg19::chr7:111234799..111234807,-p@chr7:111234799..111234807
-
Hg19::chr7:39018314..39018323,+p@chr7:39018314..39018323
+
Hg19::chr7:39018325..39018336,+p@chr7:39018325..39018336
+
Hg19::chr7:7749088..7749127,+p@chr7:7749088..7749127
+
Hg19::chr8:128311072..128311082,-p@chr8:128311072..128311082
-
Hg19::chr8:128658112..128658115,-p@chr8:128658112..128658115
-
Hg19::chr8:128658139..128658148,-p@chr8:128658139..128658148
-
Hg19::chr8:139194385..139194397,-p@chr8:139194385..139194397
-
Hg19::chr8:139510692..139510697,-p@chr8:139510692..139510697
-
Hg19::chr8:20917459..20917465,-p@chr8:20917459..20917465
-
Hg19::chr8:72252453..72252458,-p@chr8:72252453..72252458
-
Hg19::chr8:97961177..97961185,-p@chr8:97961177..97961185
-
Hg19::chr8:97961449..97961460,-p@chr8:97961449..97961460
-
Hg19::chr8:97961686..97961696,-p@chr8:97961686..97961696
-
Hg19::chr8:97962018..97962029,-p@chr8:97962018..97962029
-
Hg19::chr8:97964849..97964868,-p@chr8:97964849..97964868
-
Hg19::chr8:97965705..97965721,-p@chr8:97965705..97965721
-
Hg19::chr8:97972117..97972120,-p@chr8:97972117..97972120
-
Hg19::chr8:98014001..98014041,-p@chr8:98014001..98014041
-
Hg19::chr8:98015305..98015315,-p@chr8:98015305..98015315
-
Hg19::chr8:98015616..98015617,-p@chr8:98015616..98015617
-
Hg19::chr8:98015654..98015697,-p@chr8:98015654..98015697
-
Hg19::chr8:98043381..98043387,-p@chr8:98043381..98043387
-
Hg19::chr8:98051049..98051058,-p@chr8:98051049..98051058
-
Hg19::chr8:98065877..98065881,-p@chr8:98065877..98065881
-
Hg19::chr8:98066259..98066270,-p@chr8:98066259..98066270
-
Hg19::chr8:98070371..98070384,-p@chr8:98070371..98070384
-
Hg19::chr8:98073725..98073731,-p@chr8:98073725..98073731
-
Hg19::chr8:98075951..98075959,-p@chr8:98075951..98075959
-
Hg19::chr8:98080543..98080550,-p@chr8:98080543..98080550
-
Hg19::chr8:98103977..98103981,-p@chr8:98103977..98103981
-
Hg19::chr8:98104439..98104444,-p@chr8:98104439..98104444
-
Hg19::chr8:98108427..98108430,-p@chr8:98108427..98108430
-
Hg19::chr8:98108435..98108438,-p@chr8:98108435..98108438
-
Hg19::chr9:101928133..101928155,+p@chr9:101928133..101928155
+
Hg19::chr9:125306070..125306106,+p@chr9:125306070..125306106
+
Hg19::chr9:17454025..17454033,+p@chr9:17454025..17454033
+
Hg19::chr9:17454052..17454060,+p@chr9:17454052..17454060
+
Hg19::chr9:17454062..17454088,+p@chr9:17454062..17454088
+
Hg19::chr9:17457123..17457129,+p@chr9:17457123..17457129
+
Hg19::chr9:226208..226216,-p@chr9:226208..226216
-
Hg19::chr9:33677441..33677472,+p@chr9:33677441..33677472
+
Hg19::chrX:10852011..10852021,-p27@MID1
Hg19::chrX:114606584..114606590,+p@chrX:114606584..114606590
+
Hg19::chrX:135761733..135761754,-p@chrX:135761733..135761754
-
Hg19::chrX:135761770..135761786,-p@chrX:135761770..135761786
-
Hg19::chrX:135761795..135761849,-p@chrX:135761795..135761849
-
Hg19::chrX:135761853..135761876,-p@chrX:135761853..135761876
-
Hg19::chrX:135761931..135761934,-p@chrX:135761931..135761934
-
Hg19::chrX:135764624..135764645,-p@chrX:135764624..135764645
-
Hg19::chrX:48394285..48394295,+p@chrX:48394285..48394295
+
Hg19::chrX:64917108..64917119,+p@chrX:64917108..64917119
+
Hg19::chrX:64917135..64917146,+p@chrX:64917135..64917146
+
Hg19::chrX:97443927..97443947,+p@chrX:97443927..97443947
+


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

p.valueFDRnGenesnPathwayName
7.83036217125079e-050.0495661925440175221{POU2F1,21} (Static Module):NA



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

GO IDGO nameFDR corrected p-value
GO:0043565sequence-specific DNA binding0.00984692052000621
GO:0032501multicellular organismal process0.0184043811554295
GO:0007275multicellular organismal development0.0208285303637392
GO:0042706eye photoreceptor cell fate commitment0.0208285303637392
GO:0046552photoreceptor cell fate commitment0.0208285303637392
GO:0003700transcription factor activity0.0208285303637392
GO:0040036regulation of fibroblast growth factor receptor signaling pathway0.0434788203863315
GO:0007389pattern specification process0.0434788203863315
GO:0003828alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity0.0434788203863315
GO:0031301integral to organelle membrane0.0434788203863315
GO:0043231intracellular membrane-bound organelle0.0434788203863315
GO:0043227membrane-bound organelle0.0434788203863315
GO:0031300intrinsic to organelle membrane0.0434788203863315
GO:0008190eukaryotic initiation factor 4E binding0.0434788203863315
GO:0031369translation initiation factor binding0.0434788203863315
GO:0006349genetic imprinting0.0434788203863315
GO:0032502developmental process0.0434788203863315
GO:0008589regulation of smoothened signaling pathway0.0434788203863315
GO:0001754eye photoreceptor cell differentiation0.0434788203863315
GO:0043229intracellular organelle0.0434788203863315
GO:0043226organelle0.0434788203863315
GO:0030901midbrain development0.0434788203863315
GO:0007399nervous system development0.0434788203863315
GO:0030182neuron differentiation0.0434788203863315
GO:0016564transcription repressor activity0.0434788203863315
GO:0006688glycosphingolipid biosynthetic process0.0434788203863315
GO:0046530photoreceptor cell differentiation0.0434788203863315
GO:0004887thyroid hormone receptor activity0.0434788203863315
GO:0009790embryonic development0.0459553101092688
GO:0044424intracellular part0.0459553101092688
GO:0005720nuclear heterochromatin0.0459553101092688
GO:0048699generation of neurons0.0459553101092688
GO:0010468regulation of gene expression0.0472670367834421
GO:0007224smoothened signaling pathway0.0472670367834421
GO:0048663neuron fate commitment0.0472670367834421
GO:0022008neurogenesis0.0472670367834421
GO:0009247glycolipid biosynthetic process0.0472670367834421
GO:0001708cell fate specification0.0472670367834421
GO:0006643membrane lipid metabolic process0.0472670367834421
GO:0008543fibroblast growth factor receptor signaling pathway0.048631848475914



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><br>uberon_data<br>disease_data<br>

Uber Anatomy
Ontology termp-valuen
regional part of nervous system3.11e-2594
nervous system3.11e-2594
central nervous system5.04e-2282
neurectoderm8.48e-1890
neural tube4.29e-1757
neural rod4.29e-1757
future spinal cord4.29e-1757
neural keel4.29e-1757
neural plate6.20e-1786
presumptive neural plate6.20e-1786
brain1.80e-1669
future brain1.80e-1669
regional part of brain1.52e-1459
regional part of forebrain2.53e-1441
forebrain2.53e-1441
future forebrain2.53e-1441
ectoderm3.99e-14173
presumptive ectoderm3.99e-14173
ectoderm-derived structure2.39e-13169
pre-chordal neural plate2.73e-1361
anterior neural tube3.22e-1342
adult organism8.30e-12115
gray matter2.63e-1134
brain grey matter2.63e-1134
telencephalon5.08e-1134
regional part of telencephalon9.37e-1133
cerebral hemisphere2.39e-1032
anterior region of body3.34e-10129
craniocervical region3.34e-10129
head6.87e-10123
regional part of cerebral cortex2.63e-0822
cerebral cortex3.66e-0825
pallium3.66e-0825
neocortex1.51e-0720
Disease
Ontology termp-valuen
cancer4.26e-15235
disease of cellular proliferation2.84e-13239
cell type cancer5.88e-09143
germ cell and embryonal cancer9.14e-0822
germ cell cancer9.14e-0822
hematologic cancer9.64e-0751
immune system cancer9.64e-0751


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)

{{{tfbs_overrepresentation_jaspar}}}



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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