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Coexpression cluster:C479: Difference between revisions

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|tf_chipseq_enrich=FOS#2353;9:4.04907988900248:0.000137120465571173:0.00179233095166304!FOSL1#8061;4:7.9427159432746:0.00140810811969651:0.00915699899831778!GATA2#2624;9:5.7352192800993:8.47144559106153e-06:0.000230824238477661!JUN#3725;10:6.25641459616817:9.23595229958234e-07:3.96462647848779e-05!JUNB#3726;7:10.7137214309374:2.10748306822698e-06:7.68249298996711e-05!JUND#3727;8:2.79786557674841:0.00438315797599601:0.0207747962720693!SETDB1#9869;4:8.0640052356021:0.00133174166295161:0.00883982252046546!STAT3#6774;6:3.15583949914627:0.008838341522291:0.0335502326262694!USF2#7392;7:4.54726908477436:0.000504082156194133:0.00444193691450887
|tf_chipseq_enrich=FOS#2353;9:4.04907988900248:0.000137120465571173:0.00179233095166304!FOSL1#8061;4:7.9427159432746:0.00140810811969651:0.00915699899831778!GATA2#2624;9:5.7352192800993:8.47144559106153e-06:0.000230824238477661!JUN#3725;10:6.25641459616817:9.23595229958234e-07:3.96462647848779e-05!JUNB#3726;7:10.7137214309374:2.10748306822698e-06:7.68249298996711e-05!JUND#3727;8:2.79786557674841:0.00438315797599601:0.0207747962720693!SETDB1#9869;4:8.0640052356021:0.00133174166295161:0.00883982252046546!STAT3#6774;6:3.15583949914627:0.008838341522291:0.0335502326262694!USF2#7392;7:4.54726908477436:0.000504082156194133:0.00444193691450887
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|tfbs_overrepresentation_for_novel_motifs=0.111472,0.217429,0.107302,0.19904,1.50281,0.574869,0.253108,0.324098,0.31878,0.00692657,0.524908,0.286323,0.442397,0.684702,2.6776,0.319274,0.43322,0.0591229,0.256938,0.176245,1.16734,0.176757,0.192508,0.589118,0.134089,0.304148,1.29742,0.558352,0.0865304,0.33292,0.162709,0.465029,0.393386,0.0955518,0.0681935,0.0638435,0.0667305,0.1987,0.453893,0.282055,0.0675531,0.152186,0.210363,0.283867,0.151936,0.125045,0.253928,0.169954,0.186425,0.0865963,0.315441,0.262847,0.63074,0.532773,0.671855,0.246686,0.298409,0.222594,0.0630426,0.221865,0.500944,0.255713,0.319823,0.409576,0.269358,1.75788,0.754286,1.10771,0.456006,0.950487,0.143869,0.144782,0.105378,0.670004,0.020227,0.390082,0.351133,0.395294,1.14905,0.130356,0.266362,0.408665,0.269087,0.0355014,0.622646,0.000236156,0.00447196,0.0123399,0.336397,1.20481,0.84263,0.598,1.20603,0.409701,0.288936,0.0539379,0.25404,0.517267,0.340143,0.0485661,0.794596,0.474756,0.512318,0.436368,0.371019,0.174162,0.422802,0.67874,0.133935,0.0770225,0.364924,0.509866,0.104228,0.183573,0.797061,0.23451,0.00333426,0.487455,0.986905,3.29611,0.662347,0.889041,0.195973,0.277756,0.90249,0.395934,0.248345,0.484077,0.701879,0.200186,2.48335,0.164582,0.715286,0.275188,0.854902,0.0111458,0.932181,0.191402,0.814541,1.65405,1.25623,0.779227,0.249639,0.514137,0.372477,0.216494,4.50825,1.49614,0.457994,0.178999,0.030735,0.0117055,0.598976,0.127482,0.255347,0.980005,0.864245,0.0779979,0.134125,0.116987,0.77808,0.582159,6.39744,0.118854,0.385896,0.740042,0.375051,0.252107,0.0689247
}}
}}

Revision as of 14:15, 26 November 2012


Full id: C479_pleomorphic_mesothelioma_cholangiocellular_melanoma_Saos2_serous_glioblastoma



Phase1 CAGE Peaks

Hg19::chr11:66800552..66800553,+p@chr11:66800552..66800553
+
Hg19::chr1:224716846..224716914,+p4@CNIH3
Hg19::chr1:224716919..224716927,+p31@CNIH3
Hg19::chr1:224716955..224716961,+p30@CNIH3
Hg19::chr1:224716964..224716967,+p33@CNIH3
Hg19::chr20:44410265..44410286,-p@chr20:44410265..44410286
-
Hg19::chr2:147702122..147702148,-p@chr2:147702122..147702148
-
Hg19::chr2:147744107..147744108,-p@chr2:147744107..147744108
-
Hg19::chr2:154449717..154449762,-p3@ENST00000424322
Hg19::chr2:231825896..231825916,-p5@GPR55
Hg19::chr3:106393655..106393659,+p@chr3:106393655..106393659
+
Hg19::chr3:168808463..168808491,-p@chr3:168808463..168808491
-
Hg19::chr4:57931763..57931773,-p3@ENST00000512512
Hg19::chr4:57931786..57931797,-p2@ENST00000512512
Hg19::chr4:57931805..57931824,-p1@ENST00000512512
Hg19::chr6:55911444..55911446,-p@chr6:55911444..55911446
-
Hg19::chr6:56803369..56803378,-p@chr6:56803369..56803378
-
Hg19::chr6:56803379..56803390,-p@chr6:56803379..56803390
-
Hg19::chr6:56803460..56803471,-p@chr6:56803460..56803471
-
Hg19::chrX:31582142..31582159,+p@chrX:31582142..31582159
+


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>


Uber Anatomy
Ontology termp-valuen
intralobular bile duct9.91e-411
acinus9.91e-411
intrahepatic bile duct9.91e-411
portal lobule9.91e-411
hepatic acinus9.91e-411
liver parenchyma1.40e-143
liver lobule1.40e-143
hepatic duct1.40e-143
liver1.99e-0919
digestive gland1.99e-0919
liver bud1.99e-0919
hepatic diverticulum2.82e-0822
liver primordium2.82e-0822
digestive tract diverticulum5.87e-0823
bile duct5.92e-086
digestive system duct5.92e-086
epithelial sac2.14e-0725
epithelium of foregut-midgut junction2.14e-0725
anatomical boundary2.14e-0725
hepatobiliary system2.14e-0725
foregut-midgut junction2.14e-0725
septum transversum2.14e-0725
sac3.78e-0726
Disease
Ontology termp-valuen
pleomorphic carcinoma6.62e-411
nervous system cancer3.31e-3011


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
FOS#235394.049079889002480.0001371204655711730.00179233095166304
FOSL1#806147.94271594327460.001408108119696510.00915699899831778
GATA2#262495.73521928009938.47144559106153e-060.000230824238477661
JUN#3725106.256414596168179.23595229958234e-073.96462647848779e-05
JUNB#3726710.71372143093742.10748306822698e-067.68249298996711e-05
JUND#372782.797865576748410.004383157975996010.0207747962720693
SETDB1#986948.06400523560210.001331741662951610.00883982252046546
STAT3#677463.155839499146270.0088383415222910.0335502326262694
USF2#739274.547269084774360.0005040821561941330.00444193691450887



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


This analysis result is provided for C0 - C305 clusters.