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Coexpression cluster:C1284: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000481!2.71e-20!347;UBERON:0000475!3.06e-20!365;UBERON:0000467!8.93e-19!625;UBERON:0000480!1.27e-18!626;UBERON:0000468!1.30e-17!659;UBERON:0000062!3.34e-14!511;UBERON:0000922!5.61e-13!612;UBERON:0002050!5.45e-12!605;UBERON:0005423!5.45e-12!605;UBERON:0000033!5.76e-12!123;UBERON:0000923!1.02e-11!604;UBERON:0005291!1.02e-11!604;UBERON:0006598!1.02e-11!604;UBERON:0002532!1.02e-11!604;UBERON:0000153!5.93e-11!129;UBERON:0007811!5.93e-11!129;UBERON:0000119!7.23e-11!312;UBERON:0000924!8.02e-11!173;UBERON:0006601!8.02e-11!173;UBERON:0000477!8.05e-11!286;UBERON:0000483!1.04e-10!309;UBERON:0004121!2.55e-10!169;UBERON:0005743!8.87e-10!86;UBERON:0000064!1.24e-09!219;UBERON:0001017!1.82e-09!82;UBERON:0000073!2.80e-09!94;UBERON:0001016!2.80e-09!94;UBERON:0004111!3.82e-09!241;UBERON:0003102!4.57e-09!95;UBERON:0001007!5.20e-09!155;UBERON:0001555!5.20e-09!155;UBERON:0007026!5.20e-09!155;UBERON:0000160!6.80e-09!27;UBERON:0005409!9.07e-09!35;UBERON:0004119!4.84e-08!169;UBERON:0000925!4.84e-08!169;UBERON:0006595!4.84e-08!169;UBERON:0000914!6.53e-08!83;UBERON:0002329!6.53e-08!83;UBERON:0003077!6.53e-08!83;UBERON:0003059!6.53e-08!83;UBERON:0007282!6.53e-08!83;UBERON:0009618!6.53e-08!83;UBERON:0007285!6.53e-08!83;UBERON:0002346!1.18e-07!90;UBERON:0002100!2.28e-07!216;UBERON:0003056!3.19e-07!61;UBERON:0003075!3.52e-07!86;UBERON:0007284!3.52e-07!86;UBERON:0000955!5.96e-07!69;UBERON:0006238!5.96e-07!69
|ontology_enrichment_uberon=UBERON:0000481!2.71e-20!347;UBERON:0000475!3.06e-20!365;UBERON:0000467!8.93e-19!625;UBERON:0000480!1.27e-18!626;UBERON:0000468!1.30e-17!659;UBERON:0000062!3.34e-14!511;UBERON:0000922!5.61e-13!612;UBERON:0002050!5.45e-12!605;UBERON:0005423!5.45e-12!605;UBERON:0000033!5.76e-12!123;UBERON:0000923!1.02e-11!604;UBERON:0005291!1.02e-11!604;UBERON:0006598!1.02e-11!604;UBERON:0002532!1.02e-11!604;UBERON:0000153!5.93e-11!129;UBERON:0007811!5.93e-11!129;UBERON:0000119!7.23e-11!312;UBERON:0000924!8.02e-11!173;UBERON:0006601!8.02e-11!173;UBERON:0000477!8.05e-11!286;UBERON:0000483!1.04e-10!309;UBERON:0004121!2.55e-10!169;UBERON:0005743!8.87e-10!86;UBERON:0000064!1.24e-09!219;UBERON:0001017!1.82e-09!82;UBERON:0000073!2.80e-09!94;UBERON:0001016!2.80e-09!94;UBERON:0004111!3.82e-09!241;UBERON:0003102!4.57e-09!95;UBERON:0001007!5.20e-09!155;UBERON:0001555!5.20e-09!155;UBERON:0007026!5.20e-09!155;UBERON:0000160!6.80e-09!27;UBERON:0005409!9.07e-09!35;UBERON:0004119!4.84e-08!169;UBERON:0000925!4.84e-08!169;UBERON:0006595!4.84e-08!169;UBERON:0000914!6.53e-08!83;UBERON:0002329!6.53e-08!83;UBERON:0003077!6.53e-08!83;UBERON:0003059!6.53e-08!83;UBERON:0007282!6.53e-08!83;UBERON:0009618!6.53e-08!83;UBERON:0007285!6.53e-08!83;UBERON:0002346!1.18e-07!90;UBERON:0002100!2.28e-07!216;UBERON:0003056!3.19e-07!61;UBERON:0003075!3.52e-07!86;UBERON:0007284!3.52e-07!86;UBERON:0000955!5.96e-07!69;UBERON:0006238!5.96e-07!69
|tf_chipseq_enrich=CTCF#10664;7:5.36025637307503:7.86114662284756e-06:0.000222556327498936!EP300#2033;7:6.7739417262232:1.52695018318475e-06:5.86945712851058e-05!JUND#3727;7:6.99466394187103:1.21993360047445e-06:4.9287677098627e-05!POLR2A#5430;7:2.14745317655807:0.00474763644761028:0.0223602436505962!SIN3A#25942;7:5.40888472681514:7.3795239773719e-06:0.000211733545239765!TAF1#6872;7:3.34304628574529:0.000214233631962245:0.00246875717626668!TCF7L2#6934;7:10.7701765631373:5.9423478161588e-08:3.69852719649469e-06!TRIM28#10155;7:18.5905250452625:1.300439693691e-09:1.17488426617123e-07!ZZZ3#26009;7:239.413212435233:2.15856704034244e-17:4.51780727708064e-15
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}}
}}

Revision as of 12:44, 5 September 2012


Full id: C1284_mucinous_ductal_small_endometrial_adrenal_extraskeletal_large



Phase1 CAGE Peaks

Hg19::chr7:83824097..83824114,-p1@SEMA3A
Hg19::chr7:83824169..83824176,-p6@SEMA3A
Hg19::chr7:83824279..83824295,-p7@SEMA3A
Hg19::chr7:83824296..83824315,-p2@SEMA3A
Hg19::chr7:83824392..83824434,-p3@SEMA3A
Hg19::chr7:83824449..83824496,-p4@SEMA3A
Hg19::chr7:83824512..83824536,-p10@SEMA3A


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><br>


Cell Type
Ontology termp-valuen
non-terminally differentiated cell2.35e-15180
fibroblast6.56e-0975
electrically responsive cell2.07e-0760
electrically active cell2.07e-0760
skin fibroblast2.77e-0723
Uber Anatomy
Ontology termp-valuen
multi-tissue structure2.71e-20347
organism subdivision3.06e-20365
anatomical system8.93e-19625
anatomical group1.27e-18626
multi-cellular organism1.30e-17659
organ3.34e-14511
embryo5.61e-13612
embryonic structure5.45e-12605
developing anatomical structure5.45e-12605
head5.76e-12123
germ layer1.02e-11604
embryonic tissue1.02e-11604
presumptive structure1.02e-11604
epiblast (generic)1.02e-11604
anterior region of body5.93e-11129
craniocervical region5.93e-11129
cell layer7.23e-11312
ectoderm8.02e-11173
presumptive ectoderm8.02e-11173
anatomical cluster8.05e-11286
epithelium1.04e-10309
ectoderm-derived structure2.55e-10169
organ part1.24e-09219
central nervous system1.82e-0982
regional part of nervous system2.80e-0994
nervous system2.80e-0994
anatomical conduit3.82e-09241
surface structure4.57e-0995
digestive system5.20e-09155
digestive tract5.20e-09155
primitive gut5.20e-09155
intestine6.80e-0927
gastrointestinal system9.07e-0935
endoderm-derived structure4.84e-08169
endoderm4.84e-08169
presumptive endoderm4.84e-08169
somite6.53e-0883
paraxial mesoderm6.53e-0883
presomitic mesoderm6.53e-0883
presumptive segmental plate6.53e-0883
trunk paraxial mesoderm6.53e-0883
presumptive paraxial mesoderm6.53e-0883
neurectoderm1.18e-0790
trunk2.28e-07216
pre-chordal neural plate3.19e-0761
neural plate3.52e-0786
presumptive neural plate3.52e-0786
brain5.96e-0769
future brain5.96e-0769


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
CTCF#1066475.360256373075037.86114662284756e-060.000222556327498936
EP300#203376.77394172622321.52695018318475e-065.86945712851058e-05
JUND#372776.994663941871031.21993360047445e-064.9287677098627e-05
POLR2A#543072.147453176558070.004747636447610280.0223602436505962
SIN3A#2594275.408884726815147.3795239773719e-060.000211733545239765
TAF1#687273.343046285745290.0002142336319622450.00246875717626668
TCF7L2#6934710.77017656313735.9423478161588e-083.69852719649469e-06
TRIM28#10155718.59052504526251.300439693691e-091.17488426617123e-07
ZZZ3#260097239.4132124352332.15856704034244e-174.51780727708064e-15



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.