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|ontology_enrichment_disease=DOID:0050687!1.68e-09!143;DOID:305!4.22e-08!106
|ontology_enrichment_disease=DOID:0050687!1.68e-09!143;DOID:305!4.22e-08!106
|ontology_enrichment_uberon=UBERON:0000481!2.28e-20!347;UBERON:0000475!8.80e-14!365;UBERON:0002100!8.43e-12!216;UBERON:0000468!9.00e-12!659;UBERON:0003104!6.22e-11!238;UBERON:0009142!6.22e-11!238;UBERON:0000064!1.54e-10!219;UBERON:0001007!1.64e-10!155;UBERON:0001555!1.64e-10!155;UBERON:0007026!1.64e-10!155;UBERON:0005156!2.23e-10!59;UBERON:0000990!2.23e-10!59;UBERON:0000922!6.04e-10!612;UBERON:0003886!7.16e-10!63;UBERON:0000464!1.32e-09!104;UBERON:0004119!6.78e-09!169;UBERON:0000925!6.78e-09!169;UBERON:0006595!6.78e-09!169;UBERON:0000477!7.14e-09!286;UBERON:0000483!1.05e-08!309;UBERON:0000119!1.28e-08!312;UBERON:0003064!1.75e-08!37;UBERON:0002553!2.13e-08!70;UBERON:0004458!2.16e-08!49;UBERON:0002323!3.23e-08!46;UBERON:0000062!3.90e-08!511;UBERON:0003101!4.55e-08!22;UBERON:0000079!4.55e-08!22;UBERON:0005409!6.62e-08!35;UBERON:0002050!7.59e-08!605;UBERON:0005423!7.59e-08!605;UBERON:0000923!1.38e-07!604;UBERON:0005291!1.38e-07!604;UBERON:0006598!1.38e-07!604;UBERON:0002532!1.38e-07!604;UBERON:0000467!1.60e-07!625;UBERON:0004921!1.78e-07!129;UBERON:0004185!1.78e-07!129;UBERON:0000480!2.59e-07!626;UBERON:0000466!3.98e-07!126;UBERON:0003133!6.21e-07!48;UBERON:0000160!6.30e-07!27;UBERON:0004122!6.47e-07!15;UBERON:0000077!8.49e-07!130
|ontology_enrichment_uberon=UBERON:0000481!2.28e-20!347;UBERON:0000475!8.80e-14!365;UBERON:0002100!8.43e-12!216;UBERON:0000468!9.00e-12!659;UBERON:0003104!6.22e-11!238;UBERON:0009142!6.22e-11!238;UBERON:0000064!1.54e-10!219;UBERON:0001007!1.64e-10!155;UBERON:0001555!1.64e-10!155;UBERON:0007026!1.64e-10!155;UBERON:0005156!2.23e-10!59;UBERON:0000990!2.23e-10!59;UBERON:0000922!6.04e-10!612;UBERON:0003886!7.16e-10!63;UBERON:0000464!1.32e-09!104;UBERON:0004119!6.78e-09!169;UBERON:0000925!6.78e-09!169;UBERON:0006595!6.78e-09!169;UBERON:0000477!7.14e-09!286;UBERON:0000483!1.05e-08!309;UBERON:0000119!1.28e-08!312;UBERON:0003064!1.75e-08!37;UBERON:0002553!2.13e-08!70;UBERON:0004458!2.16e-08!49;UBERON:0002323!3.23e-08!46;UBERON:0000062!3.90e-08!511;UBERON:0003101!4.55e-08!22;UBERON:0000079!4.55e-08!22;UBERON:0005409!6.62e-08!35;UBERON:0002050!7.59e-08!605;UBERON:0005423!7.59e-08!605;UBERON:0000923!1.38e-07!604;UBERON:0005291!1.38e-07!604;UBERON:0006598!1.38e-07!604;UBERON:0002532!1.38e-07!604;UBERON:0000467!1.60e-07!625;UBERON:0004921!1.78e-07!129;UBERON:0004185!1.78e-07!129;UBERON:0000480!2.59e-07!626;UBERON:0000466!3.98e-07!126;UBERON:0003133!6.21e-07!48;UBERON:0000160!6.30e-07!27;UBERON:0004122!6.47e-07!15;UBERON:0000077!8.49e-07!130
|tf_chipseq_enrich=E2F1#1869;7:4.90738921487932:1.45832274679793e-05:0.000346858960038326!E2F6#1876;7:5.01715573169739:1.24910426162553e-05:0.000308186156342803!FOXA1#3169;4:6.33223985679169:0.00185468101692017:0.010944179373192!HEY1#23462;6:3.46295232266204:0.00126789009587212:0.00850627440886419!POLR2A#5430;7:2.14745317655807:0.00474763644761028:0.0223552030185739!RAD21#5885;7:10.3550338954563:7.82487927673307e-08:4.69938221266662e-06!REST#5978;6:8.27145318525259:7.89289295030691e-06:0.000222911261989482!SIN3A#25942;6:4.63618690869869:0.000235167814635783:0.00256669363494059!TAF1#6872;7:3.34304628574529:0.000214233631962245:0.00246794024801511!TAF7#6879;6:9.79977377564907:2.89681485118392e-06:9.95198836324991e-05!TBP#6908;7:3.70677068709639:0.000103967209750511:0.00145202345802804!TCF7L2#6934;7:10.7701765631373:5.9423478161588e-08:3.69632438101137e-06
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}}
}}

Revision as of 12:41, 5 September 2012


Full id: C1267_bile_placenta_lung_iPS_H9_clear_melanoma



Phase1 CAGE Peaks

Hg19::chr2:189156638..189156667,+p3@GULP1
Hg19::chr2:189157512..189157527,+p6@GULP1
Hg19::chr2:189157536..189157565,+p1@GULP1
Hg19::chr2:189157571..189157576,+p13@GULP1
Hg19::chr2:189157579..189157590,+p9@GULP1
Hg19::chr2:189157647..189157656,+p12@GULP1
Hg19::chr2:189157781..189157803,+p10@GULP1


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
columnar/cuboidal epithelial cell7.29e-0927
non-terminally differentiated cell5.49e-08180
neurectodermal cell2.41e-0759
neurecto-epithelial cell2.82e-0720
epithelial cell4.62e-07254
Uber Anatomy
Ontology termp-valuen
multi-tissue structure2.28e-20347
organism subdivision8.80e-14365
trunk8.43e-12216
multi-cellular organism9.00e-12659
mesenchyme6.22e-11238
entire embryonic mesenchyme6.22e-11238
organ part1.54e-10219
digestive system1.64e-10155
digestive tract1.64e-10155
primitive gut1.64e-10155
reproductive structure2.23e-1059
reproductive system2.23e-1059
embryo6.04e-10612
body cavity precursor7.16e-1063
anatomical space1.32e-09104
endoderm-derived structure6.78e-09169
endoderm6.78e-09169
presumptive endoderm6.78e-09169
anatomical cluster7.14e-09286
epithelium1.05e-08309
cell layer1.28e-08312
intermediate mesoderm1.75e-0837
anatomical cavity2.13e-0870
body cavity or lining2.16e-0849
body cavity3.23e-0846
organ3.90e-08511
male organism4.55e-0822
male reproductive system4.55e-0822
gastrointestinal system6.62e-0835
embryonic structure7.59e-08605
developing anatomical structure7.59e-08605
germ layer1.38e-07604
embryonic tissue1.38e-07604
presumptive structure1.38e-07604
epiblast (generic)1.38e-07604
anatomical system1.60e-07625
subdivision of digestive tract1.78e-07129
endodermal part of digestive tract1.78e-07129
anatomical group2.59e-07626
immaterial anatomical entity3.98e-07126
reproductive organ6.21e-0748
intestine6.30e-0727
genitourinary system6.47e-0715
mixed endoderm/mesoderm-derived structure8.49e-07130
Disease
Ontology termp-valuen
cell type cancer1.68e-09143
carcinoma4.22e-08106


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
E2F1#186974.907389214879321.45832274679793e-050.000346858960038326
E2F6#187675.017155731697391.24910426162553e-050.000308186156342803
FOXA1#316946.332239856791690.001854681016920170.010944179373192
HEY1#2346263.462952322662040.001267890095872120.00850627440886419
POLR2A#543072.147453176558070.004747636447610280.0223552030185739
RAD21#5885710.35503389545637.82487927673307e-084.69938221266662e-06
REST#597868.271453185252597.89289295030691e-060.000222911261989482
SIN3A#2594264.636186908698690.0002351678146357830.00256669363494059
TAF1#687273.343046285745290.0002142336319622450.00246794024801511
TAF7#687969.799773775649072.89681485118392e-069.95198836324991e-05
TBP#690873.706770687096390.0001039672097505110.00145202345802804
TCF7L2#6934710.77017656313735.9423478161588e-083.69632438101137e-06



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.

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