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Coexpression cluster:C3520: Difference between revisions

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|ontology_enrichment_disease=DOID:8692!8.34e-13!31;DOID:1240!2.43e-11!39;DOID:2531!1.26e-09!51;DOID:0060083!1.26e-09!51
|ontology_enrichment_disease=DOID:8692!8.34e-13!31;DOID:1240!2.43e-11!39;DOID:2531!1.26e-09!51;DOID:0060083!1.26e-09!51
|ontology_enrichment_uberon=UBERON:0005256!5.11e-16!143;UBERON:0002100!1.04e-13!216;UBERON:0003914!7.13e-12!118;UBERON:0003104!6.62e-11!238;UBERON:0009142!6.62e-11!238;UBERON:0004290!2.38e-10!70;UBERON:0000914!2.66e-10!83;UBERON:0002329!2.66e-10!83;UBERON:0003077!2.66e-10!83;UBERON:0003059!2.66e-10!83;UBERON:0007282!2.66e-10!83;UBERON:0009618!2.66e-10!83;UBERON:0007285!2.66e-10!83;UBERON:0000486!5.03e-10!82;UBERON:0000490!1.19e-09!138;UBERON:0001134!3.68e-09!61;UBERON:0002036!3.68e-09!61;UBERON:0003082!3.68e-09!61;UBERON:0002385!1.29e-08!63;UBERON:0001015!1.29e-08!63;UBERON:0000383!1.29e-08!63;UBERON:0002107!3.16e-08!19;UBERON:0006925!3.16e-08!19;UBERON:0008836!3.16e-08!19;UBERON:0005172!5.02e-08!55;UBERON:0005173!5.02e-08!55;UBERON:0002417!1.04e-07!61;UBERON:0000916!1.04e-07!61;UBERON:0005177!1.53e-07!107;UBERON:0009569!2.14e-07!113;UBERON:0007499!2.28e-07!25;UBERON:0000926!2.85e-07!448;UBERON:0004120!2.85e-07!448;UBERON:0006603!2.85e-07!448;UBERON:0009856!2.91e-07!26;UBERON:0008835!7.50e-07!22;UBERON:0003894!7.50e-07!22;UBERON:0009497!8.34e-07!25;UBERON:0000015!8.34e-07!25;UBERON:0002423!8.34e-07!25;UBERON:0006235!8.34e-07!25;UBERON:0004161!8.34e-07!25;UBERON:0009854!9.71e-07!23
|ontology_enrichment_uberon=UBERON:0005256!5.11e-16!143;UBERON:0002100!1.04e-13!216;UBERON:0003914!7.13e-12!118;UBERON:0003104!6.62e-11!238;UBERON:0009142!6.62e-11!238;UBERON:0004290!2.38e-10!70;UBERON:0000914!2.66e-10!83;UBERON:0002329!2.66e-10!83;UBERON:0003077!2.66e-10!83;UBERON:0003059!2.66e-10!83;UBERON:0007282!2.66e-10!83;UBERON:0009618!2.66e-10!83;UBERON:0007285!2.66e-10!83;UBERON:0000486!5.03e-10!82;UBERON:0000490!1.19e-09!138;UBERON:0001134!3.68e-09!61;UBERON:0002036!3.68e-09!61;UBERON:0003082!3.68e-09!61;UBERON:0002385!1.29e-08!63;UBERON:0001015!1.29e-08!63;UBERON:0000383!1.29e-08!63;UBERON:0002107!3.16e-08!19;UBERON:0006925!3.16e-08!19;UBERON:0008836!3.16e-08!19;UBERON:0005172!5.02e-08!55;UBERON:0005173!5.02e-08!55;UBERON:0002417!1.04e-07!61;UBERON:0000916!1.04e-07!61;UBERON:0005177!1.53e-07!107;UBERON:0009569!2.14e-07!113;UBERON:0007499!2.28e-07!25;UBERON:0000926!2.85e-07!448;UBERON:0004120!2.85e-07!448;UBERON:0006603!2.85e-07!448;UBERON:0009856!2.91e-07!26;UBERON:0008835!7.50e-07!22;UBERON:0003894!7.50e-07!22;UBERON:0009497!8.34e-07!25;UBERON:0000015!8.34e-07!25;UBERON:0002423!8.34e-07!25;UBERON:0006235!8.34e-07!25;UBERON:0004161!8.34e-07!25;UBERON:0009854!9.71e-07!23
|tf_chipseq_enrich=EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319928351551403!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0127854202571431!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156489525342666!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276070307475196!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246037081217192!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0139903772248733!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.010919413526017
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}}
}}

Revision as of 12:59, 5 September 2012


Full id: C3520_Mesenchymal_Hepatocyte_mature_liver_acute_Cardiac_Mesothelial



Phase1 CAGE Peaks

Hg19::chr15:80445232..80445254,+p3@FAH
Hg19::chr15:80445261..80445274,+p5@FAH
Hg19::chr15:80445320..80445379,+p1@FAH


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
somatic cell8.50e-18591
animal cell5.01e-13679
eukaryotic cell5.01e-13679
contractile cell1.33e-1059
non-terminally differentiated cell1.37e-10180
muscle cell1.25e-0954
embryonic cell1.63e-09248
muscle precursor cell1.89e-0957
myoblast1.89e-0957
multi-potent skeletal muscle stem cell1.89e-0957
mesodermal cell4.32e-09119
smooth muscle cell2.24e-0842
smooth muscle myoblast2.24e-0842
electrically responsive cell5.82e-0860
electrically active cell5.82e-0860
multi fate stem cell5.83e-08430
somatic stem cell1.08e-07436
stem cell2.51e-07444
Uber Anatomy
Ontology termp-valuen
trunk mesenchyme5.11e-16143
trunk1.04e-13216
epithelial tube7.13e-12118
mesenchyme6.62e-11238
entire embryonic mesenchyme6.62e-11238
dermomyotome2.38e-1070
somite2.66e-1083
paraxial mesoderm2.66e-1083
presomitic mesoderm2.66e-1083
presumptive segmental plate2.66e-1083
trunk paraxial mesoderm2.66e-1083
presumptive paraxial mesoderm2.66e-1083
multilaminar epithelium5.03e-1082
unilaminar epithelium1.19e-09138
skeletal muscle tissue3.68e-0961
striated muscle tissue3.68e-0961
myotome3.68e-0961
muscle tissue1.29e-0863
musculature1.29e-0863
musculature of body1.29e-0863
liver3.16e-0819
digestive gland3.16e-0819
liver bud3.16e-0819
abdomen element5.02e-0855
abdominal segment element5.02e-0855
abdominal segment of trunk1.04e-0761
abdomen1.04e-0761
trunk region element1.53e-07107
subdivision of trunk2.14e-07113
epithelial sac2.28e-0725
mesoderm2.85e-07448
mesoderm-derived structure2.85e-07448
presumptive mesoderm2.85e-07448
sac2.91e-0726
hepatic diverticulum7.50e-0722
liver primordium7.50e-0722
epithelium of foregut-midgut junction8.34e-0725
anatomical boundary8.34e-0725
hepatobiliary system8.34e-0725
foregut-midgut junction8.34e-0725
septum transversum8.34e-0725
digestive tract diverticulum9.71e-0723
Disease
Ontology termp-valuen
myeloid leukemia8.34e-1331
leukemia2.43e-1139
hematologic cancer1.26e-0951
immune system cancer1.26e-0951


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
EGR1#195834.988179094810140.008056488137383440.0319928351551403
IRF1#365937.63716375356390.002244692747297240.0127854202571431
JUND#372736.994663941871030.002921845042734990.0156489525342666
SIN3A#2594235.408884726815140.006318961977991520.0276070307475196
SP1#666735.69838137814090.005403962701712170.0246037081217192
ZBTB7A#5134137.35190930787590.002516255860282270.0139903772248733
ZNF263#1012738.221841637010680.001799043925565870.010919413526017



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.