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Coexpression cluster:C2585: Difference between revisions

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|tf_chipseq_enrich=BCL3#602;2:17.2735514018692:0.00483449420807607:0.0226762660826937!FOXA2#3170;2:12.3152318763326:0.00936191628546724:0.0353475714883017!HNF4A#3172;2:11.5661451814768:0.0105758568176249:0.0390735782572495!HNF4G#3174;2:14.3767112632234:0.00692416998043918:0.0293071282102163!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322496195462278
|tf_chipseq_enrich=BCL3#602;2:17.2735514018692:0.00483449420807607:0.0226762660826937!FOXA2#3170;2:12.3152318763326:0.00936191628546724:0.0353475714883017!HNF4A#3172;2:11.5661451814768:0.0105758568176249:0.0390735782572495!HNF4G#3174;2:14.3767112632234:0.00692416998043918:0.0293071282102163!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322496195462278
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}}
}}

Revision as of 15:35, 26 November 2012


Full id: C2585_somatostatinoma_parotid_small_pancreas_smallcell_Alveolar_salivary



Phase1 CAGE Peaks

Hg19::chr1:43736324..43736409,+p1@TMEM125
Hg19::chr1:43751230..43751274,-p1@C1orf210
Hg19::chr1:43751276..43751293,-p2@C1orf210
Hg19::chr6:27218970..27219009,+p2@PRSS16


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
epithelial cell2.52e-25253
endo-epithelial cell2.92e-1842
endodermal cell9.30e-1558
epithelial cell of alimentary canal5.12e-0920
respiratory epithelial cell1.37e-0813
germ line cell7.18e-087
germ cell7.18e-087
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure4.95e-23160
endoderm4.95e-23160
presumptive endoderm4.95e-23160
digestive system2.28e-18145
digestive tract2.28e-18145
primitive gut2.28e-18145
subdivision of digestive tract1.57e-16118
anatomical space4.21e-1395
immaterial anatomical entity1.19e-12117
endo-epithelium2.73e-1182
respiratory system8.07e-1174
reproductive structure2.78e-1059
reproductive system2.78e-1059
renal system1.13e-0948
trunk region element1.55e-09101
epithelial bud2.35e-0937
urinary system structure3.24e-0947
reproductive organ3.50e-0948
foregut4.78e-0987
organ6.14e-09503
orifice6.26e-0936
thoracic cavity element6.71e-0834
thoracic cavity6.71e-0834
organ system subdivision1.35e-07223
thoracic segment organ1.71e-0735
male organism1.73e-0722
male reproductive system1.73e-0722
epithelial fold2.17e-0747
respiratory tract2.19e-0754
subdivision of trunk2.21e-07112
organ part2.25e-07218
male reproductive organ2.40e-0711
gastrointestinal system3.35e-0725
internal genitalia3.72e-0725
intestine6.50e-0717
adult organism7.05e-07114
Disease
Ontology termp-valuen
carcinoma1.87e-18106
cell type cancer4.26e-12143
squamous cell carcinoma2.01e-1114
adenocarcinoma5.88e-0925


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)

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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
BCL3#602217.27355140186920.004834494208076070.0226762660826937
FOXA2#3170212.31523187633260.009361916285467240.0353475714883017
HNF4A#3172211.56614518147680.01057585681762490.0390735782572495
HNF4G#3174214.37671126322340.006924169980439180.0293071282102163
TAF1#687243.343046285745290.008005664898701650.0322496195462278



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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