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Coexpression cluster:C4653: Difference between revisions

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|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.01684133453057!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00584085144152027!FOXA2#3170;2:16.4203091684435:0.00481068235210548:0.0226021347866096!MAFF#23764;2:37.5435709932968:0.000934477401556032:0.00677231873854073!MAFK#7975;2:18.0671554252199:0.00398367474493681:0.0191191124804216!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00310123560957839
|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.01684133453057!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00584085144152027!FOXA2#3170;2:16.4203091684435:0.00481068235210548:0.0226021347866096!MAFF#23764;2:37.5435709932968:0.000934477401556032:0.00677231873854073!MAFK#7975;2:18.0671554252199:0.00398367474493681:0.0191191124804216!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00310123560957839
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}}
}}

Revision as of 16:52, 26 November 2012


Full id: C4653_large_lung_glioblastoma_hepatoma_mesothelioma_endometrial_pleomorphic



Phase1 CAGE Peaks

Hg19::chr7:134212296..134212311,+p2@AKR1B10
Hg19::chr7:134212312..134212329,+p1@AKR1B10
Hg19::chr7:134212586..134212595,+p6@AKR1B10


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 cell1.72e-09253
prostate stromal cell3.29e-073
endodermal cell5.46e-0758
Uber Anatomy
Ontology termp-valuen
digestive system1.19e-16145
digestive tract1.19e-16145
primitive gut1.19e-16145
endoderm-derived structure6.61e-15160
endoderm6.61e-15160
presumptive endoderm6.61e-15160
subdivision of digestive tract1.69e-14118
gut epithelium1.92e-1254
endo-epithelium2.39e-1282
prostate gland3.71e-1111
male accessory sex gland3.71e-1111
embryonic cloacal epithelium3.71e-1111
epithelium of hindgut3.71e-1111
urogenital sinus epithelium3.71e-1111
prostate bud3.71e-1111
prostate field3.71e-1111
cloaca7.04e-1114
anal region7.04e-1114
embryonic cloaca7.04e-1114
terminal part of digestive tract7.04e-1114
primitive urogenital sinus7.04e-1114
proctodeum7.04e-1114
orifice3.91e-1036
sex gland4.16e-1012
male reproductive gland4.16e-1012
genitourinary system4.93e-1015
hindgut2.19e-0919
epithelial bud2.81e-0837
epithelium of foregut-midgut junction3.37e-0725
anatomical boundary3.37e-0725
hepatobiliary system3.37e-0725
foregut-midgut junction3.37e-0725
septum transversum3.37e-0725
organ system subdivision9.05e-07223
Disease
Ontology termp-valuen
carcinoma5.36e-13106
cell type cancer1.85e-12143
cancer8.05e-09235
disease of cellular proliferation2.10e-08239
disease of anatomical entity2.41e-0839


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
EP300#203336.77394172622320.003216880500103790.01684133453057
FOXA1#3169311.08141974938550.000734755275698670.00584085144152027
FOXA2#3170216.42030916844350.004810682352105480.0226021347866096
MAFF#23764237.54357099329680.0009344774015560320.00677231873854073
MAFK#7975218.06715542521990.003983674744936810.0191191124804216
NR3C1#2908314.9730233311730.0002978331194675480.00310123560957839



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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