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Coexpression cluster:C1679: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 17:32, 8 August 2012


Full id: C1679_Endothelial_retina_Hepatic_lung_Renal_kidney_gall



Phase1 CAGE Peaks

Hg19::chr12:6025654..6025658,-p@chr12:6025654..6025658
-
Hg19::chr6:142729306..142729321,+p@chr6:142729306..142729321
+
Hg19::chr6:46922535..46922542,-p9@GPR116
Hg19::chr7:10196589..10196595,-p@chr7:10196589..10196595
-
Hg19::chr7:47988099..47988115,-p2@PKD1L1


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>

Uber Anatomy
Ontology termp-valuen
adult organism3.40e-40115
anatomical conduit2.61e-19241
tube1.34e-17194
endothelium2.02e-1718
blood vessel endothelium2.02e-1718
cardiovascular system endothelium2.02e-1718
anatomical cluster3.78e-17286
simple squamous epithelium9.66e-1522
neural tube1.48e-1357
neural rod1.48e-1357
future spinal cord1.48e-1357
neural keel1.48e-1357
squamous epithelium3.27e-1225
anterior neural tube3.70e-1242
regional part of forebrain2.46e-1141
forebrain2.46e-1141
future forebrain2.46e-1141
central nervous system5.38e-1182
neural plate7.66e-1186
presumptive neural plate7.66e-1186
regional part of brain8.10e-1159
brain1.03e-1069
future brain1.03e-1069
neurectoderm2.06e-1090
telencephalon2.90e-1034
endothelial tube3.14e-109
arterial system endothelium3.14e-109
endothelium of artery3.14e-109
gray matter3.28e-1034
brain grey matter3.28e-1034
epithelium9.02e-10309
regional part of telencephalon1.02e-0933
cell layer1.95e-09312
regional part of nervous system2.14e-0994
nervous system2.14e-0994
vessel2.68e-0969
cerebral hemisphere4.54e-0932
anatomical system1.48e-08625
multi-cellular organism1.63e-08659
anatomical group1.79e-08626
pre-chordal neural plate1.35e-0761
regional part of cerebral cortex1.62e-0722
lymphoid system3.57e-0710
vasculature6.00e-0779
vascular system6.00e-0779


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

No analysis results for this cluster

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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