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Coexpression cluster:C2646: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2646_occipital_temporal_cerebellum_postcentral_cerebral_insula_parietal
|full_id=C2646_occipital_temporal_cerebellum_postcentral_cerebral_insula_parietal
|id=C2646
|id=C2646

Revision as of 15:24, 12 September 2012


Full id: C2646_occipital_temporal_cerebellum_postcentral_cerebral_insula_parietal



Phase1 CAGE Peaks

Hg19::chr22:39548457..39548481,-p3@CBX7
Hg19::chr22:39548511..39548598,-p1@CBX7
Hg19::chr22:41763452..41763466,+p2@TEF
Hg19::chr22:41777927..41777971,+p1@TEF


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism1.55e-58115
neural tube3.97e-2457
neural rod3.97e-2457
future spinal cord3.97e-2457
neural keel3.97e-2457
anterior neural tube4.81e-1942
regional part of forebrain1.09e-1841
forebrain1.09e-1841
future forebrain1.09e-1841
brain5.09e-1869
future brain5.09e-1869
regional part of brain5.68e-1859
neural plate2.52e-1786
presumptive neural plate2.52e-1786
central nervous system6.28e-1782
neurectoderm5.36e-1690
telencephalon4.49e-1534
gray matter6.06e-1534
brain grey matter6.06e-1534
regional part of nervous system1.90e-1494
nervous system1.90e-1494
regional part of telencephalon1.93e-1433
cerebral hemisphere5.26e-1432
regional part of cerebral cortex5.81e-1322
anterior region of body8.30e-12129
craniocervical region8.30e-12129
neocortex9.03e-1220
pre-chordal neural plate2.32e-1161
head1.01e-10123
ectoderm-derived structure2.90e-10169
cerebral cortex3.73e-1025
pallium3.73e-1025
ectoderm1.06e-09173
presumptive ectoderm1.06e-09173


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
CCNT2#90534.752151182721970.01386206996689490.0487290718704992
E2F4#187439.501045236463330.001850751034728270.0109314889331515
EGR1#195844.988179094810140.001615011500076050.0101535146915749
IRF1#365947.63716375356390.0002938853996185490.00307854536115964
NRF1#489939.157709585783180.002061953791733420.0119637995586026



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.