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Coexpression cluster:C2646: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;3:4.75215118272197:0.0138620699668949:0.0487290718704992!E2F4#1874;3:9.50104523646333:0.00185075103472827:0.0109314889331515!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101535146915749!IRF1#3659;4:7.6371637535639:0.000293885399618549:0.00307854536115964!NRF1#4899;3:9.15770958578318:0.00206195379173342:0.0119637995586026
|tf_chipseq_enrich=CCNT2#905;3:4.75215118272197:0.0138620699668949:0.0487290718704992!E2F4#1874;3:9.50104523646333:0.00185075103472827:0.0109314889331515!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101535146915749!IRF1#3659;4:7.6371637535639:0.000293885399618549:0.00307854536115964!NRF1#4899;3:9.15770958578318:0.00206195379173342:0.0119637995586026
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}}
}}

Revision as of 15:38, 26 November 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 organism5.21e-55114
neural tube1.24e-2456
neural rod1.24e-2456
future spinal cord1.24e-2456
neural keel1.24e-2456
regional part of nervous system2.95e-2353
regional part of brain2.95e-2353
regional part of forebrain2.88e-1941
forebrain2.88e-1941
anterior neural tube2.88e-1941
future forebrain2.88e-1941
brain2.89e-1868
future brain2.89e-1868
central nervous system6.42e-1781
telencephalon1.48e-1534
brain grey matter1.73e-1534
gray matter1.73e-1534
cerebral hemisphere1.56e-1432
nervous system1.83e-1489
neural plate2.12e-1482
presumptive neural plate2.12e-1482
regional part of telencephalon2.16e-1432
regional part of cerebral cortex1.77e-1322
neurectoderm5.46e-1386
neocortex2.57e-1220
cerebral cortex1.45e-1025
pallium1.45e-1025
ecto-epithelium3.36e-10104
pre-chordal neural plate6.37e-1061
organ system subdivision1.08e-09223
ectoderm-derived structure9.43e-08171
ectoderm9.43e-08171
presumptive ectoderm9.43e-08171
structure with developmental contribution from neural crest1.42e-07132


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.

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