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Coexpression cluster:C1443: Difference between revisions

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|tf_chipseq_enrich=POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380296221129559
|tf_chipseq_enrich=POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380296221129559
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}}
}}

Revision as of 14:53, 26 November 2012


Full id: C1443_Endothelial_lung_left_heart_adipose_spleen_mature



Phase1 CAGE Peaks

Hg19::chr18:53177984..53178004,-p17@TCF4
Hg19::chr6:46889579..46889591,-p6@GPR116
Hg19::chr6:46889608..46889626,-p4@GPR116
Hg19::chr6:46889646..46889657,-p5@GPR116
Hg19::chr6:46889663..46889686,-p2@GPR116
Hg19::chr6:46889694..46889719,-p3@GPR116


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 organism1.37e-71114
neural tube1.92e-3156
neural rod1.92e-3156
future spinal cord1.92e-3156
neural keel1.92e-3156
regional part of nervous system5.13e-2953
regional part of brain5.13e-2953
regional part of forebrain5.68e-2741
forebrain5.68e-2741
anterior neural tube5.68e-2741
future forebrain5.68e-2741
anatomical conduit1.92e-26240
tube1.92e-23192
neural plate3.72e-2382
presumptive neural plate3.72e-2382
brain grey matter5.26e-2334
gray matter5.26e-2334
anatomical cluster6.90e-23373
telencephalon8.69e-2334
regional part of telencephalon1.41e-2132
central nervous system1.96e-2181
cerebral hemisphere2.13e-2132
neurectoderm2.95e-2186
brain5.30e-2168
future brain5.30e-2168
nervous system2.36e-1989
structure with developmental contribution from neural crest6.84e-19132
regional part of cerebral cortex8.29e-1822
pre-chordal neural plate4.86e-1761
neocortex3.11e-1620
cerebral cortex3.85e-1625
pallium3.85e-1625
ecto-epithelium1.46e-15104
organ system subdivision1.05e-13223
epithelium2.49e-11306
cell layer5.90e-11309
multi-tissue structure3.32e-10342
multi-cellular organism5.13e-10656
lymphoid system5.26e-0910
blood vessel endothelium6.14e-0918
endothelium6.14e-0918
cardiovascular system endothelium6.14e-0918
ectoderm-derived structure8.74e-09171
ectoderm8.74e-09171
presumptive ectoderm8.74e-09171
anatomical system1.15e-08624
anatomical group1.39e-08625
neural nucleus2.05e-089
nucleus of brain2.05e-089
organ part2.15e-08218
basal ganglion3.98e-089
nuclear complex of neuraxis3.98e-089
aggregate regional part of brain3.98e-089
collection of basal ganglia3.98e-089
cerebral subcortex3.98e-089
lymphatic vessel1.08e-078
lymph vasculature1.08e-078
lymphatic part of lymphoid system1.08e-078
simple squamous epithelium1.26e-0722
compound organ2.35e-0768
telencephalic nucleus5.03e-077


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
POLR2A#543062.147453176558070.01019570676818780.0380296221129559



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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