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Coexpression cluster:C4475: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327098592885558!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168126799054366!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295629521027999!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00376013493501888!YY1#7528;3:4.91117074985386:0.00844145534180826:0.03308256048794!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109903105136976
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0327098592885558!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168126799054366!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295629521027999!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00376013493501888!YY1#7528;3:4.91117074985386:0.00844145534180826:0.03308256048794!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109903105136976
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}}
}}

Revision as of 16:45, 26 November 2012


Full id: C4475_duodenum_parietal_H9_frontal_insula_immature_pons



Phase1 CAGE Peaks

Hg19::chr5:146258140..146258149,-p16@PPP2R2B
Hg19::chr5:146258158..146258169,-p11@PPP2R2B
Hg19::chr5:146258291..146258364,-p1@PPP2R2B


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>

Cell Type
Ontology termp-valuen
neural cell5.99e-0725
Uber Anatomy
Ontology termp-valuen
central nervous system7.03e-4781
nervous system1.47e-4289
neural tube3.07e-4256
neural rod3.07e-4256
future spinal cord3.07e-4256
neural keel3.07e-4256
regional part of nervous system4.14e-4053
regional part of brain4.14e-4053
brain1.03e-3968
future brain1.03e-3968
neural plate3.67e-3982
presumptive neural plate3.67e-3982
neurectoderm3.51e-3686
regional part of forebrain6.43e-3441
forebrain6.43e-3441
anterior neural tube6.43e-3441
future forebrain6.43e-3441
pre-chordal neural plate2.01e-3261
adult organism2.54e-28114
telencephalon1.45e-2734
ecto-epithelium1.98e-27104
brain grey matter2.42e-2734
gray matter2.42e-2734
cerebral hemisphere2.15e-2632
regional part of telencephalon7.05e-2632
ectoderm-derived structure5.20e-24171
ectoderm5.20e-24171
presumptive ectoderm5.20e-24171
cerebral cortex7.94e-2225
pallium7.94e-2225
organ system subdivision2.63e-21223
neocortex1.10e-2020
regional part of cerebral cortex5.30e-2022
structure with developmental contribution from neural crest3.36e-19132
organ part1.35e-11218
anatomical cluster2.44e-10373
posterior neural tube1.81e-0915
chordal neural plate1.81e-0915
diencephalon9.60e-087
future diencephalon9.60e-087
segmental subdivision of hindbrain1.57e-0712
hindbrain1.57e-0712
presumptive hindbrain1.57e-0712
gyrus1.83e-076
basal ganglion2.17e-079
nuclear complex of neuraxis2.17e-079
aggregate regional part of brain2.17e-079
collection of basal ganglia2.17e-079
cerebral subcortex2.17e-079
occipital lobe5.04e-075
neural nucleus5.30e-079
nucleus of brain5.30e-079
parietal lobe6.86e-075
tube7.87e-07192
segmental subdivision of nervous system9.97e-0713


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
E2F1#186934.907389214879320.008460985347239390.0327098592885558
EP300#203336.77394172622320.003216880500103790.0168126799054366
MYC#460935.22228187160940.007020843755740150.0295629521027999
SRF#6722313.79717826216780.0003806615025800190.00376013493501888
YY1#752834.911170749853860.008441455341808260.03308256048794
ZNF263#1012738.221841637010680.001799043925565870.0109903105136976



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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