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Coexpression cluster:C3208: Difference between revisions

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|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.0166981999279493!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00443193921575201!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156249142047209!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00641571909005896
|tf_chipseq_enrich=EP300#2033;3:6.7739417262232:0.00321688050010379:0.0166981999279493!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00443193921575201!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0156249142047209!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00641571909005896
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}}
}}

Revision as of 15:59, 26 November 2012


Full id: C3208_epithelioid_anaplastic_Pancreatic_mucinous_mesenchymal_endometrial_occipital



Phase1 CAGE Peaks

Hg19::chr11:85429930..85429939,-p14@SYTL2
Hg19::chr11:85429940..85429951,-p10@SYTL2
Hg19::chr11:85429982..85430028,-p4@SYTL2


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
cell of skeletal muscle1.48e-129
skin fibroblast5.86e-0823
Uber Anatomy
Ontology termp-valuen
regional part of nervous system2.85e-2753
regional part of brain2.85e-2753
neural tube4.66e-2756
neural rod4.66e-2756
future spinal cord4.66e-2756
neural keel4.66e-2756
brain6.60e-2668
future brain6.60e-2668
central nervous system2.22e-2581
nervous system3.59e-2489
brain grey matter1.17e-2034
gray matter1.17e-2034
telencephalon4.01e-2034
cerebral hemisphere1.77e-1832
regional part of forebrain2.46e-1841
forebrain2.46e-1841
anterior neural tube2.46e-1841
future forebrain2.46e-1841
regional part of telencephalon2.52e-1832
neural plate3.53e-1882
presumptive neural plate3.53e-1882
neurectoderm8.75e-1786
cerebral cortex3.55e-1525
pallium3.55e-1525
ecto-epithelium7.52e-15104
structure with developmental contribution from neural crest9.65e-15132
regional part of cerebral cortex4.39e-1422
adult organism4.71e-13114
pre-chordal neural plate6.51e-1361
neocortex5.43e-1220
ectoderm-derived structure2.85e-11171
ectoderm2.85e-11171
presumptive ectoderm2.85e-11171
segmental subdivision of hindbrain1.11e-1012
hindbrain1.11e-1012
presumptive hindbrain1.11e-1012
posterior neural tube5.04e-1015
chordal neural plate5.04e-1015
segmental subdivision of nervous system1.13e-0913
organ system subdivision2.02e-09223
brainstem1.10e-086
regional part of metencephalon1.69e-079
metencephalon1.69e-079
future metencephalon1.69e-079
epithelium1.81e-07306
cell layer3.11e-07309
neural nucleus5.87e-079
nucleus of brain5.87e-079
gyrus6.54e-076


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
EP300#203336.77394172622320.003216880500103790.0166981999279493
JUN#3725312.51282919233630.0005103313992726250.00443193921575201
JUND#372736.994663941871030.002921845042734990.0156249142047209
STAT3#6774310.51946499715420.0008589184530415310.00641571909005896



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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