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Coexpression cluster:C4291: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326566705599!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00388712783478599!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00155121388405847!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.0064433690789545!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00248924608288584
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326566705599!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00388712783478599!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00155121388405847!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.0064433690789545!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00248924608288584
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}}
}}

Revision as of 16:39, 26 November 2012


Full id: C4291_pleomorphic_Cardiac_breast_aorta_lung_diaphragm_mesothelioma



Phase1 CAGE Peaks

Hg19::chr3:145968857..145968899,-p1@PLSCR4
Hg19::chr3:145968900..145968915,-p3@PLSCR4
Hg19::chr3:145968923..145968935,-p4@PLSCR4


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
fibroblast4.12e-0876
Uber Anatomy
Ontology termp-valuen
adult organism6.37e-32114
anatomical cluster3.31e-22373
anatomical conduit4.04e-20240
multi-cellular organism1.60e-17656
multi-tissue structure4.79e-17342
neural tube6.98e-1756
neural rod6.98e-1756
future spinal cord6.98e-1756
neural keel6.98e-1756
tube8.40e-17192
structure with developmental contribution from neural crest5.77e-16132
brain1.62e-1568
future brain1.62e-1568
central nervous system3.79e-1581
regional part of nervous system4.20e-1553
regional part of brain4.20e-1553
cell layer5.02e-13309
epithelium6.23e-13306
nervous system7.11e-1389
neurectoderm3.10e-1286
organ system subdivision3.92e-12223
anatomical system4.79e-12624
neural plate5.57e-1282
presumptive neural plate5.57e-1282
anatomical group6.04e-12625
regional part of forebrain6.55e-1241
forebrain6.55e-1241
anterior neural tube6.55e-1241
future forebrain6.55e-1241
brain grey matter7.75e-1034
gray matter7.75e-1034
ectoderm-derived structure1.07e-09171
ectoderm1.07e-09171
presumptive ectoderm1.07e-09171
telencephalon1.77e-0934
germ layer4.32e-09560
germ layer / neural crest4.32e-09560
embryonic tissue4.32e-09560
presumptive structure4.32e-09560
germ layer / neural crest derived structure4.32e-09560
epiblast (generic)4.32e-09560
embryonic structure7.35e-09564
regional part of telencephalon7.53e-0932
cerebral hemisphere9.10e-0932
organ1.39e-08503
ecto-epithelium1.62e-08104
splanchnic layer of lateral plate mesoderm1.95e-0883
embryo1.03e-07592
developing anatomical structure1.08e-07581
regional part of cerebral cortex6.26e-0722


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#186934.907389214879320.008460985347239390.0326566705599
GATA1#2623313.56030814380040.0004009615963782630.00388712783478599
STAT1#6772320.70658749719920.0001125992441046670.00155121388405847
STAT3#6774310.51946499715420.0008589184530415310.0064433690789545
TFAP2A#7020316.5186343730450.0002218033880766340.00248924608288584



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.