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Coexpression cluster:C1653: Difference between revisions

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|tf_chipseq_enrich=TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135183588589408
|tf_chipseq_enrich=TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135183588589408
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}}
}}

Revision as of 15:01, 26 November 2012


Full id: C1653_choriocarcinoma_Endothelial_pancreatic_placenta_lung_Lymphatic_adipose



Phase1 CAGE Peaks

Hg19::chr12:10251519..10251526,-p5@CLEC1A
Hg19::chr12:10251539..10251560,-p2@CLEC1A
Hg19::chr12:10251576..10251599,-p1@CLEC1A
Hg19::chr12:10251603..10251619,-p3@CLEC1A
Hg19::chr12:10251621..10251628,-p4@CLEC1A


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 organism7.55e-46114
blood vessel endothelium7.86e-2418
endothelium7.86e-2418
cardiovascular system endothelium7.86e-2418
simple squamous epithelium2.04e-1822
anatomical conduit3.46e-18240
tube2.72e-16192
neural tube7.12e-1656
neural rod7.12e-1656
future spinal cord7.12e-1656
neural keel7.12e-1656
squamous epithelium1.62e-1525
anatomical cluster3.38e-14373
regional part of nervous system1.56e-1353
regional part of brain1.56e-1353
vessel4.07e-1268
neural plate1.93e-1182
presumptive neural plate1.93e-1182
chorion2.92e-117
endothelial tube6.85e-119
arterial system endothelium6.85e-119
endothelium of artery6.85e-119
regional part of forebrain1.32e-1041
forebrain1.32e-1041
anterior neural tube1.32e-1041
future forebrain1.32e-1041
central nervous system1.61e-1081
neurectoderm1.81e-1086
splanchnic layer of lateral plate mesoderm9.51e-1083
extraembryonic membrane1.07e-0914
membranous layer1.07e-0914
vasculature1.92e-0978
vascular system1.92e-0978
brain2.37e-0968
future brain2.37e-0968
multi-cellular organism6.26e-09656
nervous system1.33e-0889
anatomical system1.62e-08624
vein1.63e-089
venous blood vessel1.63e-089
venous system1.63e-089
anatomical group1.89e-08625
epithelial tube open at both ends3.30e-0859
blood vessel3.30e-0859
blood vasculature3.30e-0859
vascular cord3.30e-0859
brain grey matter3.86e-0834
gray matter3.86e-0834
telencephalon5.18e-0834
epithelium6.93e-08306
structure with developmental contribution from neural crest8.68e-08132
cell layer1.23e-07309
lymphatic vessel1.24e-078
lymph vasculature1.24e-078
lymphatic part of lymphoid system1.24e-078
lymphoid system1.58e-0710
brainstem1.91e-076
placenta2.30e-074
allantois2.30e-074
ecto-epithelium4.01e-07104
organ part6.19e-07218
regional part of telencephalon7.02e-0732
posterior neural tube9.00e-0715
chordal neural plate9.00e-0715
circulatory system9.02e-07112
cerebral hemisphere9.34e-0732


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
TAF1#687253.343046285745290.002394600090870310.0135183588589408



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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