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Coexpression cluster:C3643: Difference between revisions

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|tf_chipseq_enrich=E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321719825940168!USF1#7391;3:6.36149927720796:0.0038840405729056:0.019006011966157
|tf_chipseq_enrich=E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321719825940168!USF1#7391;3:6.36149927720796:0.0038840405729056:0.019006011966157
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}}
}}

Revision as of 16:15, 26 November 2012


Full id: C3643_Renal_signet_Hepatic_acute_mesothelioma_Retinal_smallcell



Phase1 CAGE Peaks

Hg19::chr17:4402141..4402158,+p2@SPNS2
Hg19::chr17:4402161..4402191,+p1@SPNS2
Hg19::chr17:4402213..4402226,+p3@SPNS2


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 organism4.65e-42114
neural tube1.28e-2556
neural rod1.28e-2556
future spinal cord1.28e-2556
neural keel1.28e-2556
regional part of nervous system8.72e-2453
regional part of brain8.72e-2453
central nervous system1.85e-2281
anatomical conduit2.20e-22240
regional part of forebrain2.29e-2141
forebrain2.29e-2141
anterior neural tube2.29e-2141
future forebrain2.29e-2141
anatomical cluster1.26e-20373
tube1.52e-20192
neural plate8.02e-2082
presumptive neural plate8.02e-2082
nervous system1.17e-1989
brain2.47e-1968
future brain2.47e-1968
telencephalon2.65e-1934
brain grey matter4.27e-1934
gray matter4.27e-1934
cerebral hemisphere7.50e-1832
neurectoderm7.91e-1886
regional part of telencephalon1.07e-1732
regional part of cerebral cortex5.74e-1622
pre-chordal neural plate1.32e-1561
ecto-epithelium3.87e-15104
neocortex1.69e-1420
organ system subdivision2.71e-13223
cerebral cortex5.70e-1325
pallium5.70e-1325
excretory tube1.41e-1116
kidney epithelium1.41e-1116
ectoderm-derived structure2.22e-11171
ectoderm2.22e-11171
presumptive ectoderm2.22e-11171
nephron epithelium2.99e-1115
renal tubule2.99e-1115
nephron tubule2.99e-1115
nephron2.99e-1115
uriniferous tubule2.99e-1115
nephrogenic mesenchyme2.99e-1115
cavitated compound organ3.26e-1131
organ part4.40e-11218
blood vessel endothelium5.15e-1018
endothelium5.15e-1018
cardiovascular system endothelium5.15e-1018
kidney6.87e-1026
kidney mesenchyme6.87e-1026
upper urinary tract6.87e-1026
kidney rudiment6.87e-1026
kidney field6.87e-1026
nephron tubule epithelium9.92e-1010
structure with developmental contribution from neural crest1.11e-09132
parenchyma2.49e-0915
epithelium6.28e-09306
cortex of kidney8.00e-0912
renal parenchyma8.00e-0912
cell layer1.64e-08309
simple squamous epithelium8.57e-0822
neural nucleus8.67e-089
nucleus of brain8.67e-089
basal ganglion9.10e-089
nuclear complex of neuraxis9.10e-089
aggregate regional part of brain9.10e-089
collection of basal ganglia9.10e-089
cerebral subcortex9.10e-089
multi-tissue structure3.76e-07342
squamous epithelium9.58e-0725


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
E2F6#187635.017155731697390.00791769806886330.0321719825940168
USF1#739136.361499277207960.00388404057290560.019006011966157



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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