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Coexpression cluster:C2514: Difference between revisions

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|tf_chipseq_enrich=CTBP2#1488;3:47.0377502544961:1.60047699357395e-05:0.000370297334363912!FOSL1#8061;3:29.7851847872798:6.26173959487248e-05:0.00102503106825844!JUND#3727;3:5.24599795640327:0.0104343275174842:0.0386944122287588!SMARCB1#6598;3:13.6895368358681:0.000630578340937934:0.00518191607122644!SUZ12#23512;3:37.5868356832972:3.12785741999833e-05:0.000631735256405347!TFAP2A#7020;3:12.3889757797837:0.00084694130358843:0.00638055996577018!TFAP2C#7022;3:8.10692145739517:0.00294701173986644:0.0157176467725417!ZEB1#6935;3:12.6663240131579:0.00079333607591285:0.00613242738748147!ZNF143#7702;3:10.1256574141709:0.00153486161068818:0.00976720763823198!ZNF263#10127;3:6.16638122775801:0.00653981434797598:0.0279762296505392
|tf_chipseq_enrich=CTBP2#1488;3:47.0377502544961:1.60047699357395e-05:0.000370297334363912!FOSL1#8061;3:29.7851847872798:6.26173959487248e-05:0.00102503106825844!JUND#3727;3:5.24599795640327:0.0104343275174842:0.0386944122287588!SMARCB1#6598;3:13.6895368358681:0.000630578340937934:0.00518191607122644!SUZ12#23512;3:37.5868356832972:3.12785741999833e-05:0.000631735256405347!TFAP2A#7020;3:12.3889757797837:0.00084694130358843:0.00638055996577018!TFAP2C#7022;3:8.10692145739517:0.00294701173986644:0.0157176467725417!ZEB1#6935;3:12.6663240131579:0.00079333607591285:0.00613242738748147!ZNF143#7702;3:10.1256574141709:0.00153486161068818:0.00976720763823198!ZNF263#10127;3:6.16638122775801:0.00653981434797598:0.0279762296505392
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}}
}}

Revision as of 15:33, 26 November 2012


Full id: C2514_Mesothelial_mesothelioma_Retinal_retina_Meningeal_Smooth_renal



Phase1 CAGE Peaks

Hg19::chr1:113051552..113051561,+p4@WNT2B
Hg19::chr1:113051579..113051596,+p1@WNT2B
Hg19::chr1:113051605..113051641,+p2@WNT2B
Hg19::chr1:113063958..113063969,+p@chr1:113063958..113063969
+


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
multi-tissue structure3.23e-20342
structure with developmental contribution from neural crest4.70e-13132
mesenchyme2.88e-12160
entire embryonic mesenchyme2.88e-12160
neural plate3.96e-1282
presumptive neural plate3.96e-1282
neurectoderm9.76e-1186
organism subdivision1.07e-10264
anatomical cluster1.93e-10373
adult organism2.00e-10114
cell layer2.79e-10309
organ part5.58e-10218
epithelium1.45e-09306
ecto-epithelium8.61e-09104
pigment epithelium of eye1.55e-0811
pre-chordal neural plate2.56e-0861
ectoderm-derived structure3.83e-08171
ectoderm3.83e-08171
presumptive ectoderm3.83e-08171
sense organ1.84e-0724
sensory system1.84e-0724
entire sense organ system1.84e-0724
eye2.83e-0721
visual system2.83e-0721
organ4.52e-07503
vasculature of organ4.70e-0711
trunk mesenchyme5.91e-07122
organ system subdivision6.14e-07223
multi-cellular organism7.44e-07656


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
CTBP2#1488347.03775025449611.60047699357395e-050.000370297334363912
FOSL1#8061329.78518478727986.26173959487248e-050.00102503106825844
JUND#372735.245997956403270.01043432751748420.0386944122287588
SMARCB1#6598313.68953683586810.0006305783409379340.00518191607122644
SUZ12#23512337.58683568329723.12785741999833e-050.000631735256405347
TFAP2A#7020312.38897577978370.000846941303588430.00638055996577018
TFAP2C#702238.106921457395170.002947011739866440.0157176467725417
ZEB1#6935312.66632401315790.000793336075912850.00613242738748147
ZNF143#7702310.12565741417090.001534861610688180.00976720763823198
ZNF263#1012736.166381227758010.006539814347975980.0279762296505392



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.