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Coexpression cluster:C4136: Difference between revisions

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|tf_chipseq_enrich=CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00661388509968301!CTCF#10664;3:5.36025637307503:0.006492509252767:0.028005582927876!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326120773796994!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00916793835245332!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167749042615508!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00582268049462731!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.0039200233850588!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173231862648405!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00614953098604641
|tf_chipseq_enrich=CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00661388509968301!CTCF#10664;3:5.36025637307503:0.006492509252767:0.028005582927876!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326120773796994!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00916793835245332!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167749042615508!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00582268049462731!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.0039200233850588!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173231862648405!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00614953098604641
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}}
}}

Revision as of 16:34, 26 November 2012


Full id: C4136_small_Intestinal_endometrial_Mesothelial_Fibroblast_Prostate_colon



Phase1 CAGE Peaks

Hg19::chr2:162930503..162930521,-p3@DPP4
Hg19::chr2:162930536..162930551,-p5@DPP4
Hg19::chr2:162930560..162930613,-p1@DPP4


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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
mesenchyme1.91e-17160
entire embryonic mesenchyme1.91e-17160
trunk mesenchyme8.60e-16122
muscle tissue4.76e-1464
musculature4.76e-1464
musculature of body4.76e-1464
somite1.10e-1371
presomitic mesoderm1.10e-1371
presumptive segmental plate1.10e-1371
dermomyotome1.10e-1371
trunk paraxial mesoderm1.10e-1371
skeletal muscle tissue1.66e-1362
striated muscle tissue1.66e-1362
myotome1.66e-1362
epithelial tube4.04e-13117
paraxial mesoderm4.75e-1372
presumptive paraxial mesoderm4.75e-1372
unilaminar epithelium7.40e-13148
dense mesenchyme tissue1.94e-1273
trunk6.64e-12199
epithelial vesicle9.77e-1278
splanchnic layer of lateral plate mesoderm1.58e-1183
multilaminar epithelium5.22e-1183
organism subdivision6.65e-09264
mesoderm9.19e-08315
mesoderm-derived structure9.19e-08315
presumptive mesoderm9.19e-08315
cardiovascular system2.44e-07109
heart4.59e-0724
primitive heart tube4.59e-0724
primary heart field4.59e-0724
anterior lateral plate mesoderm4.59e-0724
heart tube4.59e-0724
heart primordium4.59e-0724
cardiac mesoderm4.59e-0724
cardiogenic plate4.59e-0724
heart rudiment4.59e-0724
circulatory system5.09e-07112
artery6.31e-0742
arterial blood vessel6.31e-0742
arterial system6.31e-0742
gut epithelium7.79e-0754
Disease
Ontology termp-valuen
ovarian cancer2.98e-0914
reproductive organ cancer3.24e-0729
female reproductive organ cancer5.77e-0727


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)

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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
CHD2#1106310.34402283411690.0009033701102746880.00661388509968301
CTCF#1066435.360256373075030.0064925092527670.028005582927876
E2F1#186934.907389214879320.008460985347239390.0326120773796994
EBF1#187938.9064668465690.00141523283560980.00916793835245332
EP300#203336.77394172622320.003216880500103790.0167749042615508
FOXA1#3169311.08141974938550.000734755275698670.00582268049462731
HDAC2#3066313.41562023662630.0004140761399857210.0039200233850588
PAX5#507936.669565531177830.003370290999677260.0173231862648405
TCF7L2#6934310.77017656313730.0008003181298398380.00614953098604641



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.