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Coexpression cluster:C3586: Difference between revisions

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|tf_chipseq_enrich=ATF3#467;2:14.9754496840058:0.00576829454079388:0.0259535978608466!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294064528175555!SMARCB1#6598;2:12.1684771874383:0.00867500222192174:0.0329805451951252!SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457331822933716!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00541934317856543!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190015604924905!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00421246791887293!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00242489963260739
|tf_chipseq_enrich=ATF3#467;2:14.9754496840058:0.00576829454079388:0.0259535978608466!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294064528175555!SMARCB1#6598;2:12.1684771874383:0.00867500222192174:0.0329805451951252!SMC3#9126;2:10.0299552299552:0.012665637976747:0.0457331822933716!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00541934317856543!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190015604924905!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00421246791887293!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00242489963260739
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}}
}}

Revision as of 16:13, 26 November 2012


Full id: C3586_serous_breast_choriocarcinoma_pancreatic_malignant_Prostate_maxillary



Phase1 CAGE Peaks

Hg19::chr16:68771187..68771201,+p1@CDH1
Hg19::chr5:68711023..68711075,+p2@MARVELD2
Hg19::chr5:68711076..68711103,+p3@MARVELD2


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


GO IDGO nameFDR corrected p-value
GO:0030054cell junction0.00429571419202788
GO:0044459plasma membrane part0.0299164706866183
GO:0005923tight junction0.0299164706866183
GO:0043296apical junction complex0.0299164706866183
GO:0016327apicolateral plasma membrane0.0299164706866183
GO:0050954sensory perception of mechanical stimulus0.0299164706866183
GO:0007605sensory perception of sound0.0299164706866183
GO:0005911intercellular junction0.0340594182494116
GO:0007156homophilic cell adhesion0.0340594182494116
GO:0005886plasma membrane0.0340594182494116
GO:0016337cell-cell adhesion0.0498875417599653



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>


Cell Type
Ontology termp-valuen
epithelial cell2.60e-33253
endodermal cell4.22e-2458
endo-epithelial cell2.12e-2042
epithelial cell of alimentary canal7.60e-1120
respiratory epithelial cell4.96e-0913
epithelial cell of lung2.50e-0719
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.86e-28160
endoderm1.86e-28160
presumptive endoderm1.86e-28160
digestive system7.84e-23145
digestive tract7.84e-23145
primitive gut7.84e-23145
subdivision of digestive tract2.31e-21118
endo-epithelium1.19e-1782
trunk region element2.18e-16101
immaterial anatomical entity2.20e-16117
foregut4.25e-1487
anatomical space1.87e-1295
subdivision of trunk2.68e-12112
respiratory system5.90e-1274
epithelial bud1.87e-1137
renal system3.39e-1148
urinary system structure7.86e-1147
gland2.45e-1059
thoracic cavity element7.74e-1034
thoracic cavity7.74e-1034
thoracic segment organ2.47e-0935
organism subdivision4.88e-09264
epithelial fold6.43e-0947
organ9.58e-09503
exocrine gland9.66e-0931
exocrine system9.66e-0931
lung9.80e-0922
respiratory tube9.80e-0922
respiration organ9.80e-0922
pair of lungs9.80e-0922
lung primordium9.80e-0922
lung bud9.80e-0922
gut epithelium1.38e-0854
respiratory tract1.73e-0854
orifice3.01e-0836
reproductive structure8.01e-0859
reproductive system8.01e-0859
abdomen element1.31e-0754
abdominal segment element1.31e-0754
organ system subdivision1.35e-07223
respiratory system epithelium1.53e-0728
thoracic segment of trunk2.33e-0752
respiratory tract epithelium2.50e-0719
lung epithelium2.50e-0719
extraembryonic membrane3.68e-0714
membranous layer3.68e-0714
reproductive organ8.52e-0748
Disease
Ontology termp-valuen
carcinoma9.70e-26106
cell type cancer6.87e-17143
squamous cell carcinoma4.76e-1214
adenocarcinoma6.34e-0925


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
ATF3#467214.97544968400580.005768294540793880.0259535978608466
MYC#460935.22228187160940.007020843755740150.0294064528175555
SMARCB1#6598212.16847718743830.008675002221921740.0329805451951252
SMC3#9126210.02995522995520.0126656379767470.0457331822933716
TAF7#6879311.43306940492390.0006690181981945830.00541934317856543
USF1#739136.361499277207960.00388404057290560.0190015604924905
USF2#7392312.99219738506960.0004558979393427810.00421246791887293
ZEB1#6935316.88843201754390.0002075486917327580.00242489963260739



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.