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Coexpression cluster:C4669: Difference between revisions

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|tf_chipseq_enrich=GATA3#2625;2:18.1576775714707:0.00394454681927962:0.0189592031505704
|tf_chipseq_enrich=GATA3#2625;2:18.1576775714707:0.00394454681927962:0.0189592031505704
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}}
}}

Revision as of 16:53, 26 November 2012


Full id: C4669_adenocarcinoma_gastric_lung_stomach_endometrioid_trachea_Prostate



Phase1 CAGE Peaks

Hg19::chr7:16840970..16841011,-p2@AGR2
Hg19::chr7:16844611..16844628,-p1@AGR2
Hg19::chr9:128307438..128307440,+p@chr9:128307438..128307440
+


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>

Cell Type
Ontology termp-valuen
endodermal cell4.00e-1058
endo-epithelial cell4.90e-1042
epithelial cell7.05e-09253
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure9.23e-27160
endoderm9.23e-27160
presumptive endoderm9.23e-27160
digestive system1.63e-24145
digestive tract1.63e-24145
primitive gut1.63e-24145
subdivision of digestive tract1.64e-23118
endo-epithelium2.82e-1382
gastrointestinal system7.07e-1325
intestine5.67e-1217
foregut1.60e-1187
respiratory tract6.39e-1154
epithelial bud7.94e-1037
thoracic cavity element8.72e-1034
thoracic cavity8.72e-1034
immaterial anatomical entity1.67e-09117
organ system subdivision1.77e-09223
thoracic segment organ2.12e-0935
respiratory system3.65e-0974
lung9.24e-0922
respiratory tube9.24e-0922
respiration organ9.24e-0922
pair of lungs9.24e-0922
lung primordium9.24e-0922
lung bud9.24e-0922
respiratory primordium2.29e-0838
endoderm of foregut2.29e-0838
thoracic segment of trunk3.51e-0852
extraembryonic membrane4.34e-0814
membranous layer4.34e-0814
anatomical space5.09e-0895
male genital duct8.96e-083
internal male genitalia8.96e-083
trunk region element2.40e-07101
biliary system2.49e-079
biliary tree2.49e-079
biliary bud2.49e-079
amnion2.49e-077
segment of respiratory tract4.28e-0747
small intestine5.64e-074
epithelial fold6.40e-0747
Disease
Ontology termp-valuen
carcinoma1.82e-13106
cell type cancer2.54e-08143
adenocarcinoma4.68e-0825


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
GATA3#2625218.15767757147070.003944546819279620.0189592031505704



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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