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Coexpression cluster:C3975

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Full id: C3975_Urothelial_Keratinocyte_amniotic_Corneal_epidermoid_Prostate_papillotubular



Phase1 CAGE Peaks

Hg19::chr1:35225339..35225343,+p1@GJB4
Hg19::chr6:35360230..35360249,+p@chr6:35360230..35360249
+
Hg19::chr6:35360512..35360523,+p@chr6:35360512..35360523
+


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
endoderm-derived structure3.44e-20169
endoderm3.44e-20169
presumptive endoderm3.44e-20169
digestive system2.62e-13155
digestive tract2.62e-13155
primitive gut2.62e-13155
orifice1.08e-1235
respiratory system7.64e-1272
renal system2.57e-1145
anatomical space6.85e-11104
mixed endoderm/mesoderm-derived structure7.15e-11130
reproductive structure1.35e-1059
reproductive system1.35e-1059
urinary system structure1.56e-1044
extraembryonic membrane2.21e-1014
membranous layer2.21e-1014
subdivision of digestive tract6.91e-10129
endodermal part of digestive tract6.91e-10129
oral opening2.08e-0921
organ2.75e-09511
reproductive organ3.97e-0948
tracheobronchial tree4.27e-0914
lower respiratory tract4.27e-0914
immaterial anatomical entity5.01e-09126
duct1.90e-0826
urothelium2.50e-085
internal genitalia2.57e-0825
respiratory tract5.82e-0853
endo-epithelium6.76e-0882
mucosa1.90e-0712
intermediate mesoderm2.04e-0737
mouth2.46e-0728
stomodeum2.46e-0728
male organism2.57e-0722
male reproductive system2.57e-0722
biliary system3.36e-077
biliary tree3.36e-077
biliary bud3.36e-077
neck4.12e-0710
mouth mucosa7.84e-075
transitional epithelium8.30e-076
female organism8.53e-0741
surface structure9.04e-0795
chorion9.25e-077
Disease
Ontology termp-valuen
squamous cell carcinoma1.96e-1214
carcinoma1.24e-10106
adenocarcinoma5.76e-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
ESR1#2099220.51240219743630.003099741577095180.016312300240363
NR3C1#290829.982015554115360.01278474365547170.0460486219697134



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.