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Coexpression cluster:C3096

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Full id: C3096_Urothelial_Small_Corneal_Prostate_Esophageal_Bronchial_cervical



Phase1 CAGE Peaks

Hg19::chr11:119599468..119599531,-p3@PVRL1
Hg19::chr11:119599846..119599857,-p4@PVRL1
Hg19::chr11:119599869..119599934,-p1@PVRL1


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
epithelial cell1.18e-12254
endo-epithelial cell2.04e-1243
endodermal cell1.14e-1159
epithelial cell of alimentary canal4.57e-0821
respiratory epithelial cell6.92e-0713
Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure2.22e-16169
neural tube2.41e-1657
neural rod2.41e-1657
future spinal cord2.41e-1657
neural keel2.41e-1657
central nervous system3.11e-1682
anterior region of body6.69e-15129
craniocervical region6.69e-15129
ectoderm8.92e-15173
presumptive ectoderm8.92e-15173
head9.56e-15123
regional part of nervous system1.21e-1494
nervous system1.21e-1494
adult organism8.30e-14115
brain5.42e-1369
future brain5.42e-1369
anterior neural tube1.48e-1242
anatomical conduit2.10e-12241
regional part of forebrain2.74e-1241
forebrain2.74e-1241
future forebrain2.74e-1241
neural plate3.65e-1286
presumptive neural plate3.65e-1286
embryo5.71e-12612
regional part of brain6.11e-1259
telencephalon2.56e-1134
gray matter4.87e-1134
brain grey matter4.87e-1134
regional part of telencephalon7.80e-1133
cerebral hemisphere1.73e-1032
neurectoderm2.76e-1090
embryonic structure3.39e-10605
developing anatomical structure3.39e-10605
germ layer6.25e-10604
embryonic tissue6.25e-10604
presumptive structure6.25e-10604
epiblast (generic)6.25e-10604
pre-chordal neural plate8.61e-1061
regional part of cerebral cortex1.20e-0922
tube3.06e-09194
anatomical group6.33e-09626
neocortex6.52e-0920
anatomical system7.76e-09625
cerebral cortex9.96e-0925
pallium9.96e-0925
organ part2.31e-08219
multi-cellular organism2.37e-08659
epithelium2.37e-08309
cell layer2.75e-08312
endoderm-derived structure4.16e-08169
endoderm4.16e-08169
presumptive endoderm4.16e-08169
anatomical cluster1.16e-07286
organ7.67e-07511
Disease
Ontology termp-valuen
squamous cell carcinoma2.63e-0714


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
CTCFL#140690213.16431623931620.007433367036996010.0306681448991398
PAX5#507936.669565531177830.003370290999677260.0172307529721604
REST#597839.650028716128020.001112636247114590.00765296476635937
SMC3#9126210.02995522995520.0126656379767470.0457110569028088



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.