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Coexpression cluster:C1927: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 17:47, 8 August 2012


Full id: C1927_Corneal_Esophageal_Urothelial_Endothelial_Bronchial_Sebocyte_Tracheal



Phase1 CAGE Peaks

Hg19::chr3:50192438..50192447,+p5@SEMA3F
Hg19::chr3:50192457..50192498,+p2@SEMA3F
Hg19::chr3:50192499..50192534,+p1@SEMA3F
Hg19::chr3:50192537..50192563,+p3@SEMA3F
Hg19::chr3:50211299..50211317,-p@chr3:50211299..50211317
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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><br>

Uber Anatomy
Ontology termp-valuen
multi-cellular organism5.14e-29659
epithelium2.93e-26309
cell layer1.85e-25312
anatomical cluster8.28e-25286
anatomical system3.46e-24625
anatomical group6.94e-24626
embryo3.20e-23612
multi-tissue structure1.47e-22347
embryonic structure1.12e-20605
developing anatomical structure1.12e-20605
anatomical conduit1.53e-20241
germ layer2.66e-20604
embryonic tissue2.66e-20604
presumptive structure2.66e-20604
epiblast (generic)2.66e-20604
organism subdivision1.08e-17365
tube3.11e-15194
epithelial tube2.41e-14118
organ part1.37e-13219
organ4.40e-13511
compound organ4.46e-1269
vasculature2.41e-1179
vascular system2.41e-1179
subdivision of trunk2.85e-11113
endoderm-derived structure7.45e-11169
endoderm7.45e-11169
presumptive endoderm7.45e-11169
splanchnic layer of lateral plate mesoderm8.85e-1184
endothelium1.23e-1018
blood vessel endothelium1.23e-1018
cardiovascular system endothelium1.23e-1018
subdivision of head2.16e-1048
mesenchyme3.43e-10238
entire embryonic mesenchyme3.43e-10238
trunk region element4.64e-10107
vessel4.67e-1069
respiratory system1.19e-0972
blood vessel2.12e-0960
epithelial tube open at both ends2.12e-0960
blood vasculature2.12e-0960
vascular cord2.12e-0960
primordium2.65e-09168
ectoderm-derived structure3.51e-09169
mesonephros4.52e-0918
pronephros4.52e-0918
nephrogenic cord4.52e-0918
pronephric mesoderm4.52e-0918
rostral part of nephrogenic cord4.52e-0918
presumptive pronephric mesoderm4.52e-0918
intraembryonic coelom5.90e-0921
ectoderm6.27e-09173
presumptive ectoderm6.27e-09173
excretory tube1.12e-0817
mesonephric epithelium1.12e-0817
mesonephric tubule1.12e-0817
nephric duct1.12e-0817
kidney epithelium1.12e-0817
renal duct1.12e-0817
mesonephric duct1.12e-0817
pronephric duct1.12e-0817
nephron epithelium1.56e-0816
nephron1.56e-0816
uriniferous tubule1.56e-0816
metanephric mesenchyme1.56e-0816
nephrogenic mesenchyme1.56e-0816
renal system1.61e-0845
kidney2.35e-0827
kidney mesenchyme2.35e-0827
kidney rudiment2.35e-0827
kidney field2.35e-0827
squamous epithelium2.40e-0825
head2.92e-08123
ectodermal placode3.16e-0829
urinary system structure3.32e-0844
trunk5.18e-08216
urogenital ridge5.44e-0820
anterior region of body6.96e-08129
craniocervical region6.96e-08129
simple squamous epithelium1.17e-0722


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

No analysis results for this cluster

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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