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Difference between revisions of "Coexpression cluster:C2467"

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|tf_chipseq_enrich=EP300#2033;4:6.7739417262232:0.000474845982144264:0.00434297570095147!FOXA1#3169;4:11.0814197493855:6.62943068949433e-05:0.00107078736742978!FOXA2#3170;4:24.6304637526652:2.71504128667089e-06:9.42987020081878e-05!HNF4A#3172;4:23.1322903629537:3.48990320893214e-06:0.000115598478032878!HNF4G#3174;4:28.7534225264468:1.46167379934821e-06:5.66650890609235e-05!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.000743230787491224!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00391690060382102!MAFF#23764;3:42.2365173674589:2.20786227449124e-05:0.00048391800227826!MAFK#7975;2:13.550366568915:0.0077720281209805:0.0319568049183891!NR3C1#2908;4:14.973023331173:1.98868032687801e-05:0.000443131607976984!RXRA#6256;4:20.0746171391333:6.1537798808435e-06:0.000182169676013439!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00248855454441413
 
|tf_chipseq_enrich=EP300#2033;4:6.7739417262232:0.000474845982144264:0.00434297570095147!FOXA1#3169;4:11.0814197493855:6.62943068949433e-05:0.00107078736742978!FOXA2#3170;4:24.6304637526652:2.71504128667089e-06:9.42987020081878e-05!HNF4A#3172;4:23.1322903629537:3.48990320893214e-06:0.000115598478032878!HNF4G#3174;4:28.7534225264468:1.46167379934821e-06:5.66650890609235e-05!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.000743230787491224!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00391690060382102!MAFF#23764;3:42.2365173674589:2.20786227449124e-05:0.00048391800227826!MAFK#7975;2:13.550366568915:0.0077720281209805:0.0319568049183891!NR3C1#2908;4:14.973023331173:1.98868032687801e-05:0.000443131607976984!RXRA#6256;4:20.0746171391333:6.1537798808435e-06:0.000182169676013439!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00248855454441413
 
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 +
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}}
 
}}

Revision as of 06:31, 26 November 2012


Full id: C2467_Olfactory_Fibroblast_Hair_alveolar_glioblastoma_Preadipocyte_Ewing



Phase1 CAGE Peaks

  Short description
Hg19::chr18:56246745..56246774,- p11@ALPK2
Hg19::chr18:56246785..56246806,- p1@ALPK2
Hg19::chr18:56246814..56246824,- p26@ALPK2
Hg19::chr18:56246825..56246890,- p5@ALPK2


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Cell Type
Ontology termp-valuen
fibroblast3.60e-1876
skin fibroblast1.16e-1023
stromal cell7.67e-0928
mesothelial cell5.71e-0819
animal cell1.96e-07679
eukaryotic cell1.96e-07679
Uber Anatomy
Ontology termp-valuen
larynx1.43e-089
skin of body9.58e-0741


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
EP300#203346.77394172622320.0004748459821442640.00434297570095147
FOXA1#3169411.08141974938556.62943068949433e-050.00107078736742978
FOXA2#3170424.63046375266522.71504128667089e-069.42987020081878e-05
HNF4A#3172423.13229036295373.48990320893214e-060.000115598478032878
HNF4G#3174428.75342252644681.46167379934821e-065.66650890609235e-05
JUN#3725412.51282919233634.07770316866756e-050.000743230787491224
JUND#372746.994663941871030.000417684217818580.00391690060382102
MAFF#23764342.23651736745892.20786227449124e-050.00048391800227826
MAFK#7975213.5503665689150.00777202812098050.0319568049183891
NR3C1#2908414.9730233311731.98868032687801e-050.000443131607976984
RXRA#6256420.07461713913336.1537798808435e-060.000182169676013439
ZNF263#1012748.221841637010680.0002187871180958320.00248855454441413



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.