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Coexpression cluster:C2407: Difference between revisions

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|tf_chipseq_enrich=GATA3#2625;4:27.236516357206:1.81561517799785e-06:6.76734595199561e-05
|tf_chipseq_enrich=GATA3#2625;4:27.236516357206:1.81561517799785e-06:6.76734595199561e-05
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}}
}}

Revision as of 15:28, 26 November 2012


Full id: C2407_Alveolar_Tracheal_Small_Bronchial_MCF7_Amniotic_Renal



Phase1 CAGE Peaks

Hg19::chr17:39680005..39680049,-p@chr17:39680005..39680049
-
Hg19::chr17:39680672..39680701,-p4@KRT19
Hg19::chr17:39680781..39680798,-p2@KRT19
Hg19::chr17:39684550..39684567,-p1@KRT19


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 structure4.26e-19160
endoderm4.26e-19160
presumptive endoderm4.26e-19160
urinary system structure5.65e-1447
digestive system7.43e-14145
digestive tract7.43e-14145
primitive gut7.43e-14145
renal system2.05e-1348
subdivision of digestive tract7.41e-13118
anatomical space1.79e-1195
trunk region element2.84e-11101
endo-epithelium1.20e-1082
extraembryonic membrane3.37e-1014
membranous layer3.37e-1014
immaterial anatomical entity4.69e-10117
organism subdivision6.79e-10264
respiratory system7.51e-1074
thoracic cavity element2.59e-0934
thoracic cavity2.59e-0934
subdivision of trunk4.50e-09112
respiratory tract5.08e-0954
thoracic segment organ8.25e-0935
respiratory system epithelium1.36e-0828
epithelial bud8.97e-0837
nephron tubule epithelium1.09e-0710
excretory tube1.48e-0716
kidney epithelium1.48e-0716
thoracic segment of trunk2.74e-0752
foregut2.84e-0787
respiratory tract epithelium3.21e-0719
lung epithelium3.21e-0719
epithelial fold3.25e-0747
tracheobronchial tree3.50e-0715
lower respiratory tract3.50e-0715
lung4.09e-0722
respiratory tube4.09e-0722
respiration organ4.09e-0722
pair of lungs4.09e-0722
lung primordium4.09e-0722
lung bud4.09e-0722
nephron epithelium4.56e-0715
renal tubule4.56e-0715
nephron tubule4.56e-0715
nephron4.56e-0715
uriniferous tubule4.56e-0715
nephrogenic mesenchyme4.56e-0715
chorion5.41e-077
organ part8.51e-07218
Disease
Ontology termp-valuen
carcinoma1.04e-16106
cell type cancer2.84e-11143
adenocarcinoma1.86e-0925
squamous cell carcinoma9.10e-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
GATA3#2625427.2365163572061.81561517799785e-066.76734595199561e-05



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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