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Coexpression cluster:C3198

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Full id: C3198_salivary_breast_submaxillary_Intestinal_Hepatocyte_Prostate_thyroid



Phase1 CAGE Peaks

Hg19::chr11:70963538..70963630,-p1@SHANK2
Hg19::chr11:70963809..70963836,-p2@SHANK2
Hg19::chr11:70963843..70963872,-p6@SHANK2


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
endodermal cell1.06e-1458
endo-epithelial cell5.04e-1242
epithelial cell1.19e-11253
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.90e-23160
endoderm2.90e-23160
presumptive endoderm2.90e-23160
digestive system1.27e-20145
digestive tract1.27e-20145
primitive gut1.27e-20145
organism subdivision1.06e-18264
subdivision of digestive tract3.35e-17118
trunk region element1.00e-16101
immaterial anatomical entity2.50e-16117
subdivision of trunk3.98e-16112
multi-tissue structure6.62e-15342
trunk7.61e-14199
endo-epithelium3.90e-1382
organ system subdivision1.59e-12223
anatomical cluster1.88e-12373
anatomical space1.46e-1095
abdomen element4.06e-1054
abdominal segment element4.06e-1054
foregut1.32e-0987
renal system2.92e-0948
gut epithelium3.38e-0954
multi-cellular organism6.19e-09656
epithelium of foregut-midgut junction7.69e-0925
anatomical boundary7.69e-0925
hepatobiliary system7.69e-0925
foregut-midgut junction7.69e-0925
septum transversum7.69e-0925
urinary system structure7.93e-0947
abdominal segment of trunk8.88e-0960
abdomen8.88e-0960
organ3.17e-08503
thoracic segment of trunk3.98e-0852
sac6.54e-0826
digestive tract diverticulum7.76e-0823
intestine9.41e-0817
epithelial sac1.31e-0725
hepatic diverticulum1.56e-0722
liver primordium1.56e-0722
gastrointestinal system3.65e-0725
cavitated compound organ3.69e-0731
thoracic cavity element5.30e-0734
thoracic cavity5.30e-0734
mesenchyme5.64e-07160
entire embryonic mesenchyme5.64e-07160
anatomical conduit9.01e-07240
Disease
Ontology termp-valuen
carcinoma6.50e-08106
adenocarcinoma6.80e-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
FOXA2#3170216.42030916844350.004810682352105480.0225767436942367
HNF4G#3174219.16894835096450.003543986611284220.0179674960046559
TCF7L2#6934310.77017656313730.0008003181298398380.006120262514633



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.