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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2414_kidney_smallcell_seminal_somatostatinoma_ductus_small_Fibroblast
|full_id=C2414_kidney_smallcell_seminal_somatostatinoma_ductus_small_Fibroblast
|gostat_on_coexpression_clusters=GO:0030878!thyroid gland development!0.008242081714353!3213$GO:0035270!endocrine system development!0.0180540837552494!3213$GO:0048732!gland development!0.0180540837552494!3213
|gostat_on_coexpression_clusters=GO:0030878!thyroid gland development!0.008242081714353!3213$GO:0035270!endocrine system development!0.0180540837552494!3213$GO:0048732!gland development!0.0180540837552494!3213

Revision as of 15:08, 12 September 2012


Full id: C2414_kidney_smallcell_seminal_somatostatinoma_ductus_small_Fibroblast



Phase1 CAGE Peaks

Hg19::chr17:46667561..46667572,-p4@HOXB3
Hg19::chr17:46667594..46667619,-p1@HOXB3
Hg19::chr17:46667628..46667642,-p2@HOXB3
Hg19::chr17:46668194..46668198,+p1@ENST00000429755
p1@ENST00000487849
p1@ENST00000492897


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

GO IDGO nameFDR corrected p-value
GO:0030878thyroid gland development0.008242081714353
GO:0035270endocrine system development0.0180540837552494
GO:0048732gland development0.0180540837552494



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
intraembryonic coelom6.90e-1721
cavitated compound organ1.25e-1532
kidney1.80e-1527
kidney mesenchyme1.80e-1527
kidney rudiment1.80e-1527
kidney field1.80e-1527
abdominal segment of trunk1.88e-1561
abdomen1.88e-1561
mesonephros3.43e-1518
pronephros3.43e-1518
nephrogenic cord3.43e-1518
pronephric mesoderm3.43e-1518
rostral part of nephrogenic cord3.43e-1518
presumptive pronephric mesoderm3.43e-1518
excretory tube4.18e-1417
mesonephric epithelium4.18e-1417
mesonephric tubule4.18e-1417
nephric duct4.18e-1417
kidney epithelium4.18e-1417
renal duct4.18e-1417
mesonephric duct4.18e-1417
pronephric duct4.18e-1417
renal system4.28e-1445
subdivision of trunk9.60e-14113
urinary system structure1.79e-1344
urogenital ridge4.91e-1320
nephron epithelium4.94e-1316
nephron4.94e-1316
uriniferous tubule4.94e-1316
metanephric mesenchyme4.94e-1316
nephrogenic mesenchyme4.94e-1316
renal tubule9.79e-1312
nephron tubule9.79e-1312
nephron tubule epithelium9.79e-1312
trunk region element3.35e-12107
trunk9.47e-12216
abdomen element9.89e-1255
abdominal segment element9.89e-1255
duct1.17e-1126
body cavity precursor1.88e-1163
intermediate mesoderm3.45e-1137
anatomical space1.82e-10104
cortex of kidney4.62e-1013
renal parenchyma4.62e-1013
immaterial anatomical entity2.59e-09126
anatomical cavity3.45e-0970
large intestine4.93e-0911
mesenchyme1.85e-08238
entire embryonic mesenchyme1.85e-08238
cavity lining3.34e-0812
serous membrane3.34e-0812
parenchyma4.78e-0817
gastrointestinal system4.84e-0835
cortex1.81e-0716
internal genitalia2.12e-0725
trunk mesenchyme2.30e-07143
colon4.12e-079


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
ESR1#2099323.07645247211590.0001339105244968570.0017578533519265
TRIM28#10155418.59052504526258.36730015875654e-060.00023002697059236
USF1#739134.771124457905970.01370465887188020.0482976503431852
ZNF263#1012736.166381227758010.006539814347975980.027970501277213



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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