Personal tools

Coexpression cluster:C727

From FANTOM5_SSTAR

Revision as of 16:38, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C727_colon_smooth_rectum_duodenum_bladder_esophagus_prostate



Phase1 CAGE Peaks

Hg19::chr10:71175837..71175884,-p8@TACR2
Hg19::chr10:71176135..71176147,-p6@TACR2
Hg19::chr10:71176561..71176571,-p4@TACR2
Hg19::chr10:71176580..71176586,-p7@TACR2
Hg19::chr10:71176627..71176638,-p3@TACR2
Hg19::chr10:71176667..71176679,-p2@TACR2
Hg19::chr12:95775013..95775020,-p1@ENST00000549961
Hg19::chr22:31487193..31487207,+p19@SMTN
Hg19::chr22:31487784..31487801,+p@chr22:31487784..31487801
+
Hg19::chr2:74143846..74143862,+p@chr2:74143846..74143862
+
Hg19::chr9:139442039..139442067,+p1@uc004cib.1


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:0003012muscle system process0.000656532722588068
GO:0006936muscle contraction0.000656532722588068
GO:0004995tachykinin receptor activity0.00549439764808921
GO:0007217tachykinin signaling pathway0.00659298603237552
GO:0003008system process0.0161430672631361
GO:0006939smooth muscle contraction0.0161430672631361
GO:0007588excretion0.0161430672631361
GO:0008307structural constituent of muscle0.0161430672631361
GO:0008188neuropeptide receptor activity0.0161430672631361
GO:0042923neuropeptide binding0.0161430672631361
GO:0030594neurotransmitter receptor activity0.0347768246083993
GO:0042165neurotransmitter binding0.0347768246083993
GO:0001653peptide receptor activity0.0347768246083993
GO:0008528peptide receptor activity, G-protein coupled0.0347768246083993
GO:0007517muscle development0.0377085351688235
GO:0042277peptide binding0.0416847670934325
GO:0032501multicellular organismal process0.0416847670934325



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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
intestine7.67e-2617
gastrointestinal system3.57e-2225
adult organism8.64e-18114
large intestine2.15e-1711
colon5.23e-149
small intestine6.52e-144
male reproductive organ8.24e-1111
male genital duct1.20e-103
internal male genitalia1.20e-103
subdivision of digestive tract9.17e-10118
vermiform appendix5.70e-091
caecum5.70e-091
midgut5.70e-091
penis6.16e-091
intromittent organ6.16e-091
lateral plate mesenchyme6.16e-091
undifferentiated genital tubercle6.16e-091
somatopleure6.16e-091
uterus or analog7.18e-091
digestive system9.80e-09145
digestive tract9.80e-09145
primitive gut9.80e-09145
vas deferens1.22e-081
spermatic cord1.22e-081
epididymis1.42e-081
male organism3.25e-0822
male reproductive system3.25e-0822
duct of male reproductive system3.34e-084
endoderm-derived structure1.16e-07160
endoderm1.16e-07160
presumptive endoderm1.16e-07160
lower digestive tract5.57e-075
reproductive structure6.79e-0759
reproductive system6.79e-0759


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


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.