Personal tools

Coexpression cluster:C4739

From FANTOM5_SSTAR

Revision as of 14:52, 21 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C4739_heart_vagina_bile_pineal_pancreas_lung_bladder



Phase1 CAGE Peaks

Hg19::chr8:17658704..17658715,-p10@MTUS1
Hg19::chr8:17658721..17658766,-p3@MTUS1
Hg19::chr8:17658793..17658804,-p9@MTUS1


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
epithelial cell1.39e-12254
endodermal cell2.18e-0959
endo-epithelial cell5.94e-0743
Uber Anatomy
Ontology termp-valuen
adult organism8.41e-40115
organ1.21e-24511
digestive system1.10e-21155
digestive tract1.10e-21155
primitive gut1.10e-21155
endoderm-derived structure3.61e-21169
endoderm3.61e-21169
presumptive endoderm3.61e-21169
multi-tissue structure3.34e-20347
subdivision of digestive tract1.65e-18129
endodermal part of digestive tract1.65e-18129
head4.94e-18123
anterior region of body5.41e-18129
craniocervical region5.41e-18129
neurectoderm5.82e-1790
neural plate1.04e-1686
presumptive neural plate1.04e-1686
neural tube2.27e-1657
neural rod2.27e-1657
future spinal cord2.27e-1657
neural keel2.27e-1657
multi-cellular organism1.82e-15659
ectoderm4.19e-15173
presumptive ectoderm4.19e-15173
embryo5.61e-15612
mixed endoderm/mesoderm-derived structure7.37e-15130
ectoderm-derived structure9.91e-15169
organ part1.23e-14219
central nervous system2.10e-1482
brain4.49e-1469
future brain4.49e-1469
anatomical system5.79e-14625
embryonic structure6.55e-14605
developing anatomical structure6.55e-14605
regional part of nervous system9.02e-1494
nervous system9.02e-1494
anatomical group9.49e-14626
anatomical cluster1.08e-13286
germ layer1.30e-13604
embryonic tissue1.30e-13604
presumptive structure1.30e-13604
epiblast (generic)1.30e-13604
regional part of brain2.01e-1359
organism subdivision6.49e-13365
anterior neural tube3.22e-1242
pre-chordal neural plate5.11e-1261
regional part of forebrain1.04e-1141
forebrain1.04e-1141
future forebrain1.04e-1141
foregut1.39e-1198
anatomical conduit2.59e-11241
primordium2.32e-10168
respiratory system6.79e-1072
endo-epithelium8.25e-1082
immaterial anatomical entity1.73e-09126
epithelium4.88e-09309
orifice5.88e-0935
gland7.33e-0959
cell layer7.48e-09312
gray matter9.70e-0934
brain grey matter9.70e-0934
telencephalon1.54e-0834
gut epithelium2.52e-0854
regional part of telencephalon2.85e-0833
trunk region element4.16e-08107
organ segment6.82e-0897
cerebral hemisphere1.44e-0732
epithelium of foregut-midgut junction6.74e-0725
anatomical boundary6.74e-0725
hepatobiliary system6.74e-0725
foregut-midgut junction6.74e-0725
septum transversum6.74e-0725
regional part of cerebral cortex7.29e-0722
Disease
Ontology termp-valuen
carcinoma5.62e-20106
cell type cancer3.32e-18143
adenocarcinoma1.05e-0725
cancer7.15e-07235


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.