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Coexpression cluster:C4786

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Full id: C4786_occipital_H9_parietal_Neural_duodenum_Neurons_temporal



Phase1 CAGE Peaks

Hg19::chr9:103235365..103235419,+p1@TMEFF1
Hg19::chr9:103235423..103235444,+p4@TMEFF1
Hg19::chr9:103235453..103235470,+p3@TMEFF1


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
regional part of nervous system9.76e-3494
nervous system9.76e-3494
central nervous system1.77e-2982
neural tube7.48e-2357
neural rod7.48e-2357
future spinal cord7.48e-2357
neural keel7.48e-2357
brain9.61e-2369
future brain9.61e-2369
neurectoderm1.33e-2290
neural plate4.98e-2186
presumptive neural plate4.98e-2186
ectoderm2.88e-20173
presumptive ectoderm2.88e-20173
pre-chordal neural plate2.82e-1961
regional part of brain4.17e-1959
ectoderm-derived structure6.97e-19169
tube1.36e-18194
telencephalon1.75e-1834
gray matter1.84e-1834
brain grey matter1.84e-1834
cell layer3.05e-18312
regional part of forebrain3.53e-1841
forebrain3.53e-1841
future forebrain3.53e-1841
anterior neural tube4.51e-1842
regional part of telencephalon5.99e-1833
epithelium7.10e-18309
cerebral hemisphere3.17e-1732
anatomical conduit8.53e-16241
head1.29e-15123
anterior region of body5.91e-15129
craniocervical region5.91e-15129
cerebral cortex2.52e-1325
pallium2.52e-1325
organism subdivision1.37e-12365
anatomical cluster2.17e-12286
regional part of cerebral cortex4.09e-1222
neocortex4.32e-1120
multi-cellular organism4.63e-09659
endothelium1.27e-0718
blood vessel endothelium1.27e-0718
cardiovascular system endothelium1.27e-0718
embryo1.89e-07612
organ part2.29e-07219
vasculature5.57e-0779
vascular system5.57e-0779
Disease
Ontology termp-valuen
germ cell and embryonal cancer4.47e-1122
germ cell cancer4.47e-1122


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
CTCF#1066435.360256373075030.0064925092527670.0281602713505434
E2F6#187635.017155731697390.00791769806886330.0324688420219104
EGR1#195834.988179094810140.008056488137383440.0322800416089998
MAX#414936.452555509007120.003721913834265510.0187548470007167
RAD21#5885310.35503389545630.0009004912073565420.0066917889003209
USF1#739136.361499277207960.00388404057290560.0191324079517823
ZBTB7A#5134137.35190930787590.002516255860282270.0141075394992495



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.