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Coexpression cluster:C3611

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Full id: C3611_Mesenchymal_brain_pineal_amygdala_tenocyte_occipital_breast



Phase1 CAGE Peaks

Hg19::chr17:1928587..1928602,-p2@RTN4RL1
Hg19::chr17:1928607..1928617,-p3@RTN4RL1
Hg19::chr17:1928621..1928641,-p1@RTN4RL1


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism5.81e-27115
central nervous system6.27e-2382
brain1.42e-2169
future brain1.42e-2169
neural tube3.03e-2157
neural rod3.03e-2157
future spinal cord3.03e-2157
neural keel3.03e-2157
regional part of brain9.81e-2059
anterior neural tube3.80e-1942
regional part of forebrain1.32e-1841
forebrain1.32e-1841
future forebrain1.32e-1841
regional part of nervous system2.23e-1894
nervous system2.23e-1894
ectoderm-derived structure1.43e-17169
ectoderm2.29e-17173
presumptive ectoderm2.29e-17173
regional part of cerebral cortex2.61e-1622
head1.40e-15123
anterior region of body1.40e-15129
craniocervical region1.40e-15129
telencephalon2.56e-1534
cerebral hemisphere3.56e-1532
neocortex4.05e-1520
neural plate4.69e-1586
presumptive neural plate4.69e-1586
gray matter9.50e-1534
brain grey matter9.50e-1534
regional part of telencephalon1.19e-1433
neurectoderm1.29e-1490
cerebral cortex8.38e-1325
pallium8.38e-1325
pre-chordal neural plate1.22e-1261
organism subdivision7.33e-10365


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#1066435.360256373075030.0064925092527670.0279110551514668
E2F1#186934.907389214879320.008460985347239390.0324826072886463
EGR1#195834.988179094810140.008056488137383440.032017182822686
ZNF263#1012738.221841637010680.001799043925565870.0109289407016155



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.