Personal tools

Coexpression cluster:C3204

From FANTOM5_SSTAR

Revision as of 14:33, 21 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3204_brain_non_parietal_temporal_duodenum_occipital_thalamus



Phase1 CAGE Peaks

Hg19::chr11:79032682..79032686,-p@chr11:79032682..79032686
-
Hg19::chr11:79081820..79081824,-p@chr11:79081820..79081824
-
Hg19::chr11:79109778..79109782,-p@chr11:79109778..79109782
-


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
regional part of nervous system3.78e-3594
nervous system3.78e-3594
central nervous system4.36e-3482
neural tube1.59e-3257
neural rod1.59e-3257
future spinal cord1.59e-3257
neural keel1.59e-3257
regional part of brain3.96e-2959
neural plate8.59e-2986
presumptive neural plate8.59e-2986
neurectoderm2.58e-2790
regional part of forebrain5.35e-2741
forebrain5.35e-2741
future forebrain5.35e-2741
brain7.56e-2769
future brain7.56e-2769
anterior neural tube6.46e-2642
ectoderm-derived structure2.66e-25169
gray matter8.95e-2534
brain grey matter8.95e-2534
ectoderm1.36e-24173
presumptive ectoderm1.36e-24173
telencephalon1.52e-2434
regional part of telencephalon7.61e-2433
cerebral hemisphere1.08e-2332
pre-chordal neural plate2.70e-2361
anterior region of body6.39e-21129
craniocervical region6.39e-21129
cerebral cortex1.27e-2025
pallium1.27e-2025
head1.74e-20123
regional part of cerebral cortex1.98e-1822
adult organism1.15e-17115
neocortex1.02e-1620
organism subdivision9.02e-11365
posterior neural tube8.44e-0815
chordal neural plate8.44e-0815
temporal lobe3.04e-077
cell layer9.73e-07312


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.