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Coexpression cluster:C4649

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Full id: C4649_H9_iPS_HES3GFP_Hepatocyte_mature_heart_anaplastic



Phase1 CAGE Peaks

Hg19::chr7:121738923..121738927,-p@chr7:121738923..121738927
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Hg19::chr7:121784265..121784276,-p2@AASS
Hg19::chr7:121784285..121784350,-p1@AASS


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 organism6.72e-19114
nervous system6.88e-1789
central nervous system6.42e-1681
neural tube7.85e-1556
neural rod7.85e-1556
future spinal cord7.85e-1556
neural keel7.85e-1556
neurectoderm9.35e-1586
ectoderm-derived structure6.08e-14171
ectoderm6.08e-14171
presumptive ectoderm6.08e-14171
organ system subdivision2.41e-13223
regional part of nervous system2.94e-1353
regional part of brain2.94e-1353
neural plate4.05e-1382
presumptive neural plate4.05e-1382
brain5.28e-1368
future brain5.28e-1368
regional part of forebrain4.24e-1241
forebrain4.24e-1241
anterior neural tube4.24e-1241
future forebrain4.24e-1241
anatomical cluster1.48e-11373
structure with developmental contribution from neural crest1.21e-10132
pre-chordal neural plate1.11e-0961
brain grey matter1.70e-0934
gray matter1.70e-0934
telencephalon5.65e-0934
ecto-epithelium8.59e-09104
regional part of telencephalon1.29e-0832
multi-cellular organism2.50e-08656
multi-tissue structure3.47e-08342
cerebral hemisphere4.82e-0832
anatomical conduit3.59e-07240


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
FOXA2#3170216.42030916844350.004810682352105480.0226011180464033
HNF4A#3172215.42152690863580.005444210486686610.0246922264740983
HNF4G#3174219.16894835096450.003543986611284220.0179805886663062
NFYA#4800212.28372046655370.008516011403724430.0324979434008176
NFYB#4801211.17319550235760.01025467135054530.0381609699333546
NR3C1#290829.982015554115360.01278474365547170.0460772255722897



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.