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Coexpression cluster:C4483

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Full id: C4483_caudate_Fibroblast_acute_putamen_pituitary_mesenchymal_occipital



Phase1 CAGE Peaks

Hg19::chr5:163723701..163723725,+p2@ENST00000517508
Hg19::chr5:163723738..163723786,+p1@ENST00000517508
Hg19::chr5:163723787..163723799,+p3@ENST00000517508


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><br>


Cell Type
Ontology termp-valuen
non-terminally differentiated cell7.28e-09180
preadipocyte1.12e-0712
Uber Anatomy
Ontology termp-valuen
neural tube7.04e-3057
neural rod7.04e-3057
future spinal cord7.04e-3057
neural keel7.04e-3057
regional part of forebrain1.09e-2841
forebrain1.09e-2841
future forebrain1.09e-2841
anterior neural tube1.10e-2742
cerebral hemisphere9.30e-2732
regional part of brain9.89e-2759
gray matter2.57e-2634
brain grey matter2.57e-2634
regional part of nervous system4.48e-2694
nervous system4.48e-2694
telencephalon4.50e-2634
brain8.88e-2669
future brain8.88e-2669
neural plate1.17e-2586
presumptive neural plate1.17e-2586
regional part of telencephalon4.81e-2533
central nervous system6.25e-2582
pre-chordal neural plate1.17e-2461
neurectoderm1.21e-2390
neocortex2.51e-2020
regional part of cerebral cortex1.21e-1922
cerebral cortex1.97e-1925
pallium1.97e-1925
head1.08e-17123
anterior region of body5.97e-16129
craniocervical region5.97e-16129
tube2.78e-14194
adult organism6.38e-14115
ectoderm-derived structure5.33e-12169
epithelium7.73e-12309
cell layer1.90e-11312
organism subdivision2.83e-11365
ectoderm2.85e-11173
presumptive ectoderm2.85e-11173
cavity lining2.39e-0912
serous membrane2.39e-0912
anatomical cluster3.59e-09286
anatomical conduit6.34e-09241
nucleus of brain2.56e-089
neural nucleus2.56e-089
multi-tissue structure3.21e-08347
gyrus3.97e-086
basal ganglion7.37e-089
nuclear complex of neuraxis7.37e-089
aggregate regional part of brain7.37e-089
collection of basal ganglia7.37e-089
cerebral subcortex7.37e-089
parietal lobe4.53e-075
occipital lobe5.47e-075
omentum7.26e-076
peritoneum7.26e-076
abdominal cavity7.26e-076
visceral peritoneum7.26e-076


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
NANOG#79923329.24477848101273.99627955670032e-050.000739882007839435
SRF#6722313.79717826216780.0003806615025800190.00376049060423331
TRIM28#10155318.59052504526250.0001555969297255280.00197717334756106



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.