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Coexpression cluster:C1476

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Full id: C1476_Neurons_iPS_occipital_temporal_parietal_duodenum_spinal



Phase1 CAGE Peaks

Hg19::chr1:32799593..32799616,-p2@BX648622
Hg19::chr1:32799709..32799739,-p1@BX648622
Hg19::chr1:32799803..32799823,-p@chr1:32799803..32799823
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Hg19::chr1:32799908..32799938,-p@chr1:32799908..32799938
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Hg19::chr1:32800048..32800094,-p@chr1:32800048..32800094
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Hg19::chr1:32800303..32800316,-p@chr1:32800303..32800316
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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
central nervous system5.02e-1782
regional part of nervous system1.27e-1694
nervous system1.27e-1694
neural tube2.32e-1257
neural rod2.32e-1257
future spinal cord2.32e-1257
neural keel2.32e-1257
neurectoderm7.24e-1290
tube8.05e-12194
epithelium8.09e-12309
cell layer9.28e-12312
brain1.49e-1169
future brain1.49e-1169
neural plate4.45e-1186
presumptive neural plate4.45e-1186
regional part of brain1.78e-1059
gray matter1.04e-0934
brain grey matter1.04e-0934
anatomical conduit1.97e-09241
telencephalon2.46e-0934
regional part of telencephalon2.47e-0933
anatomical cluster9.24e-09286
embryo1.17e-08612
cerebral hemisphere2.21e-0832
pre-chordal neural plate2.25e-0861
anterior neural tube1.03e-0742
regional part of forebrain1.20e-0741
forebrain1.20e-0741
future forebrain1.20e-0741
cerebral cortex2.43e-0725
pallium2.43e-0725
embryonic structure4.25e-07605
developing anatomical structure4.25e-07605
germ layer6.23e-07604
embryonic tissue6.23e-07604
presumptive structure6.23e-07604
epiblast (generic)6.23e-07604


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
POLR2A#543062.147453176558070.01019570676818780.0380459275104604



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.