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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>cell_data<br>uberon_data<br><br>


Cell Type
Ontology termp-valuen
endothelial cell8.94e-0736
Uber Anatomy
Ontology termp-valuen
central nervous system4.30e-1781
nervous system1.84e-1689
anatomical cluster1.23e-13373
neurectoderm7.27e-1386
neural tube1.76e-1256
neural rod1.76e-1256
future spinal cord1.76e-1256
neural keel1.76e-1256
neural plate4.95e-1282
presumptive neural plate4.95e-1282
tube7.40e-12192
epithelium1.29e-11306
cell layer1.45e-11309
brain1.53e-1168
future brain1.53e-1168
regional part of nervous system5.10e-1153
regional part of brain5.10e-1153
brain grey matter6.98e-1034
gray matter6.98e-1034
telencephalon1.31e-0934
anatomical conduit2.47e-09240
pre-chordal neural plate3.29e-0961
regional part of telencephalon4.60e-0932
cerebral hemisphere1.18e-0832
embryo1.78e-08592
organ system subdivision4.00e-08223
regional part of forebrain5.01e-0841
forebrain5.01e-0841
anterior neural tube5.01e-0841
future forebrain5.01e-0841
developing anatomical structure9.57e-08581
ecto-epithelium1.05e-07104
cerebral cortex2.20e-0725
pallium2.20e-0725
structure with developmental contribution from neural crest2.92e-07132
germ layer4.37e-07560
germ layer / neural crest4.37e-07560
embryonic tissue4.37e-07560
presumptive structure4.37e-07560
germ layer / neural crest derived structure4.37e-07560
epiblast (generic)4.37e-07560
multi-cellular organism5.20e-07656
embryonic structure5.65e-07564


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.