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Coexpression cluster:C4672

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Full id: C4672_Fibroblast_CD14_clear_retina_immature_CD34_endometrial



Phase1 CAGE Peaks

Hg19::chr7:20371003..20371017,+p13@ITGB8
Hg19::chr7:20371023..20371030,+p25@ITGB8
Hg19::chr7:20371040..20371070,+p7@ITGB8


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
anatomical system1.48e-12625
regional part of nervous system2.31e-1294
nervous system2.31e-1294
anatomical group2.40e-12626
central nervous system6.15e-1282
embryo2.54e-11612
neural tube4.37e-1157
neural rod4.37e-1157
future spinal cord4.37e-1157
neural keel4.37e-1157
embryonic structure8.92e-11605
developing anatomical structure8.92e-11605
germ layer1.00e-10604
embryonic tissue1.00e-10604
presumptive structure1.00e-10604
epiblast (generic)1.00e-10604
head2.26e-10123
multi-cellular organism3.55e-10659
anterior region of body5.87e-10129
craniocervical region5.87e-10129
organ6.47e-10511
ectoderm-derived structure3.21e-09169
ectoderm4.24e-09173
presumptive ectoderm4.24e-09173
neural plate5.77e-0986
presumptive neural plate5.77e-0986
neurectoderm1.08e-0890
regional part of forebrain1.36e-0841
forebrain1.36e-0841
future forebrain1.36e-0841
brain1.75e-0869
future brain1.75e-0869
anatomical cluster1.80e-08286
anatomical conduit1.96e-08241
anterior neural tube4.74e-0842
regional part of brain6.25e-0859
gray matter6.65e-0834
brain grey matter6.65e-0834
telencephalon6.96e-0834
adult organism1.12e-07115
regional part of telencephalon1.24e-0733
pre-chordal neural plate3.18e-0761
cerebral hemisphere5.13e-0732


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
SMARCB1#6598318.25271578115740.000164397760679890.00203986428984757



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.