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Coexpression cluster:C4444

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Full id: C4444_Nucleus_small_Pericytes_Anulus_colon_skeletal_lung



Phase1 CAGE Peaks

Hg19::chr5:10307849..10307873,-p3@CMBL
Hg19::chr5:10307874..10307930,-p2@CMBL
Hg19::chr5:10307933..10308038,-p1@CMBL


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
multi-tissue structure1.39e-18347
organism subdivision8.06e-15365
mesenchyme8.14e-12238
entire embryonic mesenchyme8.14e-12238
trunk1.13e-11216
multi-cellular organism7.90e-11659
digestive system1.63e-08155
digestive tract1.63e-08155
primitive gut1.63e-08155
anatomical cluster1.98e-08286
subdivision of digestive tract3.03e-08129
endodermal part of digestive tract3.03e-08129
embryo3.14e-08612
cell layer3.18e-08312
embryonic structure4.55e-08605
developing anatomical structure4.55e-08605
germ layer6.29e-08604
embryonic tissue6.29e-08604
presumptive structure6.29e-08604
epiblast (generic)6.29e-08604
trunk mesenchyme6.95e-08143
epithelium7.54e-08309
anatomical system1.32e-07625
anatomical group1.75e-07626
intestine1.96e-0727
organ3.25e-07511
endoderm-derived structure4.58e-07169
endoderm4.58e-07169
presumptive endoderm4.58e-07169


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
CCNT2#90536.336201576962630.003930750035764890.0190799220573178
HMGN3#932438.178547723350590.001827766942164210.010902401717556
SIN3A#2594235.408884726815140.006318961977991520.0277860330099556
SMARCB1#6598318.25271578115740.000164397760679890.00203647701668213
SMARCC1#6599343.66335931963151.20046018043203e-050.000302399567737918
SPI1#668838.204323508522730.001810593189410520.0109335959588809
TFAP2A#7020316.5186343730450.0002218033880766340.00249165580803868
TFAP2C#7022310.80922860986020.0007916746575753130.0061804237974666
ZNF263#1012738.221841637010680.001799043925565870.0109858123453297



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.