Personal tools

Coexpression cluster:C933

From FANTOM5_SSTAR

Revision as of 14:34, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C933_skeletal_heart_left_penis_Cardiac_Preadipocyte_tongue



Phase1 CAGE Peaks

Hg19::chr1:78354243..78354293,+p2@NEXN
Hg19::chr1:78354297..78354320,+p1@NEXN
Hg19::chr1:78354330..78354366,+p3@NEXN
Hg19::chr1:78381736..78381749,+p@chr1:78381736..78381749
+
Hg19::chr1:78383815..78383829,+p12@NEXN
Hg19::chr1:78390864..78390882,+p@chr1:78390864..78390882
+
Hg19::chr1:78392094..78392114,+p5@NEXN
Hg19::chr1:78398956..78398980,+p6@NEXN
Hg19::chr1:78401567..78401585,+p@chr1:78401567..78401585
+


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>


Uber Anatomy
Ontology termp-valuen
multi-tissue structure4.34e-13342
multi-cellular organism2.14e-12656
muscle tissue2.31e-1264
musculature2.31e-1264
musculature of body2.31e-1264
dense mesenchyme tissue5.59e-1273
skeletal muscle tissue1.10e-1162
striated muscle tissue1.10e-1162
myotome1.10e-1162
paraxial mesoderm1.35e-1172
presumptive paraxial mesoderm1.35e-1172
mesenchyme1.45e-11160
entire embryonic mesenchyme1.45e-11160
somite1.62e-1171
presomitic mesoderm1.62e-1171
presumptive segmental plate1.62e-1171
dermomyotome1.62e-1171
trunk paraxial mesoderm1.62e-1171
surface structure3.85e-1199
organism subdivision2.14e-10264
multilaminar epithelium3.29e-1083
epithelial vesicle1.05e-0978
anatomical system1.07e-09624
trunk mesenchyme1.46e-09122
anatomical group1.82e-09625
anatomical cluster7.11e-08373
primary circulatory organ3.91e-0727


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#7992339.748259493670880.002874553687984370.015572959467756
TRIM28#1015536.196841681754170.0102278065029780.038085423872946



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.