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Coexpression cluster:C2420

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Full id: C2420_Smooth_osteosarcoma_Fibroblast_Preadipocyte_mesenchymal_thyroid_osteoclastoma



Phase1 CAGE Peaks

Hg19::chr17:4872260..4872292,-p@chr17:4872260..4872292
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Hg19::chr17:4872322..4872330,-p@chr17:4872322..4872330
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Hg19::chr17:4872340..4872347,-p@chr17:4872340..4872347
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Hg19::chr17:4872349..4872405,-p@chr17:4872349..4872405
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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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
epithelial vesicle9.16e-1378
dense mesenchyme tissue1.49e-1273
somite1.81e-1271
presomitic mesoderm1.81e-1271
presumptive segmental plate1.81e-1271
dermomyotome1.81e-1271
trunk paraxial mesoderm1.81e-1271
paraxial mesoderm3.29e-1272
presumptive paraxial mesoderm3.29e-1272
multilaminar epithelium2.48e-1183
skeletal muscle tissue2.58e-1162
striated muscle tissue2.58e-1162
myotome2.58e-1162
muscle tissue1.91e-1064
musculature1.91e-1064
musculature of body1.91e-1064
mesenchyme3.06e-10160
entire embryonic mesenchyme3.06e-10160
organism subdivision1.22e-09264
multi-tissue structure1.56e-09342
trunk2.27e-08199
trunk mesenchyme1.33e-07122
Disease
Ontology termp-valuen
ovarian cancer8.81e-0714


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
CEBPB#105135.978360719368610.007153832484726970.029726231832275
EP300#203346.77394172622320.0004748459821442640.00434069492596628
FOSL2#2355312.69765045342130.000787568572975710.0061663448679069
GTF2F1#2962412.73966087675773.79492332235515e-050.000717613610109451
JUN#372539.384621894252250.001918994502030470.0112847897971599
JUND#372735.245997956403270.01043432751748420.0386847970038528
STAT3#677437.889598747865680.003190760481680130.0167406728597504
TAF1#687243.343046285745290.008005664898701650.0322024201338585
TBP#690843.706770687096390.005296377814784350.0244032471257009
TFAP2A#7020416.5186343730451.34240829060362e-050.000326425563358211
TFAP2C#7022410.80922860986027.32289634782688e-050.00114507556770578



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.