Personal tools

Coexpression cluster:C2835

From FANTOM5_SSTAR

Revision as of 14:28, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2835_Melanocyte_myxofibrosarcoma_placenta_cervical_Corneal_breast_salivary



Phase1 CAGE Peaks

Hg19::chr6:10412576..10412599,-p5@TFAP2A
Hg19::chr6:10412600..10412637,-p1@TFAP2A
Hg19::chr6:10415263..10415274,-p8@TFAP2A
Hg19::chr6:10415276..10415341,-p2@TFAP2A


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
surface structure1.49e-1399
respiratory system1.18e-1274
endoderm-derived structure2.46e-10160
endoderm2.46e-10160
presumptive endoderm2.46e-10160
respiratory tract2.97e-0854
skin of body6.55e-0841
extraembryonic membrane7.63e-0814
membranous layer7.63e-0814
orifice1.64e-0736
respiratory primordium2.12e-0738
endoderm of foregut2.12e-0738
renal system5.04e-0748
oral opening5.12e-0722
urinary system structure7.68e-0747
digestive system9.64e-07145
digestive tract9.64e-07145
primitive gut9.64e-07145
Disease
Ontology termp-valuen
cell type cancer1.16e-21143
carcinoma1.14e-16106
disease of cellular proliferation4.69e-13239
cancer1.11e-12235


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
CTBP2#1488231.35850016966410.001492676882047230.00954353724420757
SMARCC1#6599221.83167965981570.003051207456162050.0160941947229348
SUZ12#23512450.11578091106291.5827390373096e-078.83955520414855e-06
TAF1#687243.343046285745290.008005664898701650.0323194293140898
TBP#690843.706770687096390.005296377814784350.0244929331649957



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.