Personal tools

Coexpression cluster:C4049

From FANTOM5_SSTAR

Revision as of 14:44, 21 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C4049_choriocarcinoma_MCF7_pancreatic_Hair_breast_testicular_gall



Phase1 CAGE Peaks

Hg19::chr20:55204351..55204377,+p1@TFAP2C
Hg19::chr20:55213326..55213338,+p@chr20:55213326..55213338
+
Hg19::chr20:55213735..55213739,+p@chr20:55213735..55213739
+


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>


Cell Type
Ontology termp-valuen
epithelial cell4.30e-16254
endo-epithelial cell1.09e-1243
ectodermal cell4.34e-1171
ecto-epithelial cell1.64e-0833
neurectodermal cell7.86e-0859
epithelial cell of alimentary canal8.75e-0821
endodermal cell5.10e-0759
Uber Anatomy
Ontology termp-valuen
surface structure1.24e-2295
ectoderm-derived structure1.53e-15169
organ2.75e-15511
ectoderm4.15e-15173
presumptive ectoderm4.15e-15173
endoderm-derived structure1.38e-14169
endoderm1.38e-14169
presumptive endoderm1.38e-14169
mouth2.64e-1428
stomodeum2.64e-1428
digestive system2.22e-12155
digestive tract2.22e-12155
primitive gut2.22e-12155
orifice7.65e-1235
oral opening5.34e-1121
skin of body7.20e-1140
organ part1.84e-10219
respiratory system3.50e-1072
head4.88e-10123
anterior region of body6.61e-10129
craniocervical region6.61e-10129
subdivision of head1.08e-0948
organism subdivision1.25e-08365
reproductive structure1.54e-0859
reproductive system1.54e-0859
integument1.70e-0845
integumental system1.70e-0845
mixed endoderm/mesoderm-derived structure2.02e-08130
extraembryonic membrane8.95e-0814
membranous layer8.95e-0814
reproductive organ2.18e-0748
multi-cellular organism3.65e-07659
organ component layer3.80e-0757
Disease
Ontology termp-valuen
carcinoma2.17e-10106
cell type cancer5.10e-10143
squamous cell carcinoma5.31e-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


No analysis results for this cluster

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.