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Coexpression cluster:C2976: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2976_Small_Gingival_Urothelial_keratoacanthoma_Keratinocyte_neuroectodermal_Bronchial
|full_id=C2976_Small_Gingival_Urothelial_keratoacanthoma_Keratinocyte_neuroectodermal_Bronchial
|id=C2976
|id=C2976

Revision as of 15:48, 12 September 2012


Full id: C2976_Small_Gingival_Urothelial_keratoacanthoma_Keratinocyte_neuroectodermal_Bronchial



Phase1 CAGE Peaks

Hg19::chr10:105615282..105615323,-p6@SH3PXD2A
Hg19::chr10:105615327..105615342,-p8@SH3PXD2A
Hg19::chr10:105615456..105615531,-p3@SH3PXD2A


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>

Cell Type
Ontology termp-valuen
endo-epithelial cell6.73e-0843
endodermal cell1.93e-0759
Uber Anatomy
Ontology termp-valuen
ectoderm3.17e-15173
presumptive ectoderm3.17e-15173
ectoderm-derived structure5.53e-14169
anatomical system1.04e-13625
multi-cellular organism1.18e-13659
anatomical group2.18e-13626
organism subdivision6.06e-13365
surface structure8.13e-1295
adult organism1.96e-11115
embryo1.79e-10612
head6.63e-10123
embryonic structure7.28e-10605
developing anatomical structure7.28e-10605
anterior region of body7.56e-10129
craniocervical region7.56e-10129
germ layer1.37e-09604
embryonic tissue1.37e-09604
presumptive structure1.37e-09604
epiblast (generic)1.37e-09604
anatomical conduit1.54e-09241
multi-tissue structure1.05e-08347
epithelium1.09e-08309
organ part1.15e-08219
cell layer2.67e-08312
endoderm-derived structure4.43e-08169
endoderm4.43e-08169
presumptive endoderm4.43e-08169
mouth6.00e-0828
stomodeum6.00e-0828
organ6.07e-08511
oral opening9.99e-0821
neural tube1.43e-0757
neural rod1.43e-0757
future spinal cord1.43e-0757
neural keel1.43e-0757
orifice3.36e-0735
regional part of nervous system9.07e-0794
nervous system9.07e-0794


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
CTCF#1066435.360256373075030.0064925092527670.0278103180153282
RAD21#5885310.35503389545630.0009004912073565420.00661506655448476



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.

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