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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4392_Mammary_Burkitt_pharyngeal_Keratinocyte_Sebocyte_Corneal_salivary
|full_id=C4392_Mammary_Burkitt_pharyngeal_Keratinocyte_Sebocyte_Corneal_salivary
|id=C4392
|id=C4392

Revision as of 17:27, 12 September 2012


Full id: C4392_Mammary_Burkitt_pharyngeal_Keratinocyte_Sebocyte_Corneal_salivary



Phase1 CAGE Peaks

Hg19::chr4:169575836..169575859,+p24@PALLD
Hg19::chr4:169575875..169575902,+p12@PALLD
Hg19::chr4:169575903..169575919,+p22@PALLD


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
respiratory system2.06e-2472
endoderm-derived structure1.11e-23169
endoderm1.11e-23169
presumptive endoderm1.11e-23169
digestive system4.17e-22155
digestive tract4.17e-22155
primitive gut4.17e-22155
subdivision of digestive tract2.64e-20129
endodermal part of digestive tract2.64e-20129
respiratory tract4.37e-1953
segment of respiratory tract7.31e-1746
respiratory primordium8.03e-1738
endoderm of foregut8.03e-1738
mixed endoderm/mesoderm-derived structure3.59e-15130
foregut5.30e-1598
upper respiratory tract1.74e-1119
oral opening7.65e-1121
thoracic cavity element4.16e-1034
thoracic cavity4.16e-1034
orifice7.64e-1035
larynx1.14e-099
thoracic segment organ1.20e-0935
organ segment1.67e-0997
epithelial bud1.95e-0937
saliva-secreting gland1.46e-086
gland of oral region1.46e-086
gland of foregut1.46e-086
oral gland1.46e-086
oral cavity1.46e-086
gland of gut2.39e-0810
mouth2.53e-0828
stomodeum2.53e-0828
endo-epithelium6.31e-0882
epithelial fold9.29e-0851
respiratory system epithelium3.89e-0728
lung6.14e-0722
respiratory tube6.14e-0722
respiration organ6.14e-0722
pair of lungs6.14e-0722
lung primordium6.14e-0722
lung bud6.14e-0722
thoracic segment of trunk7.86e-0752
organ7.87e-07511
uterine cervix8.72e-076
neck of organ8.72e-076
Disease
Ontology termp-valuen
carcinoma3.11e-17106
cell type cancer3.42e-11143
squamous cell carcinoma4.08e-0914


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.

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