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Revision as of 05:31, 21 May 2012

Full id: C3027_Mammary_keratoacanthoma_Gingival_Prostate_tongue_esophagus_oral

Phase1 CAGE Peaks

  Short description
Hg19::chr10:5566916..5566932,+ p1@CALML3
Hg19::chr10:5567551..5567579,+ p@chr10:5567551..5567579
Hg19::chr10:5567644..5567657,+ p@chr10:5567644..5567657

Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset

No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset

No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset


Uber Anatomy
Ontology termp-valuen
oral opening1.96e-1721
respiratory system1.82e-1672
endoderm-derived structure7.20e-12169
presumptive endoderm7.20e-12169
surface structure2.58e-1195
gland of gut6.92e-1110
saliva-secreting gland1.53e-106
gland of oral region1.53e-106
gland of foregut1.53e-106
oral gland1.53e-106
oral cavity1.53e-106
mixed ectoderm/mesoderm/endoderm-derived structure2.81e-1018
subdivision of head2.43e-0948
anterior region of body1.87e-08129
craniocervical region1.87e-08129
respiratory tract7.11e-0853
digestive system1.21e-07155
digestive tract1.21e-07155
primitive gut1.21e-07155
tracheobronchial tree2.02e-0714
lower respiratory tract2.02e-0714
gingival epithelium2.88e-073
chordate pharynx6.86e-0710
pharyngeal region of foregut6.86e-0710
gustatory system7.04e-073
future tongue7.04e-073

Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs

Jaspar motifs

Novel motifs

JASPAR motifs



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset


No analysis results for this cluster

Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.

link to data source

This analysis result is provided for C0 - C305 clusters.