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Coexpression cluster:C3144

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Full id: C3144_cervical_pharyngeal_oral_amniotic_keratoacanthoma_esophagus_squamous



Phase1 CAGE Peaks

Hg19::chr11:32851437..32851446,+p5@PRRG4
Hg19::chr11:32851450..32851485,+p1@PRRG4
Hg19::chr11:32851487..32851496,+p4@PRRG4


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 cell1.89e-22253
endodermal cell6.51e-1958
endo-epithelial cell2.99e-1842
epithelial cell of alimentary canal6.06e-1420
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure5.14e-30160
endoderm5.14e-30160
presumptive endoderm5.14e-30160
digestive system3.25e-25145
digestive tract3.25e-25145
primitive gut3.25e-25145
subdivision of digestive tract4.30e-22118
respiratory system4.47e-1874
foregut1.36e-1487
respiratory tract2.05e-1254
orifice3.68e-1236
endo-epithelium4.58e-1282
oral opening3.70e-1022
immaterial anatomical entity8.69e-09117
respiratory primordium1.38e-0838
endoderm of foregut1.38e-0838
gland2.63e-0859
segment of respiratory tract2.69e-0847
mouth8.56e-0829
stomodeum8.56e-0829
mucosa1.05e-0720
anatomical space1.21e-0795
epithelial bud1.44e-0737
extraembryonic membrane5.60e-0714
membranous layer5.60e-0714
anterior region of body6.43e-0762
craniocervical region6.43e-0762
trunk region element7.34e-07101
Disease
Ontology termp-valuen
carcinoma9.51e-19106
cell type cancer6.98e-13143
squamous cell carcinoma1.12e-1214


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#1066435.360256373075030.0064925092527670.0278388624974231
E2F1#186934.907389214879320.008460985347239390.0323719400915974
EBF1#187938.9064668465690.00141523283560980.00912492296075147
PAX5#507936.669565531177830.003370290999677260.0172332838049103
ZEB1#6935316.88843201754390.0002075486917327580.00241948630604727



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.