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Coexpression cluster:C2305

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Full id: C2305_thyroid_pituitary_small_parotid_choriocarcinoma_salivary_bile



Phase1 CAGE Peaks

Hg19::chr14:61748076..61748115,-p3@TMEM30B
Hg19::chr14:61748121..61748145,-p8@TMEM30B
Hg19::chr14:61748147..61748187,-p4@TMEM30B
Hg19::chr14:61748188..61748205,-p6@TMEM30B


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 cell2.24e-16254
endo-epithelial cell1.73e-1543
endodermal cell4.42e-1159
epithelial cell of alimentary canal8.46e-0821
respiratory epithelial cell1.68e-0713
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.17e-20169
endoderm1.17e-20169
presumptive endoderm1.17e-20169
digestive system6.50e-16155
digestive tract6.50e-16155
primitive gut6.50e-16155
subdivision of digestive tract2.94e-13129
endodermal part of digestive tract2.94e-13129
mixed endoderm/mesoderm-derived structure2.69e-12130
endo-epithelium1.02e-1182
respiratory system4.62e-1172
anatomical space1.51e-10104
immaterial anatomical entity1.99e-10126
orifice2.09e-0935
epithelial bud3.05e-0937
extraembryonic membrane1.35e-0714
membranous layer1.35e-0714
adult organism1.69e-07115
respiratory tract1.95e-0753
reproductive structure1.98e-0759
reproductive system1.98e-0759
foregut2.51e-0798
neck3.05e-0710
thoracic cavity element6.00e-0734
thoracic cavity6.00e-0734
oral opening6.88e-0721
epithelial fold8.60e-0751
Disease
Ontology termp-valuen
squamous cell carcinoma1.16e-1014
carcinoma1.27e-10106


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
E2F1#186944.907389214879320.001724022357361790.0106346447924226
MYC#460945.22228187160940.001344309395272740.00886465014098304
TAF1#687243.343046285745290.008005664898701650.0321640175555107
TBP#690843.706770687096390.005296377814784350.0243763618278804
ZEB1#6935416.88843201754391.22862303393937e-050.000303706890039276



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.