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Coexpression cluster:C4669

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Full id: C4669_adenocarcinoma_gastric_lung_stomach_endometrioid_trachea_Prostate



Phase1 CAGE Peaks

Hg19::chr7:16840970..16841011,-p2@AGR2
Hg19::chr7:16844611..16844628,-p1@AGR2
Hg19::chr9:128307438..128307440,+p@chr9:128307438..128307440
+


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 cell7.14e-20254
endodermal cell3.57e-1659
endo-epithelial cell5.23e-1643
respiratory epithelial cell1.20e-0813
epithelial cell of alimentary canal2.05e-0721
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure5.71e-33169
endoderm5.71e-33169
presumptive endoderm5.71e-33169
digestive system5.79e-27155
digestive tract5.79e-27155
primitive gut5.79e-27155
subdivision of digestive tract7.90e-25129
endodermal part of digestive tract7.90e-25129
mixed endoderm/mesoderm-derived structure1.10e-21130
foregut5.03e-1698
trunk region element6.23e-16107
immaterial anatomical entity6.30e-16126
endo-epithelium2.99e-1582
respiratory system3.34e-1472
anatomical space2.07e-13104
organ1.16e-12511
multi-tissue structure1.84e-12347
mesenchyme3.92e-11238
entire embryonic mesenchyme3.92e-11238
subdivision of trunk6.13e-11113
respiratory tract6.28e-1153
gastrointestinal system2.97e-1035
thoracic segment organ3.00e-1035
thoracic cavity element6.41e-1034
thoracic cavity6.41e-1034
epithelial bud6.69e-1037
embryo7.77e-09612
epithelial fold8.11e-0951
multi-cellular organism1.35e-08659
adult organism1.59e-08115
intestine1.64e-0827
lung1.78e-0822
respiratory tube1.78e-0822
respiration organ1.78e-0822
pair of lungs1.78e-0822
lung primordium1.78e-0822
lung bud1.78e-0822
respiratory primordium3.79e-0838
endoderm of foregut3.79e-0838
embryonic structure3.87e-08605
developing anatomical structure3.87e-08605
organ part4.30e-08219
thoracic segment of trunk4.73e-0852
germ layer7.15e-08604
embryonic tissue7.15e-08604
presumptive structure7.15e-08604
epiblast (generic)7.15e-08604
extraembryonic membrane1.48e-0714
membranous layer1.48e-0714
orifice1.56e-0735
trunk1.68e-07216
anatomical system2.42e-07625
anatomical group3.02e-07626
segment of respiratory tract3.21e-0746
gut epithelium5.24e-0754
mucosa6.29e-0712
Disease
Ontology termp-valuen
carcinoma2.14e-18106
cell type cancer2.09e-09143
squamous cell carcinoma3.06e-0914
adenocarcinoma1.80e-0825


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
GATA3#2625218.15767757147070.003944546819279620.0189592031505704



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.