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Coexpression cluster:C4016

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Full id: C4016_gastrointestinal_anaplastic_maxillary_small_smallcell_argyrophil_Bronchial



Phase1 CAGE Peaks

Hg19::chr20:22565370..22565388,-p2@FOXA2
Hg19::chr20:22565612..22565627,-p@chr20:22565612..22565627
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Hg19::chr20:22565646..22565665,-p@chr20:22565646..22565665
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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 cell1.65e-15253
endodermal cell3.37e-1558
endo-epithelial cell1.80e-1142
respiratory epithelial cell1.86e-1013
epithelial cell of lung2.18e-0819
metabolising cell5.05e-0712
endopolyploid cell5.05e-0712
parenchymal cell5.05e-0712
polyploid cell5.05e-0712
hepatocyte5.05e-0712
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.50e-18160
endoderm1.50e-18160
presumptive endoderm1.50e-18160
digestive system4.02e-18145
digestive tract4.02e-18145
primitive gut4.02e-18145
subdivision of digestive tract2.05e-17118
endo-epithelium9.00e-1682
trunk region element1.12e-12101
foregut4.57e-1287
immaterial anatomical entity1.55e-11117
gut epithelium2.23e-0954
epithelium of foregut-midgut junction3.21e-0925
anatomical boundary3.21e-0925
hepatobiliary system3.21e-0925
foregut-midgut junction3.21e-0925
septum transversum3.21e-0925
respiratory tract4.98e-0954
epithelial bud8.42e-0937
lung1.30e-0822
respiratory tube1.30e-0822
respiration organ1.30e-0822
pair of lungs1.30e-0822
lung primordium1.30e-0822
lung bud1.30e-0822
thoracic cavity element1.88e-0834
thoracic cavity1.88e-0834
respiratory tract epithelium2.18e-0819
lung epithelium2.18e-0819
thoracic segment organ3.98e-0835
epithelial sac8.15e-0825
sac1.97e-0726
epithelial fold2.21e-0747
hepatic diverticulum2.26e-0722
liver primordium2.26e-0722
respiratory primordium2.97e-0738
endoderm of foregut2.97e-0738
subdivision of trunk3.00e-07112
respiratory system3.93e-0774
digestive tract diverticulum5.68e-0723
gastrointestinal system8.47e-0725
Disease
Ontology termp-valuen
carcinoma5.69e-17106
cell type cancer8.35e-14143
cancer4.18e-09235
disease of cellular proliferation1.10e-08239
respiratory system cancer2.78e-0816
gastrointestinal system cancer1.56e-0714
disease of anatomical entity4.83e-0739
lung cancer9.19e-0715


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
HDAC2#3066313.41562023662630.0004140761399857210.00391611862573293
SREBF1#6720347.00584944048839.62099323994382e-060.000254768487065541
SUZ12#23512233.41052060737530.00117826764536030.00799955110276175
ZNF263#1012738.221841637010680.001799043925565870.0109563443082497



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.