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Coexpression cluster:C3539

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Full id: C3539_lung_adenocarcinoma_trachea_gastric_somatostatinoma_Hep2_signet



Phase1 CAGE Peaks

Hg19::chr16:19421803..19421848,+p4@TMC5
Hg19::chr16:19421885..19421901,+p10@TMC5
Hg19::chr16:19421906..19421915,+p15@TMC5


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 cell2.62e-09253
Uber Anatomy
Ontology termp-valuen
respiratory primordium7.76e-2638
endoderm of foregut7.76e-2638
larynx5.23e-249
respiratory tract6.40e-2454
endoderm-derived structure1.50e-20160
endoderm1.50e-20160
presumptive endoderm1.50e-20160
subdivision of digestive tract3.57e-20118
respiratory system4.61e-2074
digestive system6.12e-19145
digestive tract6.12e-19145
primitive gut6.12e-19145
foregut8.07e-1887
segment of respiratory tract1.83e-1547
upper respiratory tract1.20e-1219
epithelial bud3.39e-1037
lung7.84e-1022
respiratory tube7.84e-1022
respiration organ7.84e-1022
pair of lungs7.84e-1022
lung primordium7.84e-1022
lung bud7.84e-1022
biliary system8.65e-109
biliary tree8.65e-109
biliary bud8.65e-109
primordium9.04e-09160
organ system subdivision1.72e-08223
thoracic cavity element1.92e-0834
thoracic cavity1.92e-0834
endo-epithelium3.51e-0882
thoracic segment organ4.00e-0835
organ segment5.60e-0898
gallbladder6.50e-083
gall bladder primordium6.50e-083
immaterial anatomical entity9.58e-08117
epithelial fold2.44e-0747
anatomical space3.99e-0795
Disease
Ontology termp-valuen
carcinoma3.06e-26106
cell type cancer9.68e-22143
cancer2.04e-12235
disease of cellular proliferation6.49e-12239
adenocarcinoma1.67e-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
CEBPB#105137.971147625824820.001974187055288560.0115101949348117
CTCF#1066435.360256373075030.0064925092527670.0279041635329108
RAD21#5885310.35503389545630.0009004912073565420.00663185961533812
SMC3#9126315.04493284493280.0002935825420371870.0030862070566504
TFAP2A#7020316.5186343730450.0002218033880766340.00247885757595886
TFAP2C#7022310.80922860986020.0007916746575753130.0061450545940177



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.