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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3539_lung_adenocarcinoma_trachea_gastric_somatostatinoma_Hep2_signet
|full_id=C3539_lung_adenocarcinoma_trachea_gastric_somatostatinoma_Hep2_signet
|id=C3539
|id=C3539

Revision as of 16:28, 12 September 2012


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 cell7.11e-11254
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure8.80e-22169
endoderm8.80e-22169
presumptive endoderm8.80e-22169
subdivision of digestive tract2.84e-21129
endodermal part of digestive tract2.84e-21129
digestive system1.00e-20155
digestive tract1.00e-20155
primitive gut1.00e-20155
mixed endoderm/mesoderm-derived structure2.99e-19130
adult organism9.97e-17115
respiratory tract1.74e-1653
respiratory primordium5.93e-1638
endoderm of foregut5.93e-1638
respiratory system8.82e-1672
foregut1.54e-1498
larynx1.12e-129
segment of respiratory tract3.76e-1146
multi-tissue structure2.41e-09347
upper respiratory tract3.14e-0819
epithelial bud1.73e-0737
organ segment1.84e-0797
anatomical space1.99e-07104
lung3.60e-0722
respiratory tube3.60e-0722
respiration organ3.60e-0722
pair of lungs3.60e-0722
lung primordium3.60e-0722
lung bud3.60e-0722
biliary system5.85e-077
biliary tree5.85e-077
biliary bud5.85e-077
immaterial anatomical entity5.97e-07126
mesenchyme9.01e-07238
entire embryonic mesenchyme9.01e-07238
thoracic cavity element9.60e-0734
thoracic cavity9.60e-0734
Disease
Ontology termp-valuen
carcinoma1.20e-31106
cell type cancer5.19e-27143
cancer6.60e-13235
disease of cellular proliferation3.66e-12239
squamous cell carcinoma7.86e-1014
adenocarcinoma7.24e-0925


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.

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