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Coexpression cluster:C1727: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;5:4.90738921487932:0.000351281809925646:0.00352595107610039!MYC#4609;4:4.17782549728752:0.00569196903682344:0.0256765529646166!ZEB1#6935;3:10.1330592105263:0.00189555692435707:0.0111601595142301
|tf_chipseq_enrich=E2F1#1869;5:4.90738921487932:0.000351281809925646:0.00352595107610039!MYC#4609;4:4.17782549728752:0.00569196903682344:0.0256765529646166!ZEB1#6935;3:10.1330592105263:0.00189555692435707:0.0111601595142301
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}}
}}

Revision as of 15:04, 26 November 2012


Full id: C1727_colon_small_stomach_papillotubular_breast_duodenum_prostate



Phase1 CAGE Peaks

Hg19::chr14:61747949..61747974,-p2@TMEM30B
Hg19::chr14:61747978..61747991,-p7@TMEM30B
Hg19::chr14:61748025..61748074,-p1@TMEM30B
Hg19::chr15:41136563..41136613,-p@chr15:41136563..41136613
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Hg19::chr5:68711211..68711238,+p4@MARVELD2


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


GO IDGO nameFDR corrected p-value
GO:0005923tight junction0.0279220393075104
GO:0043296apical junction complex0.0279220393075104
GO:0016327apicolateral plasma membrane0.0279220393075104
GO:0050954sensory perception of mechanical stimulus0.0279220393075104
GO:0007605sensory perception of sound0.0279220393075104
GO:0005911intercellular junction0.0304772232795939



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
endo-epithelial cell1.62e-1942
epithelial cell9.69e-19253
endodermal cell1.52e-1358
respiratory epithelial cell9.82e-1013
epithelial cell of alimentary canal1.32e-0920
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure5.82e-26160
endoderm5.82e-26160
presumptive endoderm5.82e-26160
digestive system8.75e-21145
digestive tract8.75e-21145
primitive gut8.75e-21145
subdivision of digestive tract7.88e-19118
endo-epithelium2.67e-1382
respiratory system1.20e-1274
epithelial bud4.98e-1137
foregut7.44e-1187
anatomical space3.04e-1095
immaterial anatomical entity1.08e-09117
orifice1.64e-0936
respiratory tract1.98e-0954
epithelial fold2.24e-0947
thoracic cavity element2.44e-0934
thoracic cavity2.44e-0934
thoracic segment organ7.25e-0935
renal system8.50e-0848
gastrointestinal system9.38e-0825
reproductive structure1.00e-0759
reproductive system1.00e-0759
thoracic segment of trunk1.46e-0752
trunk region element1.51e-07101
urinary system structure2.02e-0747
lung2.57e-0722
respiratory tube2.57e-0722
respiration organ2.57e-0722
pair of lungs2.57e-0722
lung primordium2.57e-0722
lung bud2.57e-0722
respiratory system epithelium3.94e-0728
male organism6.97e-0722
male reproductive system6.97e-0722
oral opening8.97e-0722
Disease
Ontology termp-valuen
carcinoma1.38e-12106
squamous cell carcinoma5.62e-1214
adenocarcinoma1.69e-0725
cell type cancer4.12e-07143


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#186954.907389214879320.0003512818099256460.00352595107610039
MYC#460944.177825497287520.005691969036823440.0256765529646166
ZEB1#6935310.13305921052630.001895556924357070.0111601595142301



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.