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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C819_Alveolar_MCF7_mesothelioma_endometrioid_signet_Renal_gastric
|full_id=C819_Alveolar_MCF7_mesothelioma_endometrioid_signet_Renal_gastric
|gostat_on_coexpression_clusters=GO:0005882!intermediate filament!0.00163391453254799!3856;3875$GO:0045111!intermediate filament cytoskeleton!0.00163391453254799!3856;3875$GO:0043000!Golgi to plasma membrane CFTR protein transport!0.00266882527361085!3875$GO:0043001!Golgi to plasma membrane protein transport!0.0030023842411101!3875$GO:0006893!Golgi to plasma membrane transport!0.00560412061869646!3875$GO:0044430!cytoskeletal part!0.00756000214426228!3856;3875$GO:0030018!Z disc!0.00756000214426228!3856$GO:0042383!sarcolemma!0.00756000214426228!3856$GO:0031674!I band!0.00756000214426228!3856$GO:0006892!post-Golgi vesicle-mediated transport!0.00840444861332212!3875$GO:0005856!cytoskeleton!0.0107478076253176!3856;3875$GO:0030017!sarcomere!0.0160021099440816!3856$GO:0030016!myofibril!0.0163086417198209!3856$GO:0044449!contractile fiber part!0.0170648948467576!3856$GO:0043292!contractile fiber!0.0170648948467576!3856$GO:0005200!structural constituent of cytoskeleton!0.0197684410496945!3875$GO:0045095!keratin filament!0.0197684410496945!3875$GO:0048193!Golgi vesicle transport!0.0197684410496945!3875$GO:0043232!intracellular non-membrane-bound organelle!0.0251111392713346!3856;3875$GO:0043228!non-membrane-bound organelle!0.0251111392713346!3856;3875$GO:0016043!cellular component organization and biogenesis!0.0301217712229689!3856;3875$GO:0051707!response to other organism!0.0372143670088532!3856$GO:0043066!negative regulation of apoptosis!0.0372143670088532!3875$GO:0043069!negative regulation of programmed cell death!0.0372143670088532!3875$GO:0045045!secretory pathway!0.0372143670088532!3875$GO:0044446!intracellular organelle part!0.0372143670088532!3856;3875$GO:0044422!organelle part!0.0372143670088532!3856;3875$GO:0009607!response to biotic stimulus!0.0408206615432263!3856$GO:0032940!secretion by cell!0.0408206615432263!3875$GO:0051704!multi-organism process!0.0442194544953417!3856$GO:0046903!secretion!0.0493096828301634!3875
|id=C819
|id=C819
}}
}}

Revision as of 17:41, 18 May 2012


Full id: C819_Alveolar_MCF7_mesothelioma_endometrioid_signet_Renal_gastric



Phase1 CAGE Peaks

Hg19::chr12:53298570..53298600,-p5@KRT8
Hg19::chr12:53298672..53298713,-p7@KRT8
Hg19::chr12:53342893..53342911,+p1@KRT18
Hg19::chr12:53343121..53343150,+p6@KRT18
Hg19::chr12:53344588..53344613,+p4@KRT18
Hg19::chr12:53344624..53344654,-p@chr12:53344624..53344654
-
Hg19::chr12:53345928..53345949,+p3@KRT18
Hg19::chr2:203706578..203706583,-p1@KRT8P15
Hg19::chr2:236715167..236715174,+p@chr2:236715167..236715174
+
Hg19::chr3:170213152..170213154,+p1@KRT8P13


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:0005882intermediate filament0.00163391453254799
GO:0045111intermediate filament cytoskeleton0.00163391453254799
GO:0043000Golgi to plasma membrane CFTR protein transport0.00266882527361085
GO:0043001Golgi to plasma membrane protein transport0.0030023842411101
GO:0006893Golgi to plasma membrane transport0.00560412061869646
GO:0044430cytoskeletal part0.00756000214426228
GO:0030018Z disc0.00756000214426228
GO:0042383sarcolemma0.00756000214426228
GO:0031674I band0.00756000214426228
GO:0006892post-Golgi vesicle-mediated transport0.00840444861332212
GO:0005856cytoskeleton0.0107478076253176
GO:0030017sarcomere0.0160021099440816
GO:0030016myofibril0.0163086417198209
GO:0044449contractile fiber part0.0170648948467576
GO:0043292contractile fiber0.0170648948467576
GO:0005200structural constituent of cytoskeleton0.0197684410496945
GO:0045095keratin filament0.0197684410496945
GO:0048193Golgi vesicle transport0.0197684410496945
GO:0043232intracellular non-membrane-bound organelle0.0251111392713346
GO:0043228non-membrane-bound organelle0.0251111392713346
GO:0016043cellular component organization and biogenesis0.0301217712229689
GO:0051707response to other organism0.0372143670088532
GO:0043066negative regulation of apoptosis0.0372143670088532
GO:0043069negative regulation of programmed cell death0.0372143670088532
GO:0045045secretory pathway0.0372143670088532
GO:0044446intracellular organelle part0.0372143670088532
GO:0044422organelle part0.0372143670088532
GO:0009607response to biotic stimulus0.0408206615432263
GO:0032940secretion by cell0.0408206615432263
GO:0051704multi-organism process0.0442194544953417
GO:0046903secretion0.0493096828301634



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

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


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


No analysis results for this cluster

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.