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Coexpression cluster:C889: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0007172!signal complex assembly!0.0300359574741371!5747$GO:0042169!SH2 domain binding!0.0300359574741371!5747$GO:0005925!focal adhesion!0.0300359574741371!5747$GO:0005924!cell-substrate adherens junction!0.0300359574741371!5747$GO:0004672!protein kinase activity!0.0300359574741371!5747;9891$GO:0006937!regulation of muscle contraction!0.0300359574741371!4659$GO:0006468!protein amino acid phosphorylation!0.0300359574741371!5747;9891$GO:0004715!non-membrane spanning protein tyrosine kinase activity!0.0300359574741371!5747$GO:0030055!cell-matrix junction!0.0300359574741371!5747$GO:0005912!adherens junction!0.0300359574741371!5747$GO:0016310!phosphorylation!0.0300359574741371!5747;9891$GO:0016773!phosphotransferase activity, alcohol group as acceptor!0.0300359574741371!5747;9891$GO:0005856!cytoskeleton!0.0300359574741371!5747;4659$GO:0043623!cellular protein complex assembly!0.030700721916763!5747$GO:0016301!kinase activity!0.030700721916763!5747;9891$GO:0006793!phosphorus metabolic process!0.030700721916763!5747;9891$GO:0006796!phosphate metabolic process!0.030700721916763!5747;9891$GO:0016323!basolateral plasma membrane!0.030700721916763!5747$GO:0007229!integrin-mediated signaling pathway!0.030700721916763!5747$GO:0016772!transferase activity, transferring phosphorus-containing groups!0.0369879296170742!5747;9891$GO:0019904!protein domain specific binding!0.0409697638742895!5747$GO:0043687!post-translational protein modification!0.0434369027088801!5747;9891$GO:0003012!muscle system process!0.0465227350691899!4659$GO:0006936!muscle contraction!0.0465227350691899!4659$GO:0006464!protein modification process!0.0492255124386033!5747;9891$GO:0007169!transmembrane receptor protein tyrosine kinase signaling pathway!0.0492255124386033!5747$GO:0005515!protein binding!0.0492255124386033!5747;4659;9891$GO:0005524!ATP binding!0.0492255124386033!5747;9891$GO:0043412!biopolymer modification!0.0492255124386033!5747;9891$GO:0032559!adenyl ribonucleotide binding!0.0492255124386033!5747;9891$GO:0043232!intracellular non-membrane-bound organelle!0.0492255124386033!5747;4659$GO:0043228!non-membrane-bound organelle!0.0492255124386033!5747;4659$GO:0030554!adenyl nucleotide binding!0.0492255124386033!5747;9891
|gostat_on_coexpression_clusters=GO:0007172!signal complex assembly!0.0300359574741371!5747$GO:0042169!SH2 domain binding!0.0300359574741371!5747$GO:0005925!focal adhesion!0.0300359574741371!5747$GO:0005924!cell-substrate adherens junction!0.0300359574741371!5747$GO:0004672!protein kinase activity!0.0300359574741371!5747;9891$GO:0006937!regulation of muscle contraction!0.0300359574741371!4659$GO:0006468!protein amino acid phosphorylation!0.0300359574741371!5747;9891$GO:0004715!non-membrane spanning protein tyrosine kinase activity!0.0300359574741371!5747$GO:0030055!cell-matrix junction!0.0300359574741371!5747$GO:0005912!adherens junction!0.0300359574741371!5747$GO:0016310!phosphorylation!0.0300359574741371!5747;9891$GO:0016773!phosphotransferase activity, alcohol group as acceptor!0.0300359574741371!5747;9891$GO:0005856!cytoskeleton!0.0300359574741371!5747;4659$GO:0043623!cellular protein complex assembly!0.030700721916763!5747$GO:0016301!kinase activity!0.030700721916763!5747;9891$GO:0006793!phosphorus metabolic process!0.030700721916763!5747;9891$GO:0006796!phosphate metabolic process!0.030700721916763!5747;9891$GO:0016323!basolateral plasma membrane!0.030700721916763!5747$GO:0007229!integrin-mediated signaling pathway!0.030700721916763!5747$GO:0016772!transferase activity, transferring phosphorus-containing groups!0.0369879296170742!5747;9891$GO:0019904!protein domain specific binding!0.0409697638742895!5747$GO:0043687!post-translational protein modification!0.0434369027088801!5747;9891$GO:0003012!muscle system process!0.0465227350691899!4659$GO:0006936!muscle contraction!0.0465227350691899!4659$GO:0006464!protein modification process!0.0492255124386033!5747;9891$GO:0007169!transmembrane receptor protein tyrosine kinase signaling pathway!0.0492255124386033!5747$GO:0005515!protein binding!0.0492255124386033!5747;4659;9891$GO:0005524!ATP binding!0.0492255124386033!5747;9891$GO:0043412!biopolymer modification!0.0492255124386033!5747;9891$GO:0032559!adenyl ribonucleotide binding!0.0492255124386033!5747;9891$GO:0043232!intracellular non-membrane-bound organelle!0.0492255124386033!5747;4659$GO:0043228!non-membrane-bound organelle!0.0492255124386033!5747;4659$GO:0030554!adenyl nucleotide binding!0.0492255124386033!5747;9891
|id=C889
|id=C889
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=CL:0000077!2.15e-20!19;CL:0002097!3.71e-09!2
|ontology_enrichment_disease=
|ontology_enrichment_disease=DOID:3112!1.04e-16!1
|ontology_enrichment_uberon=UBERON:0007023!2.97e-08!115
|ontology_enrichment_uberon=UBERON:0001255!6.94e-09!2;UBERON:0001556!6.94e-09!2
|pathway_enrichment=0.000145853209864357;0.0264257502200088;2;200;Focal adhesion (KEGG):04510!0.000166987363159613;0.0264257502200088;2;214;Regulation of actin cytoskeleton (KEGG):04810!0.000128870835041632;0.0264257502200088;2;188;Focal Adhesion (Wikipathways):WP306!7.66167144514812e-05;0.0264257502200088;2;145;Regulation of Actin Cytoskeleton (Wikipathways):WP51
|pathway_enrichment=0.000145853209864357;0.0264257502200088;2;200;Focal adhesion (KEGG):04510!0.000166987363159613;0.0264257502200088;2;214;Regulation of actin cytoskeleton (KEGG):04810!0.000128870835041632;0.0264257502200088;2;188;Focal Adhesion (Wikipathways):WP306!7.66167144514812e-05;0.0264257502200088;2;145;Regulation of Actin Cytoskeleton (Wikipathways):WP51
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}}
}}

Revision as of 16:50, 19 October 2012


Full id: C889_mesothelioma_mesodermal_lung_placenta_umbilical_Urothelial_Mallassezderived



Phase1 CAGE Peaks

Hg19::chr12:106477805..106477824,-p13@NUAK1
Hg19::chr12:80175910..80175928,-p31@PPP1R12A
Hg19::chr17:26890530..26890545,-p@chr17:26890530..26890545
-
Hg19::chr17:26890583..26890593,-p@chr17:26890583..26890593
-
Hg19::chr17:67586124..67586131,+p1@uc002jil.2
Hg19::chr3:129023260..129023267,+p3@AF035296
Hg19::chr4:23022304..23022336,+p@chr4:23022304..23022336
+
Hg19::chr8:141728444..141728461,-p23@PTK2
Hg19::chr8:141728472..141728496,-p19@PTK2


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


p.valueFDRnGenesnPathwayName
0.0001458532098643570.02642575022000882200Focal adhesion (KEGG):04510
0.0001669873631596130.02642575022000882214Regulation of actin cytoskeleton (KEGG):04810
0.0001288708350416320.02642575022000882188Focal Adhesion (Wikipathways):WP306
7.66167144514812e-050.02642575022000882145Regulation of Actin Cytoskeleton (Wikipathways):WP51



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:0007172signal complex assembly0.0300359574741371
GO:0042169SH2 domain binding0.0300359574741371
GO:0005925focal adhesion0.0300359574741371
GO:0005924cell-substrate adherens junction0.0300359574741371
GO:0004672protein kinase activity0.0300359574741371
GO:0006937regulation of muscle contraction0.0300359574741371
GO:0006468protein amino acid phosphorylation0.0300359574741371
GO:0004715non-membrane spanning protein tyrosine kinase activity0.0300359574741371
GO:0030055cell-matrix junction0.0300359574741371
GO:0005912adherens junction0.0300359574741371
GO:0016310phosphorylation0.0300359574741371
GO:0016773phosphotransferase activity, alcohol group as acceptor0.0300359574741371
GO:0005856cytoskeleton0.0300359574741371
GO:0043623cellular protein complex assembly0.030700721916763
GO:0016301kinase activity0.030700721916763
GO:0006793phosphorus metabolic process0.030700721916763
GO:0006796phosphate metabolic process0.030700721916763
GO:0016323basolateral plasma membrane0.030700721916763
GO:0007229integrin-mediated signaling pathway0.030700721916763
GO:0016772transferase activity, transferring phosphorus-containing groups0.0369879296170742
GO:0019904protein domain specific binding0.0409697638742895
GO:0043687post-translational protein modification0.0434369027088801
GO:0003012muscle system process0.0465227350691899
GO:0006936muscle contraction0.0465227350691899
GO:0006464protein modification process0.0492255124386033
GO:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.0492255124386033
GO:0005515protein binding0.0492255124386033
GO:0005524ATP binding0.0492255124386033
GO:0043412biopolymer modification0.0492255124386033
GO:0032559adenyl ribonucleotide binding0.0492255124386033
GO:0043232intracellular non-membrane-bound organelle0.0492255124386033
GO:0043228non-membrane-bound organelle0.0492255124386033
GO:0030554adenyl nucleotide binding0.0492255124386033



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
mesothelial cell2.15e-2019
cortical cell of adrenal gland3.71e-092
Uber Anatomy
Ontology termp-valuen
urinary bladder6.94e-092
lower urinary tract6.94e-092
Disease
Ontology termp-valuen
papillary adenocarcinoma1.04e-161


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.