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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C3414_Smooth_Alveolar_Mallassezderived_mucinous_Placental_Bronchial_hepatocellular
|full_id=C3414_Smooth_Alveolar_Mallassezderived_mucinous_Placental_Bronchial_hepatocellular
|gostat_on_coexpression_clusters=GO:0004298!threonine endopeptidase activity!2.90963365692439e-05!5693;5694$GO:0005839!proteasome core complex (sensu Eukaryota)!2.90963365692439e-05!5693;5694$GO:0000502!proteasome complex (sensu Eukaryota)!6.0851107296576e-05!5693;5694$GO:0006511!ubiquitin-dependent protein catabolic process!0.000358939301823721!5693;5694$GO:0043632!modification-dependent macromolecule catabolic process!0.000358939301823721!5693;5694$GO:0019941!modification-dependent protein catabolic process!0.000358939301823721!5693;5694$GO:0051603!proteolysis involved in cellular protein catabolic process!0.000358939301823721!5693;5694$GO:0044257!cellular protein catabolic process!0.000358939301823721!5693;5694$GO:0030163!protein catabolic process!0.000474538006919738!5693;5694$GO:0043285!biopolymer catabolic process!0.000695007058246673!5693;5694$GO:0044265!cellular macromolecule catabolic process!0.000838715495874038!5693;5694$GO:0005829!cytosol!0.000906954100865701!5693;5694$GO:0009057!macromolecule catabolic process!0.00101380963655902!5693;5694$GO:0004175!endopeptidase activity!0.00147266438388624!5693;5694$GO:0044248!cellular catabolic process!0.00147266438388624!5693;5694$GO:0009056!catabolic process!0.00199753447215315!5693;5694$GO:0008233!peptidase activity!0.00303930587302639!5693;5694$GO:0006508!proteolysis!0.0032539008803968!5693;5694$GO:0043234!protein complex!0.0147781536685955!5693;5694$GO:0032991!macromolecular complex!0.0248985563881076!5693;5694$GO:0016787!hydrolase activity!0.0248985563881076!5693;5694$GO:0044444!cytoplasmic part!0.0323833408943997!5693;5694$GO:0044267!cellular protein metabolic process!0.0450366344531342!5693;5694$GO:0044260!cellular macromolecule metabolic process!0.0450366344531342!5693;5694$GO:0019538!protein metabolic process!0.0463788251414518!5693;5694$GO:0005634!nucleus!0.0476923425897552!5693;5694
|id=C3414
|id=C3414
}}
}}

Revision as of 17:38, 18 May 2012


Full id: C3414_Smooth_Alveolar_Mallassezderived_mucinous_Placental_Bronchial_hepatocellular



Phase1 CAGE Peaks

Hg19::chr14:23504087..23504118,-p1@PSMB5
Hg19::chr14:24701539..24701583,-p1@NEDD8-MDP1
p1@NEDD8
Hg19::chr17:4699451..4699490,+p1@PSMB6


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:0004298threonine endopeptidase activity2.90963365692439e-05
GO:0005839proteasome core complex (sensu Eukaryota)2.90963365692439e-05
GO:0000502proteasome complex (sensu Eukaryota)6.0851107296576e-05
GO:0006511ubiquitin-dependent protein catabolic process0.000358939301823721
GO:0043632modification-dependent macromolecule catabolic process0.000358939301823721
GO:0019941modification-dependent protein catabolic process0.000358939301823721
GO:0051603proteolysis involved in cellular protein catabolic process0.000358939301823721
GO:0044257cellular protein catabolic process0.000358939301823721
GO:0030163protein catabolic process0.000474538006919738
GO:0043285biopolymer catabolic process0.000695007058246673
GO:0044265cellular macromolecule catabolic process0.000838715495874038
GO:0005829cytosol0.000906954100865701
GO:0009057macromolecule catabolic process0.00101380963655902
GO:0004175endopeptidase activity0.00147266438388624
GO:0044248cellular catabolic process0.00147266438388624
GO:0009056catabolic process0.00199753447215315
GO:0008233peptidase activity0.00303930587302639
GO:0006508proteolysis0.0032539008803968
GO:0043234protein complex0.0147781536685955
GO:0032991macromolecular complex0.0248985563881076
GO:0016787hydrolase activity0.0248985563881076
GO:0044444cytoplasmic part0.0323833408943997
GO:0044267cellular protein metabolic process0.0450366344531342
GO:0044260cellular macromolecule metabolic process0.0450366344531342
GO:0019538protein metabolic process0.0463788251414518
GO:0005634nucleus0.0476923425897552



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.