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Coexpression cluster:C2248: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!2.91e-17!114;UBERON:0001017!1.86e-10!81;UBERON:0001016!1.29e-09!89;UBERON:0000073!7.52e-09!53;UBERON:0002616!7.52e-09!53;UBERON:0001049!1.52e-08!56;UBERON:0005068!1.52e-08!56;UBERON:0006241!1.52e-08!56;UBERON:0007135!1.52e-08!56;UBERON:0000955!1.04e-07!68;UBERON:0006238!1.04e-07!68;UBERON:0011216!8.14e-07!223
|ontology_enrichment_uberon=UBERON:0007023!2.91e-17!114;UBERON:0001017!1.86e-10!81;UBERON:0001016!1.29e-09!89;UBERON:0000073!7.52e-09!53;UBERON:0002616!7.52e-09!53;UBERON:0001049!1.52e-08!56;UBERON:0005068!1.52e-08!56;UBERON:0006241!1.52e-08!56;UBERON:0007135!1.52e-08!56;UBERON:0000955!1.04e-07!68;UBERON:0006238!1.04e-07!68;UBERON:0011216!8.14e-07!223
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}}
}}

Revision as of 15:23, 26 November 2012


Full id: C2248_anaplastic_cord_Mast_leukemia_mycosis_chronic_Fibroblast



Phase1 CAGE Peaks

Hg19::chr12:93965704..93965728,+p6@SOCS2
Hg19::chr12:93966292..93966306,+p15@SOCS2
Hg19::chr12:93968004..93968009,+p@chr12:93968004..93968009
+
Hg19::chr6:88876353..88876383,-p4@CNR1


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:0005148prolactin receptor binding0.00329678416151928
GO:0004949cannabinoid receptor activity0.00329678416151928
GO:0008269JAK pathway signal transduction adaptor activity0.00329678416151928
GO:0008268receptor signaling protein tyrosine kinase signaling protein activity0.00370882759195954
GO:0005131growth hormone receptor binding0.00395602453569053
GO:0005159insulin-like growth factor receptor binding0.00906495546968549
GO:0007259JAK-STAT cascade0.0269506616453008
GO:0005070SH3/SH2 adaptor activity0.0269506616453008
GO:0007242intracellular signaling cascade0.0269506616453008
GO:0005126hematopoietin/interferon-class (D200-domain) cytokine receptor binding0.0269506616453008
GO:0060090molecular adaptor activity0.0269506616453008
GO:0030674protein binding, bridging0.0374517951281148
GO:0009968negative regulation of signal transduction0.0395020162906004
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0401497273096432
GO:0019935cyclic-nucleotide-mediated signaling0.0401497273096432
GO:0001558regulation of cell growth0.0441585883937592
GO:0006916anti-apoptosis0.0441585883937592
GO:0005057receptor signaling protein activity0.0441585883937592
GO:0016049cell growth0.0441585883937592
GO:0040008regulation of growth0.0441585883937592
GO:0060089molecular transducer activity0.0441585883937592
GO:0004871signal transducer activity0.0441585883937592
GO:0008361regulation of cell size0.0441585883937592
GO:0043066negative regulation of apoptosis0.0453429448171146
GO:0043069negative regulation of programmed cell death0.0453429448171146



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><br>


Cell Type
Ontology termp-valuen
skin fibroblast1.54e-0823
Uber Anatomy
Ontology termp-valuen
adult organism2.91e-17114
central nervous system1.86e-1081
nervous system1.29e-0989
regional part of nervous system7.52e-0953
regional part of brain7.52e-0953
neural tube1.52e-0856
neural rod1.52e-0856
future spinal cord1.52e-0856
neural keel1.52e-0856
brain1.04e-0768
future brain1.04e-0768
organ system subdivision8.14e-07223


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)

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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.