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Coexpression cluster:C2955: Difference between revisions

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|tf_chipseq_enrich=ESRRA#2101;1:120.960078534031:0.00824166246177904:0.0324860728353616!NR3C1#2908;3:11.2297674983798:0.00113167206806385:0.00775682215111379!PPARGC1A#10891;1:87.5127840909091:0.0113781217638372:0.0417056701257641
|tf_chipseq_enrich=ESRRA#2101;1:120.960078534031:0.00824166246177904:0.0324860728353616!NR3C1#2908;3:11.2297674983798:0.00113167206806385:0.00775682215111379!PPARGC1A#10891;1:87.5127840909091:0.0113781217638372:0.0417056701257641
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}}
}}

Revision as of 15:50, 26 November 2012


Full id: C2955_Adipocyte_Endothelial_Osteoblast_neuroectodermal_salivary_Smooth_Fibroblast



Phase1 CAGE Peaks

Hg19::chrX:1508197..1508219,-p@chrX:1508197..1508219
-
Hg19::chrX:1508481..1508521,-p2@SLC25A6
Hg19::chrX:1510994..1511012,-p1@SLC25A6
Hg19::chrX:1571759..1571808,-p1@ASMTL


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:0005471ATP:ADP antiporter activity0.00244315254826876
GO:0017096acetylserotonin O-methyltransferase activity0.00244315254826876
GO:0030186melatonin metabolic process0.00244315254826876
GO:0030187melatonin biosynthetic process0.00244315254826876
GO:0042435indole derivative biosynthetic process0.00488601741722185
GO:0046219indolalkylamine biosynthetic process0.00488601741722185
GO:0042430indole and derivative metabolic process0.00597135955542775
GO:0006586indolalkylamine metabolic process0.00597135955542775
GO:0042434indole derivative metabolic process0.00597135955542775
GO:0008171O-methyltransferase activity0.0066618683710385
GO:0005744mitochondrial inner membrane presequence translocase complex0.0066618683710385
GO:0042401biogenic amine biosynthetic process0.013838010375701
GO:0042398amino acid derivative biosynthetic process0.0149988803209093
GO:0042446hormone biosynthetic process0.0149988803209093
GO:0006839mitochondrial transport0.0155638645169341
GO:0015300solute:solute antiporter activity0.0155638645169341
GO:0006576biogenic amine metabolic process0.0201850584132047
GO:0008757S-adenosylmethionine-dependent methyltransferase activity0.0201850584132047
GO:0042445hormone metabolic process0.0201850584132047
GO:0007005mitochondrion organization and biogenesis0.0201850584132047
GO:0006575amino acid derivative metabolic process0.0201850584132047
GO:0015297antiporter activity0.0201850584132047
GO:0009309amine biosynthetic process0.0245919726276852
GO:0044455mitochondrial membrane part0.0245919726276852
GO:0046483heterocycle metabolic process0.025360916663867
GO:0044271nitrogen compound biosynthetic process0.0275674568476008
GO:0006725aromatic compound metabolic process0.0330300604508557
GO:0008168methyltransferase activity0.0466508466277305
GO:0016741transferase activity, transferring one-carbon groups0.0466508466277305



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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
female organism3.95e-1141
female reproductive organ9.87e-1037
female reproductive system9.87e-1037
breast2.31e-0710
embryonic uterus2.32e-0722
internal female genitalia2.39e-0722
uterus5.92e-0721


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ESRRA#21011120.9600785340310.008241662461779040.0324860728353616
NR3C1#2908311.22976749837980.001131672068063850.00775682215111379
PPARGC1A#10891187.51278409090910.01137812176383720.0417056701257641



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.