MCL coexpression mm9:2358: Difference between revisions

Revision as of 13:11, 11 October 2012

Phase1 CAGE Peaks

	Short description
Mm9::chr3:108525199..108525229,-	p1@Gpsm2
Mm9::chr5:144578655..144578687,+	p2@Eif2ak1
Mm9::chr5:73583087..73583161,-	p@chr5:73583087..73583161 -
Mm9::chrX:8849886..8849931,+	p1@Xk

Enriched pathways on this co-expression clusterSummary: 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. Analyst: Emmanuel Dimont link to source dataset data

GO ID	GO name	FDR corrected p-value
GO:0046986	negative regulation of hemoglobin biosynthetic process	0.00756040102996767
GO:0046984	regulation of hemoglobin biosynthetic process	0.00756040102996767
GO:0042541	hemoglobin biosynthetic process	0.0188968605703257
GO:0020027	hemoglobin metabolic process	0.0188968605703257

Relative expression of the co-expression cluster over median Analyst:

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji links to source dataset cell_data uberon_data disease_data

Cell Type
Ontology term	p-value	n

Uber Anatomy
Ontology term	p-value	n

Disease
Ontology term	p-value	n

TFBS overrepresentationSummary: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. Analyst: Michiel de Hoon link to source data Novel motifs data Jaspar motifs data

Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
{{{tfbs_overrepresentation_jaspar}}}

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 |gostat_on_MCL_coexpression=GO:0046986;negative regulation of hemoglobin biosynthetic process;0.00756040102996767;15467!GO:0046984;regulation of hemoglobin biosynthetic process;0.00756040102996767;15467!GO:0042541;hemoglobin biosynthetic process;0.0188968605703257;15467!GO:0020027;hemoglobin metabolic process;0.0188968605703257;15467!
 }}

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MCL coexpression mm9:2358: Difference between revisions

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Revision as of 13:11, 11 October 2012

Phase1 CAGE Peaks

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	Mozilla Cavendish skin modified by DaSch for the Web Community Wiki GitHub project page – Report a bug – Skin version: 2.6.0