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Coexpression cluster:C3411: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000178!7.35e-22!15;UBERON:0000179!7.35e-22!15;UBERON:0000463!7.35e-22!15;UBERON:0004177!1.88e-12!7;UBERON:0005057!1.88e-12!7;UBERON:0002370!6.96e-11!4;UBERON:0005058!6.96e-11!4;UBERON:0009113!6.96e-11!4;UBERON:0003295!6.96e-11!4;UBERON:0005562!6.96e-11!4;UBERON:0007023!5.18e-08!114;UBERON:0003351!3.30e-07!6
|ontology_enrichment_uberon=UBERON:0000178!7.35e-22!15;UBERON:0000179!7.35e-22!15;UBERON:0000463!7.35e-22!15;UBERON:0004177!1.88e-12!7;UBERON:0005057!1.88e-12!7;UBERON:0002370!6.96e-11!4;UBERON:0005058!6.96e-11!4;UBERON:0009113!6.96e-11!4;UBERON:0003295!6.96e-11!4;UBERON:0005562!6.96e-11!4;UBERON:0007023!5.18e-08!114;UBERON:0003351!3.30e-07!6
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}}
}}

Revision as of 16:07, 26 November 2012


Full id: C3411_NK_anaplastic_acute_thymus_Natural_Whole_CD8



Phase1 CAGE Peaks

Hg19::chr14:22925581..22925592,+p2@uc001wdz.3
p2@uc010tms.1
Hg19::chr14:22925600..22925628,+p1@uc001wdz.3
p1@uc010tms.1
Hg19::chr14:22925634..22925675,+p1@TRDJ2


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

No GOStat results

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
mature alpha-beta T cell2.65e-1418
alpha-beta T cell2.65e-1418
immature T cell2.65e-1418
mature T cell2.65e-1418
immature alpha-beta T cell2.65e-1418
CD8-positive, alpha-beta T cell4.97e-1011
T cell1.44e-0925
pro-T cell1.44e-0925
natural killer cell8.45e-093
pro-NK cell8.45e-093
basophil4.69e-083
hematopoietic stem cell5.21e-08168
angioblastic mesenchymal cell5.21e-08168
naive T cell6.09e-083
single nucleate cell9.74e-083
mononuclear cell9.74e-083
hematopoietic cell3.44e-07177
Uber Anatomy
Ontology termp-valuen
blood7.35e-2215
haemolymphatic fluid7.35e-2215
organism substance7.35e-2215
hemopoietic organ1.88e-127
immune organ1.88e-127
thymus6.96e-114
hemolymphoid system gland6.96e-114
thymic region6.96e-114
pharyngeal gland6.96e-114
thymus primordium6.96e-114
adult organism5.18e-08114
pharyngeal epithelium3.30e-076


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.

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