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Coexpression cluster:C3928: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000178!2.27e-26!15;UBERON:0000179!2.27e-26!15;UBERON:0000463!2.27e-26!15;UBERON:0002390!2.26e-12!98;UBERON:0003061!2.26e-12!98;UBERON:0002193!2.32e-11!108;UBERON:0004177!2.29e-07!7;UBERON:0005057!2.29e-07!7
|ontology_enrichment_uberon=UBERON:0000178!2.27e-26!15;UBERON:0000179!2.27e-26!15;UBERON:0000463!2.27e-26!15;UBERON:0002390!2.26e-12!98;UBERON:0003061!2.26e-12!98;UBERON:0002193!2.32e-11!108;UBERON:0004177!2.29e-07!7;UBERON:0005057!2.29e-07!7
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}}
}}

Revision as of 16:26, 26 November 2012


Full id: C3928_cord_CD8_Natural_small_CD19_CD4_Whole



Phase1 CAGE Peaks

Hg19::chr1:205744205..205744244,-p2@RAB7L1
Hg19::chr7:142251148..142251182,-p1@TRBV6-4
Hg19::chr7:142251189..142251208,-p2@TRBV6-4


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 cell4.69e-3318
alpha-beta T cell4.69e-3318
immature T cell4.69e-3318
mature T cell4.69e-3318
immature alpha-beta T cell4.69e-3318
T cell5.80e-2525
pro-T cell5.80e-2525
CD8-positive, alpha-beta T cell3.27e-2411
leukocyte3.04e-17136
nongranular leukocyte1.73e-15115
lymphoid lineage restricted progenitor cell8.09e-1552
lymphocyte2.04e-1453
common lymphoid progenitor2.04e-1453
nucleate cell1.16e-1355
circulating cell1.20e-136
hematopoietic cell3.36e-13177
CD4-positive, alpha-beta T cell9.92e-136
hematopoietic stem cell9.46e-12168
angioblastic mesenchymal cell9.46e-12168
hematopoietic lineage restricted progenitor cell1.84e-11120
hematopoietic oligopotent progenitor cell2.71e-10161
hematopoietic multipotent progenitor cell2.71e-10161
granulocyte1.43e-088
blood cell2.37e-0811
natural killer cell1.91e-073
pro-NK cell1.91e-073
naive T cell2.13e-073
single nucleate cell3.85e-073
mononuclear cell3.85e-073
Uber Anatomy
Ontology termp-valuen
blood2.27e-2615
haemolymphatic fluid2.27e-2615
organism substance2.27e-2615
hematopoietic system2.26e-1298
blood island2.26e-1298
hemolymphoid system2.32e-11108
hemopoietic organ2.29e-077
immune organ2.29e-077


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.