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Coexpression cluster:C3828: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3828_Neutrophils_Whole_Eosinophils_CD8_CD4_Natural_small
|full_id=C3828_Neutrophils_Whole_Eosinophils_CD8_CD4_Natural_small
|id=C3828
|id=C3828

Revision as of 16:48, 12 September 2012


Full id: C3828_Neutrophils_Whole_Eosinophils_CD8_CD4_Natural_small



Phase1 CAGE Peaks

Hg19::chr19:58326267..58326292,-p1@ZNF552
Hg19::chr3:36949995..36950042,-p1@TRANK1
Hg19::chr6:26402517..26402535,+p2@BTN3A1


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
leukocyte1.06e-30140
nongranular leukocyte1.62e-23119
hematopoietic lineage restricted progenitor cell6.02e-23124
hematopoietic stem cell5.56e-21172
angioblastic mesenchymal cell5.56e-21172
hematopoietic oligopotent progenitor cell1.27e-18165
hematopoietic multipotent progenitor cell1.27e-18165
lymphocyte1.69e-1853
common lymphoid progenitor1.69e-1853
lymphoid lineage restricted progenitor cell3.26e-1852
hematopoietic cell4.84e-18182
mature alpha-beta T cell4.26e-1218
alpha-beta T cell4.26e-1218
immature T cell4.26e-1218
mature T cell4.26e-1218
immature alpha-beta T cell4.26e-1218
myeloid leukocyte1.57e-1076
T cell5.78e-1025
pro-T cell5.78e-1025
CD8-positive, alpha-beta T cell2.16e-0811
lymphocyte of B lineage5.89e-0824
pro-B cell5.89e-0824
B cell1.11e-0714
mesenchymal cell2.78e-07358
myeloid lineage restricted progenitor cell3.01e-0770
granulocyte monocyte progenitor cell5.00e-0771
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.01e-12102
blood island2.01e-12102
hemolymphoid system2.54e-12112
blood4.09e-0715
haemolymphatic fluid4.09e-0715
organism substance4.09e-0715


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


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

TF#promotersEnrichmentp-valueq-value
NFYA#4800212.28372046655370.008516011403724430.0324777693990716



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.