Personal tools

Coexpression cluster:C762


Revision as of 07:40, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search

Full id: C762_splenic_migratory_b_B_cord_CD14_mycosis

Phase1 CAGE Peaks


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>disease_data<br>

Cell Type
Ontology termp-valuen
nongranular leukocyte9.83e-33115
common lymphoid progenitor9.58e-2953
hematopoietic cell1.40e-27177
nucleate cell2.02e-2755
lymphoid lineage restricted progenitor cell3.44e-2752
hematopoietic lineage restricted progenitor cell3.66e-26120
hematopoietic stem cell2.76e-25168
angioblastic mesenchymal cell2.76e-25168
hematopoietic oligopotent progenitor cell6.10e-23161
hematopoietic multipotent progenitor cell6.10e-23161
T cell2.99e-1725
pro-T cell2.99e-1725
circulating cell7.02e-166
mature alpha-beta T cell3.50e-1518
alpha-beta T cell3.50e-1518
immature T cell3.50e-1518
mature T cell3.50e-1518
immature alpha-beta T cell3.50e-1518
CD8-positive, alpha-beta T cell1.49e-1011
Langerhans cell1.02e-095
classical monocyte1.90e-0942
CD14-positive, CD16-negative classical monocyte1.90e-0942
lymphocyte of B lineage2.51e-0924
pro-B cell2.51e-0924
single nucleate cell3.58e-083
mononuclear cell3.58e-083
defensive cell7.42e-0848
CD4-positive, alpha-beta T cell2.70e-076
Uber Anatomy
Ontology termp-valuen
hemolymphoid system6.42e-15108
hematopoietic system1.14e-1498
blood island1.14e-1498
hemopoietic organ3.11e-127
immune organ3.11e-127
haemolymphatic fluid4.09e-1015
organism substance4.09e-1015
immune system8.11e-0993
gastrointestinal system mesentery3.49e-083
stomach region3.49e-083
gastrointestinal system serosa3.49e-083
mesentery of stomach3.49e-083
gut mesentery3.49e-083
dorsal mesentery3.49e-083
dorsal mesogastrium3.49e-083
peritoneal cavity3.49e-083
spleen primordium3.49e-083
Ontology termp-valuen

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



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)


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.