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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4583_lymphoma_hairy_b_CD4_CD8_Natural_Burkitt
|full_id=C4583_lymphoma_hairy_b_CD4_CD8_Natural_Burkitt
|id=C4583
|id=C4583

Revision as of 17:41, 12 September 2012


Full id: C4583_lymphoma_hairy_b_CD4_CD8_Natural_Burkitt



Phase1 CAGE Peaks

Hg19::chr6:25042390..25042405,-p6@FAM65B
Hg19::chr6:25042412..25042446,-p4@FAM65B
Hg19::chr6:25042510..25042521,-p11@FAM65B


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
hematopoietic stem cell8.55e-53172
angioblastic mesenchymal cell8.55e-53172
hematopoietic cell1.65e-47182
hematopoietic oligopotent progenitor cell5.75e-47165
hematopoietic multipotent progenitor cell5.75e-47165
leukocyte6.46e-47140
lymphocyte2.18e-3753
common lymphoid progenitor2.18e-3753
lymphoid lineage restricted progenitor cell1.55e-3652
hematopoietic lineage restricted progenitor cell1.62e-36124
nongranular leukocyte4.51e-35119
T cell1.79e-1825
pro-T cell1.79e-1825
mature alpha-beta T cell8.60e-1718
alpha-beta T cell8.60e-1718
immature T cell8.60e-1718
mature T cell8.60e-1718
immature alpha-beta T cell8.60e-1718
lymphocyte of B lineage5.68e-1624
pro-B cell5.68e-1624
myeloid cell5.08e-15112
common myeloid progenitor5.08e-15112
CD8-positive, alpha-beta T cell1.68e-1011
B cell1.88e-1014
myeloid leukocyte7.41e-0976
granulocyte monocyte progenitor cell4.68e-0871
mesenchymal cell4.89e-08358
connective tissue cell2.48e-07365
CD4-positive, alpha-beta T cell4.42e-076
myeloid lineage restricted progenitor cell6.39e-0770
Uber Anatomy
Ontology termp-valuen
hematopoietic system7.31e-14102
blood island7.31e-14102
hemolymphoid system1.46e-12112
adult organism2.88e-08115
blood4.58e-0715
haemolymphatic fluid4.58e-0715
organism substance4.58e-0715
Disease
Ontology termp-valuen
hematologic cancer1.95e-0751
immune system cancer1.95e-0751


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
POU2F2#545239.106124057742520.001324165192682130.00885311366484405



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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