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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1032_Mast_Natural_CD4_CD8_CD19_Basophils_CD14
|full_id=C1032_Mast_Natural_CD4_CD8_CD19_Basophils_CD14
|id=C1032
|id=C1032

Revision as of 13:27, 12 September 2012


Full id: C1032_Mast_Natural_CD4_CD8_CD19_Basophils_CD14



Phase1 CAGE Peaks

Hg19::chr14:50101931..50101969,-p4@DNAAF2
Hg19::chr15:86250415..86250426,-p@chr15:86250415..86250426
-
Hg19::chr16:27247011..27247032,+p@chr16:27247011..27247032
+
Hg19::chr19:16435987..16435993,+p@chr19:16435987..16435993
+
Hg19::chr19:18415466..18415480,-p@chr19:18415466..18415480
-
Hg19::chr2:25195104..25195126,+p5@DNAJC27-AS1
Hg19::chr8:38243836..38243862,+p10@LETM2
Hg19::chr9:129485649..129485680,-p@chr9:129485649..129485680
-


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
leukocyte1.01e-24140
hematopoietic stem cell7.48e-20172
angioblastic mesenchymal cell7.48e-20172
hematopoietic lineage restricted progenitor cell6.98e-19124
hematopoietic cell9.88e-19182
nongranular leukocyte2.12e-18119
hematopoietic oligopotent progenitor cell5.73e-17165
hematopoietic multipotent progenitor cell5.73e-17165
lymphoid lineage restricted progenitor cell5.39e-1452
lymphocyte5.92e-1453
common lymphoid progenitor5.92e-1453
T cell2.72e-1025
pro-T cell2.72e-1025
mature alpha-beta T cell5.14e-1018
alpha-beta T cell5.14e-1018
immature T cell5.14e-1018
mature T cell5.14e-1018
immature alpha-beta T cell5.14e-1018
CD14-positive, CD16-negative classical monocyte8.67e-1042
classical monocyte2.48e-0945
myeloid leukocyte4.24e-0976
granulocyte monocyte progenitor cell4.97e-0871
CD8-positive, alpha-beta T cell6.00e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.74e-09102
blood island2.74e-09102
hemolymphoid system3.89e-07112


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
E2F6#187653.135722332310870.01024880501420960.0381486544614384
POLR2A#543082.147453176558070.002210725788971910.0127174877815718



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.