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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1576_Mast_CD4_Natural_CD19_Basophils_CD8_CD34
|full_id=C1576_Mast_CD4_Natural_CD19_Basophils_CD8_CD34
|id=C1576
|id=C1576

Revision as of 14:09, 12 September 2012


Full id: C1576_Mast_CD4_Natural_CD19_Basophils_CD8_CD34



Phase1 CAGE Peaks

Hg19::chr10:32621291..32621298,-p@chr10:32621291..32621298
-
Hg19::chr14:50329808..50329834,+p@chr14:50329808..50329834
+
Hg19::chr1:144520117..144520134,+p@chr1:144520117..144520134
+
Hg19::chr4:40198691..40198704,+p2@RHOH
Hg19::chr5:109026781..109026805,-p@chr5:109026781..109026805
-


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
leukocyte6.25e-44140
hematopoietic stem cell2.41e-37172
angioblastic mesenchymal cell2.41e-37172
hematopoietic cell1.77e-35182
hematopoietic lineage restricted progenitor cell9.01e-35124
hematopoietic oligopotent progenitor cell1.07e-33165
hematopoietic multipotent progenitor cell1.07e-33165
nongranular leukocyte4.53e-33119
lymphocyte3.71e-2753
common lymphoid progenitor3.71e-2753
lymphoid lineage restricted progenitor cell8.23e-2752
CD14-positive, CD16-negative classical monocyte8.64e-1442
T cell3.18e-1325
pro-T cell3.18e-1325
myeloid leukocyte4.56e-1376
lymphocyte of B lineage9.76e-1324
pro-B cell9.76e-1324
mature alpha-beta T cell4.40e-1218
alpha-beta T cell4.40e-1218
immature T cell4.40e-1218
mature T cell4.40e-1218
immature alpha-beta T cell4.40e-1218
classical monocyte1.97e-1145
myeloid cell5.21e-11112
common myeloid progenitor5.21e-11112
granulocyte monocyte progenitor cell5.40e-1171
myeloid lineage restricted progenitor cell4.03e-1070
B cell4.31e-0914
macrophage dendritic cell progenitor1.20e-0865
CD8-positive, alpha-beta T cell5.30e-0811
monopoietic cell5.44e-0863
monocyte5.44e-0863
monoblast5.44e-0863
promonocyte5.44e-0863
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.15e-17102
blood island1.15e-17102
hemolymphoid system7.75e-16112
bone marrow1.35e-0980
bone element2.11e-0886
blood3.52e-0815
haemolymphatic fluid3.52e-0815
organism substance3.52e-0815
immune system4.13e-08115
adult organism2.96e-07115


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
BCL11A#53335211.34778204144280.01157056933741320.0422819695951748
BCL3#602320.7282616822430.0002320005217689230.00254997921416802
BDP1#558141210.0306818181820.00475220144180810.0223354109347462
BRF2#552901214.915116279070.004644397888135530.0219244382136588
EBF1#187935.34388010794140.01187615563868110.0432262430734028
GATA2#262437.64695904013240.004279061879252130.0203256898898082
NFKB1#479044.390450739355070.004707732692524960.0221943255845535
TAF1#687253.343046285745290.002394600090870310.0135095958778308



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.