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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3381_CD14_Neutrophils_Eosinophils_Peripheral_CD4_CD19_CD14CD16
|full_id=C3381_CD14_Neutrophils_Eosinophils_Peripheral_CD4_CD19_CD14CD16
|id=C3381
|id=C3381

Revision as of 16:17, 12 September 2012


Full id: C3381_CD14_Neutrophils_Eosinophils_Peripheral_CD4_CD19_CD14CD16



Phase1 CAGE Peaks

Hg19::chr13:50700157..50700171,+p3@FLJ31945
Hg19::chr1:65532758..65532804,+p@chr1:65532758..65532804
+
Hg19::chr3:13044044..13044048,-p@chr3:13044044..13044048
-


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
leukocyte2.15e-58140
hematopoietic stem cell2.69e-55172
angioblastic mesenchymal cell2.69e-55172
hematopoietic oligopotent progenitor cell1.21e-51165
hematopoietic multipotent progenitor cell1.21e-51165
hematopoietic cell6.04e-50182
hematopoietic lineage restricted progenitor cell4.14e-48124
nongranular leukocyte7.38e-47119
myeloid leukocyte1.91e-3176
CD14-positive, CD16-negative classical monocyte5.16e-3042
myeloid cell9.05e-30112
common myeloid progenitor9.05e-30112
classical monocyte1.59e-2745
granulocyte monocyte progenitor cell7.22e-2771
myeloid lineage restricted progenitor cell2.08e-2670
macrophage dendritic cell progenitor7.22e-2565
monopoietic cell6.25e-2463
monocyte6.25e-2463
monoblast6.25e-2463
promonocyte6.25e-2463
lymphocyte1.76e-1953
common lymphoid progenitor1.76e-1953
lymphoid lineage restricted progenitor cell2.44e-1952
mesenchymal cell6.37e-14358
mature alpha-beta T cell6.47e-1318
alpha-beta T cell6.47e-1318
immature T cell6.47e-1318
mature T cell6.47e-1318
immature alpha-beta T cell6.47e-1318
connective tissue cell1.08e-12365
motile cell4.83e-12390
T cell5.80e-1225
pro-T cell5.80e-1225
B cell8.16e-1014
intermediate monocyte4.05e-099
CD14-positive, CD16-positive monocyte4.05e-099
CD8-positive, alpha-beta T cell3.19e-0811
granulocyte7.15e-088
lymphocyte of B lineage7.13e-0724
pro-B cell7.13e-0724
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.18e-33102
blood island3.18e-33102
hemolymphoid system1.08e-27112
bone marrow3.78e-2580
bone element4.12e-2286
skeletal element1.02e-17101
skeletal system1.02e-17101
immune system2.31e-16115
connective tissue8.60e-12375
blood8.70e-0815
haemolymphatic fluid8.70e-0815
organism substance8.70e-0815
lateral plate mesoderm4.31e-07216


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
FOXA2#3170216.42030916844350.004810682352105480.0225808024346761



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.