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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3584_Whole_CD14CD16_Neutrophils_Eosinophils_CD4_CD14_Basophils
|full_id=C3584_Whole_CD14CD16_Neutrophils_Eosinophils_CD4_CD14_Basophils
|id=C3584
|id=C3584

Revision as of 16:31, 12 September 2012


Full id: C3584_Whole_CD14CD16_Neutrophils_Eosinophils_CD4_CD14_Basophils



Phase1 CAGE Peaks

Hg19::chr16:68034452..68034466,-p4@DPEP2
Hg19::chr16:68034470..68034496,-p2@DPEP2
Hg19::chr16:68034504..68034527,-p3@DPEP2


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
leukocyte5.25e-42140
myeloid leukocyte2.20e-3876
nongranular leukocyte3.76e-37119
macrophage dendritic cell progenitor2.77e-3565
monopoietic cell6.05e-3463
monocyte6.05e-3463
monoblast6.05e-3463
promonocyte6.05e-3463
hematopoietic lineage restricted progenitor cell1.27e-33124
granulocyte monocyte progenitor cell1.63e-3171
CD14-positive, CD16-negative classical monocyte2.61e-3142
hematopoietic stem cell2.99e-31172
angioblastic mesenchymal cell2.99e-31172
classical monocyte1.96e-3045
myeloid lineage restricted progenitor cell1.80e-2970
hematopoietic oligopotent progenitor cell3.78e-29165
hematopoietic multipotent progenitor cell3.78e-29165
hematopoietic cell1.44e-27182
myeloid cell7.35e-24112
common myeloid progenitor7.35e-24112
mature alpha-beta T cell2.08e-1218
alpha-beta T cell2.08e-1218
immature T cell2.08e-1218
mature T cell2.08e-1218
immature alpha-beta T cell2.08e-1218
intermediate monocyte5.78e-109
CD14-positive, CD16-positive monocyte5.78e-109
T cell6.78e-1025
pro-T cell6.78e-1025
granulocyte3.18e-098
CD8-positive, alpha-beta T cell2.10e-0811
CD4-positive, alpha-beta T cell9.07e-076
Uber Anatomy
Ontology termp-valuen
hematopoietic system7.16e-38102
blood island7.16e-38102
hemolymphoid system4.27e-36112
bone marrow2.34e-2780
bone element6.51e-2486
immune system9.57e-23115
skeletal element4.56e-18101
skeletal system4.56e-18101
adult organism1.55e-16115
lateral plate mesoderm8.92e-12216
blood1.17e-0915
haemolymphatic fluid1.17e-0915
organism substance1.17e-0915


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

No analysis results for this cluster

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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