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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3533_Neutrophils_CD14_Eosinophils_Monocytederived_lymph_blood_optic
|full_id=C3533_Neutrophils_CD14_Eosinophils_Monocytederived_lymph_blood_optic
|id=C3533
|id=C3533

Revision as of 16:28, 12 September 2012


Full id: C3533_Neutrophils_CD14_Eosinophils_Monocytederived_lymph_blood_optic



Phase1 CAGE Peaks

Hg19::chr16:11643014..11643095,-p@chr16:11643014..11643095
-
Hg19::chr1:111435023..111435051,+p@chr1:111435023..111435051
+
Hg19::chr21:46330677..46330701,-p5@ITGB2


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
leukocyte7.59e-52140
nongranular leukocyte1.45e-45119
hematopoietic lineage restricted progenitor cell9.29e-45124
hematopoietic stem cell4.63e-40172
angioblastic mesenchymal cell4.63e-40172
hematopoietic oligopotent progenitor cell1.33e-39165
hematopoietic multipotent progenitor cell1.33e-39165
hematopoietic cell2.64e-36182
myeloid leukocyte4.84e-3676
granulocyte monocyte progenitor cell9.18e-3171
macrophage dendritic cell progenitor3.30e-3065
monopoietic cell1.29e-2963
monocyte1.29e-2963
monoblast1.29e-2963
promonocyte1.29e-2963
myeloid lineage restricted progenitor cell1.50e-2970
CD14-positive, CD16-negative classical monocyte5.42e-2742
classical monocyte9.69e-2645
myeloid cell5.61e-24112
common myeloid progenitor5.61e-24112
lymphocyte3.83e-1453
common lymphoid progenitor3.83e-1453
lymphoid lineage restricted progenitor cell5.04e-1452
mature alpha-beta T cell2.14e-0718
alpha-beta T cell2.14e-0718
immature T cell2.14e-0718
mature T cell2.14e-0718
immature alpha-beta T cell2.14e-0718
T cell2.73e-0725
pro-T cell2.73e-0725
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.95e-34102
blood island2.95e-34102
hemolymphoid system2.00e-28112
bone marrow3.55e-2580
bone element4.29e-2286
immune system5.90e-18115
skeletal element1.22e-15101
skeletal system1.22e-15101
blood1.67e-0715
haemolymphatic fluid1.67e-0715
organism substance1.67e-0715


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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