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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2197_Natural_CD8_CD4_Basophils_CD14_CD19_Mast
|full_id=C2197_Natural_CD8_CD4_Basophils_CD14_CD19_Mast
|id=C2197
|id=C2197

Revision as of 14:53, 12 September 2012


Full id: C2197_Natural_CD8_CD4_Basophils_CD14_CD19_Mast



Phase1 CAGE Peaks

Hg19::chr12:14520115..14520131,-p@chr12:14520115..14520131
-
Hg19::chr17:62966372..62966382,+p@chr17:62966372..62966382
+
Hg19::chr5:49860626..49860631,+p@chr5:49860626..49860631
+
Hg19::chr7:76993644..76993691,-p@chr7:76993644..76993691
-


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
leukocyte1.22e-46140
hematopoietic lineage restricted progenitor cell2.77e-39124
nongranular leukocyte2.07e-36119
hematopoietic stem cell3.76e-33172
angioblastic mesenchymal cell3.76e-33172
hematopoietic cell1.88e-32182
hematopoietic oligopotent progenitor cell4.49e-30165
hematopoietic multipotent progenitor cell4.49e-30165
lymphoid lineage restricted progenitor cell9.72e-2652
lymphocyte5.73e-2553
common lymphoid progenitor5.73e-2553
CD14-positive, CD16-negative classical monocyte1.51e-1942
mature alpha-beta T cell2.64e-1918
alpha-beta T cell2.64e-1918
immature T cell2.64e-1918
mature T cell2.64e-1918
immature alpha-beta T cell2.64e-1918
classical monocyte1.75e-1745
T cell4.64e-1625
pro-T cell4.64e-1625
myeloid leukocyte1.92e-1576
granulocyte monocyte progenitor cell4.88e-1571
myeloid lineage restricted progenitor cell3.14e-1370
CD8-positive, alpha-beta T cell8.60e-1311
macrophage dendritic cell progenitor4.46e-1265
monopoietic cell9.80e-1163
monocyte9.80e-1163
monoblast9.80e-1163
promonocyte9.80e-1163
myeloid cell1.18e-09112
common myeloid progenitor1.18e-09112
intermediate monocyte1.31e-099
CD14-positive, CD16-positive monocyte1.31e-099
B cell1.68e-0914
lymphocyte of B lineage2.36e-0824
pro-B cell2.36e-0824
mesenchymal cell6.27e-08358
connective tissue cell6.80e-08365
CD4-positive, alpha-beta T cell8.08e-086
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.30e-21102
blood island3.30e-21102
hemolymphoid system4.30e-20112
bone marrow7.05e-1380
immune system2.80e-11115
bone element4.28e-1186
skeletal element9.42e-09101
skeletal system9.42e-09101
blood1.54e-0815
haemolymphatic fluid1.54e-0815
organism substance1.54e-0815
connective tissue2.65e-07375


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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