Coexpression cluster:C597

Full id: C597_CD14_mature_immature_Eosinophils_Mast_embryonic_chorionic

Phase1 CAGE Peaks

Hg19::chr13:28615672..28615689,-	p@chr13:28615672..28615689 -
Hg19::chr17:19091325..19091326,+	p1@SNORD3A
Hg19::chr17:76320827..76320838,+	p@chr17:76320827..76320838 +
Hg19::chr19:2476116..2476132,+	p1@GADD45B
Hg19::chr19:41222998..41223057,+	p1@ITPKC
Hg19::chr19:45350840..45350859,-	p@chr19:45350840..45350859 -
Hg19::chr19:45947096..45947113,+	p@chr19:45947096..45947113 +
Hg19::chr1:39324762..39324790,+	p@chr1:39324762..39324790 +
Hg19::chr1:85461941..85461949,+	p@chr1:85461941..85461949 +
Hg19::chr21:38740608..38740619,-	p@chr21:38740608..38740619 -
Hg19::chr2:102759127..102759136,-	p@chr2:102759127..102759136 -
Hg19::chr5:395563..395569,+	p@chr5:395563..395569 +
Hg19::chr6:14109177..14109181,+	p@chr6:14109177..14109181 +
Hg19::chr7:151033644..151033667,+	p@chr7:151033644..151033667 +
Hg19::chrX:20284429..20284435,+	p@chrX:20284429..20284435 +

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

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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

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GO ID	GO name	FDR corrected p-value
GO:0000185	activation of MAPKKK activity	0.0119487317818538
GO:0000186	activation of MAPKK activity	0.0119487317818538
GO:0008440	inositol trisphosphate 3-kinase activity	0.0119487317818538
GO:0051766	inositol trisphosphate kinase activity	0.0119487317818538
GO:0006469	negative regulation of protein kinase activity	0.0265308474773421
GO:0033673	negative regulation of kinase activity	0.0265308474773421
GO:0051348	negative regulation of transferase activity	0.0265308474773421
GO:0004428	inositol or phosphatidylinositol kinase activity	0.0265308474773421
GO:0032147	activation of protein kinase activity	0.0265308474773421
GO:0043086	negative regulation of catalytic activity	0.0296692149196469
GO:0045860	positive regulation of protein kinase activity	0.0340708838298483
GO:0005516	calmodulin binding	0.0340708838298483
GO:0033674	positive regulation of kinase activity	0.0340708838298483
GO:0051347	positive regulation of transferase activity	0.0340708838298483
GO:0000165	MAPKKK cascade	0.0340708838298483
GO:0045859	regulation of protein kinase activity	0.0458342550450001
GO:0043549	regulation of kinase activity	0.0458342550450001
GO:0051338	regulation of transferase activity	0.0458342550450001
GO:0043085	positive regulation of catalytic activity	0.0458342550450001

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>

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Cell Type

Ontology term	p-value	n
CD14-positive, CD16-negative classical monocyte	3.34e-20	42
classical monocyte	7.72e-17	45
myeloid leukocyte	2.92e-13	76
granulocyte monocyte progenitor cell	8.84e-11	71
macrophage dendritic cell progenitor	3.05e-10	65
monopoietic cell	2.74e-09	63
monocyte	2.74e-09	63
monoblast	2.74e-09	63
promonocyte	2.74e-09	63
myeloid lineage restricted progenitor cell	4.80e-09	70

Uber Anatomy

Ontology term	p-value	n
immune system	2.59e-10	115
organ	7.89e-10	511
bone marrow	4.72e-09	80
multi-cellular organism	4.66e-08	659
bone element	5.59e-08	86
anatomical system	1.20e-07	625
anatomical group	1.95e-07	626
hemolymphoid system	2.44e-07	112
lateral plate mesoderm	8.44e-07	216

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

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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

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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
ETS1#2113	5	3.24292030740078	0.0142357715348991	0.0499334926392386
NFKB1#4790	7	2.56109626462379	0.0108752592113249	0.0401031423194533
REST#5978	6	3.86001148645121	0.00270193564832292	0.014863705934959
STAT3#6774	5	3.50648833238475	0.0103118355458907	0.0383013654092497

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

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This analysis result is provided for C0 - C305 clusters.