Coexpression cluster:C1311

Full id: C1311_Neutrophils_Whole_Eosinophils_Basophils_blood_CD4_CD14

Phase1 CAGE Peaks

Hg19::chr10:31876301..31876306,-	p@chr10:31876301..31876306 -
Hg19::chr15:58443521..58443530,+	p7@ENST00000559334
Hg19::chr3:46283839..46283854,+	p4@CCR3
Hg19::chr3:46283863..46283874,+	p6@CCR3
Hg19::chr3:46283880..46283890,+	p7@CCR3
Hg19::chr3:46283916..46283927,+	p2@CCR3

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:0016493	C-C chemokine receptor activity	0.0136919479907823
GO:0019957	C-C chemokine binding	0.0136919479907823
GO:0001637	G-protein chemoattractant receptor activity	0.0136919479907823
GO:0004950	chemokine receptor activity	0.0136919479907823
GO:0019956	chemokine binding	0.0136919479907823
GO:0051480	cytosolic calcium ion homeostasis	0.0136919479907823
GO:0007204	elevation of cytosolic calcium ion concentration	0.0136919479907823
GO:0006968	cellular defense response	0.0136919479907823
GO:0007188	G-protein signaling, coupled to cAMP nucleotide second messenger	0.0136919479907823
GO:0019933	cAMP-mediated signaling	0.0136919479907823
GO:0019955	cytokine binding	0.0136919479907823
GO:0055074	calcium ion homeostasis	0.0136919479907823
GO:0006874	cellular calcium ion homeostasis	0.0136919479907823
GO:0007187	G-protein signaling, coupled to cyclic nucleotide second messenger	0.0136919479907823
GO:0019935	cyclic-nucleotide-mediated signaling	0.0136919479907823
GO:0006875	cellular metal ion homeostasis	0.0136919479907823
GO:0055065	metal ion homeostasis	0.0136919479907823
GO:0042330	taxis	0.0136919479907823
GO:0006935	chemotaxis	0.0136919479907823
GO:0001653	peptide receptor activity	0.0136919479907823
GO:0008528	peptide receptor activity, G-protein coupled	0.0136919479907823
GO:0030005	cellular di-, tri-valent inorganic cation homeostasis	0.0148136700812434
GO:0007626	locomotory behavior	0.0148136700812434
GO:0055066	di-, tri-valent inorganic cation homeostasis	0.0148136700812434
GO:0030003	cellular cation homeostasis	0.014966573779714
GO:0055080	cation homeostasis	0.014966573779714
GO:0042277	peptide binding	0.014966573779714
GO:0055082	cellular chemical homeostasis	0.0158771726817623
GO:0006873	cellular ion homeostasis	0.0158771726817623
GO:0050801	ion homeostasis	0.0167956153644557
GO:0019932	second-messenger-mediated signaling	0.0167956153644557
GO:0006954	inflammatory response	0.0172564257069836
GO:0007610	behavior	0.0172564257069836
GO:0048878	chemical homeostasis	0.0172564257069836
GO:0019725	cellular homeostasis	0.0208154614724731
GO:0009611	response to wounding	0.0228276227481455
GO:0042592	homeostatic process	0.0252035857828864
GO:0006952	defense response	0.0293409051798313
GO:0042221	response to chemical stimulus	0.0293409051798313
GO:0009605	response to external stimulus	0.0307444365948428
GO:0065008	regulation of biological quality	0.0433736127426417
GO:0022610	biological adhesion	0.0433736127426417
GO:0007155	cell adhesion	0.0433736127426417

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
myeloid leukocyte	2.19e-48	76
CD14-positive, CD16-negative classical monocyte	5.30e-46	42
leukocyte	4.82e-45	140
classical monocyte	7.20e-42	45
hematopoietic stem cell	4.12e-41	172
angioblastic mesenchymal cell	4.12e-41	172
myeloid cell	5.34e-41	112
common myeloid progenitor	5.34e-41	112
myeloid lineage restricted progenitor cell	1.17e-40	70
hematopoietic cell	3.07e-38	182
hematopoietic oligopotent progenitor cell	9.10e-38	165
hematopoietic multipotent progenitor cell	9.10e-38	165
granulocyte monocyte progenitor cell	3.41e-36	71
monopoietic cell	6.76e-36	63
monocyte	6.76e-36	63
monoblast	6.76e-36	63
promonocyte	6.76e-36	63
macrophage dendritic cell progenitor	2.83e-34	65
hematopoietic lineage restricted progenitor cell	9.10e-33	124
nongranular leukocyte	1.86e-31	119
granulocyte	8.21e-12	8
intermediate monocyte	6.87e-11	9
CD14-positive, CD16-positive monocyte	6.87e-11	9
blood cell	1.05e-09	11
mesenchymal cell	6.83e-07	358

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	6.43e-47	102
blood island	6.43e-47	102
hemolymphoid system	8.90e-42	112
bone marrow	4.21e-30	80
bone element	9.01e-27	86
immune system	6.06e-22	115
skeletal element	3.60e-21	101
skeletal system	3.60e-21	101
blood	1.76e-14	15
haemolymphatic fluid	1.76e-14	15
organism substance	1.76e-14	15
lateral plate mesoderm	1.45e-12	216
adult organism	4.60e-12	115
musculoskeletal system	2.79e-07	167

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)
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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
PBX3#5090	4	14.6096751244961	6.03404227507469e-05	0.000991019564658792
SPI1#6688	4	5.46954900568182	0.0026973005361414	0.0148389891853177

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.