Coexpression cluster:C3806

Full id: C3806_CD14_Eosinophils_CD14CD16_Neutrophils_Whole_lymph_Basophils

Phase1 CAGE Peaks

Hg19::chr19:47234972..47234989,-	p@chr19:47234972..47234989 -
Hg19::chr1:12185978..12185991,+	p9@TNFRSF8
Hg19::chr2:32490833..32490846,-	p3@NLRC4

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:0001816	cytokine production	0.00103446535802594
GO:0043065	positive regulation of apoptosis	0.00103446535802594
GO:0043068	positive regulation of programmed cell death	0.00103446535802594
GO:0045554	regulation of TRAIL biosynthetic process	0.00103446535802594
GO:0032639	TRAIL production	0.00103446535802594
GO:0045556	positive regulation of TRAIL biosynthetic process	0.00103446535802594
GO:0045553	TRAIL biosynthetic process	0.00103446535802594
GO:0042981	regulation of apoptosis	0.00362041559311593
GO:0043067	regulation of programmed cell death	0.00362041559311593
GO:0042535	positive regulation of tumor necrosis factor biosynthetic process	0.00362041559311593
GO:0042533	tumor necrosis factor biosynthetic process	0.00445569935155049
GO:0042534	regulation of tumor necrosis factor biosynthetic process	0.00445569935155049
GO:0016045	detection of bacterium	0.00445569935155049
GO:0050702	interleukin-1 beta secretion	0.00460719125131041
GO:0006915	apoptosis	0.00460719125131041
GO:0012501	programmed cell death	0.00460719125131041
GO:0050701	interleukin-1 secretion	0.00460719125131041
GO:0016265	death	0.00460719125131041
GO:0008219	cell death	0.00460719125131041
GO:0032640	tumor necrosis factor production	0.00460719125131041
GO:0048522	positive regulation of cellular process	0.00460719125131041
GO:0009595	detection of biotic stimulus	0.00460719125131041
GO:0048518	positive regulation of biological process	0.0052214091912989
GO:0050663	cytokine secretion	0.00603269373868363
GO:0048468	cell development	0.00657096317561614
GO:0042108	positive regulation of cytokine biosynthetic process	0.0114121833297713
GO:0006919	caspase activation	0.0116710243335441
GO:0048869	cellular developmental process	0.0116710243335441
GO:0030154	cell differentiation	0.0116710243335441
GO:0009581	detection of external stimulus	0.0116710243335441
GO:0043280	positive regulation of caspase activity	0.0116710243335441
GO:0045727	positive regulation of translation	0.0119841535431956
GO:0009306	protein secretion	0.0120582821448717
GO:0042035	regulation of cytokine biosynthetic process	0.0120582821448717
GO:0043281	regulation of caspase activity	0.0120582821448717
GO:0031328	positive regulation of cellular biosynthetic process	0.0120582821448717
GO:0042089	cytokine biosynthetic process	0.012945261368358
GO:0042107	cytokine metabolic process	0.012945261368358
GO:0009891	positive regulation of biosynthetic process	0.0129839293357284
GO:0051345	positive regulation of hydrolase activity	0.0137432016135358
GO:0051606	detection of stimulus	0.0141128540237549
GO:0051247	positive regulation of protein metabolic process	0.0146368073075038
GO:0008632	apoptotic program	0.0149683065950834
GO:0042742	defense response to bacterium	0.0156129023590789
GO:0009617	response to bacterium	0.0170308235643359
GO:0042803	protein homodimerization activity	0.0248146709306179
GO:0032502	developmental process	0.0253956571749537
GO:0006417	regulation of translation	0.0276833879125117
GO:0031326	regulation of cellular biosynthetic process	0.0293226689605162
GO:0051707	response to other organism	0.0297439634680821
GO:0032501	multicellular organismal process	0.0301222550321238
GO:0009889	regulation of biosynthetic process	0.0301222550321238
GO:0008285	negative regulation of cell proliferation	0.0306398359910231
GO:0043085	positive regulation of catalytic activity	0.0342000811111639
GO:0009607	response to biotic stimulus	0.037888228250408
GO:0032940	secretion by cell	0.0382372110621555
GO:0051336	regulation of hydrolase activity	0.0388255038108474
GO:0051704	multi-organism process	0.0413716498701346
GO:0042802	identical protein binding	0.0432141348646109
GO:0031325	positive regulation of cellular metabolic process	0.0432141348646109
GO:0046983	protein dimerization activity	0.0432141348646109
GO:0046903	secretion	0.0440225673836635
GO:0009893	positive regulation of metabolic process	0.0440225673836635
GO:0007165	signal transduction	0.0440225673836635
GO:0051246	regulation of protein metabolic process	0.0467211608289428
GO:0000287	magnesium ion binding	0.0487211228152806
GO:0007154	cell communication	0.0491668435042182
GO:0042127	regulation of cell proliferation	0.0495993575852572

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	5.04e-50	42
myeloid leukocyte	6.06e-50	76
monopoietic cell	1.51e-45	63
monocyte	1.51e-45	63
monoblast	1.51e-45	63
promonocyte	1.51e-45	63
classical monocyte	1.70e-45	45
macrophage dendritic cell progenitor	1.59e-43	65
myeloid lineage restricted progenitor cell	5.59e-39	70
granulocyte monocyte progenitor cell	3.78e-38	71
myeloid cell	1.07e-36	112
common myeloid progenitor	1.07e-36	112
leukocyte	1.02e-31	140
nongranular leukocyte	3.54e-26	119
hematopoietic stem cell	5.62e-26	172
angioblastic mesenchymal cell	5.62e-26	172
hematopoietic oligopotent progenitor cell	3.08e-24	165
hematopoietic multipotent progenitor cell	3.08e-24	165
hematopoietic cell	4.48e-23	182
hematopoietic lineage restricted progenitor cell	5.27e-21	124
intermediate monocyte	5.47e-12	9
CD14-positive, CD16-positive monocyte	5.47e-12	9
granulocyte	7.32e-11	8
blood cell	2.88e-07	11

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	1.06e-42	102
blood island	1.06e-42	102
hemolymphoid system	3.04e-39	112
adult organism	2.99e-34	115
bone marrow	1.24e-31	80
bone element	4.49e-28	86
immune system	2.76e-25	115
skeletal element	4.47e-22	101
skeletal system	4.47e-22	101
lateral plate mesoderm	9.03e-16	216
regional part of forebrain	3.19e-14	41
forebrain	3.19e-14	41
future forebrain	3.19e-14	41
regional part of cerebral cortex	5.83e-14	22
anterior neural tube	1.11e-13	42
telencephalon	1.89e-13	34
gray matter	2.13e-13	34
brain grey matter	2.13e-13	34
regional part of telencephalon	9.13e-13	33
neocortex	2.64e-12	20
cerebral hemisphere	2.76e-12	32
regional part of brain	8.46e-12	59
neural tube	1.04e-11	57
neural rod	1.04e-11	57
future spinal cord	1.04e-11	57
neural keel	1.04e-11	57
cerebral cortex	1.20e-11	25
pallium	1.20e-11	25
blood	1.96e-10	15
haemolymphatic fluid	1.96e-10	15
organism substance	1.96e-10	15
brain	5.70e-10	69
future brain	5.70e-10	69
neural plate	2.53e-09	86
presumptive neural plate	2.53e-09	86
pre-chordal neural plate	7.87e-09	61
musculoskeletal system	1.19e-08	167
neurectoderm	1.92e-08	90
central nervous system	3.31e-08	82
tissue	7.21e-07	787

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
ESRRA#2101	1	161.280104712042	0.00618762008021956	0.0273501292347236

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.