Coexpression cluster:C560

Full id: C560_Neutrophils_Eosinophils_CD14CD16_Whole_CD14_acute_Dendritic

Phase1 CAGE Peaks

Hg19::chr11:3862154..3862165,-	p3@RHOG
Hg19::chr15:40600066..40600089,-	p3@PLCB2
Hg19::chr16:3137080..3137121,-	p@chr16:3137080..3137121 -
Hg19::chr19:2282186..2282208,-	p1@C19orf35
Hg19::chr19:48753064..48753095,-	p1@CARD8
Hg19::chr1:161039493..161039519,-	p3@ARHGAP30
Hg19::chr1:161039535..161039544,-	p11@ARHGAP30
Hg19::chr20:62708698..62708701,+	p@chr20:62708698..62708701 +
Hg19::chr20:62710832..62710879,-	p1@RGS19
Hg19::chr20:62710880..62710898,-	p3@RGS19
Hg19::chr20:62711425..62711470,+	p2@OPRL1
Hg19::chr22:40859415..40859478,-	p2@MKL1
Hg19::chr2:220042536..220042549,-	p5@CNPPD1
Hg19::chr6:31554456..31554512,+	p6@LST1
Hg19::chrX:109245878..109245916,+	p2@TMEM164
Hg19::chrX:77583054..77583100,-	p1@CYSLTR1

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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p.value	FDR	nGenes	nPathway	Name
1.43919346767955e-05	0.00911009465041154	5	932	Signaling by GPCR (Reactome):REACT_14797
0.000123219497261582	0.0389989708832906	4	733	{ARRB2,743} (Static Module):NA

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:0065007	biological regulation	0.00768606826536886
GO:0007242	intracellular signaling cascade	0.00768606826536886
GO:0007165	signal transduction	0.00768606826536886
GO:0051480	cytosolic calcium ion homeostasis	0.00768606826536886
GO:0007204	elevation of cytosolic calcium ion concentration	0.00768606826536886
GO:0051345	positive regulation of hydrolase activity	0.00768606826536886
GO:0007154	cell communication	0.00768606826536886
GO:0008047	enzyme activator activity	0.00768606826536886
GO:0032089	NACHT domain binding	0.00768606826536886
GO:0009968	negative regulation of signal transduction	0.00963686219868977
GO:0006874	cellular calcium ion homeostasis	0.00963686219868977
GO:0055074	calcium ion homeostasis	0.00963686219868977
GO:0006875	cellular metal ion homeostasis	0.00963686219868977
GO:0055065	metal ion homeostasis	0.00963686219868977
GO:0007186	G-protein coupled receptor protein signaling pathway	0.0153133997986742
GO:0015051	X-opioid receptor activity	0.0164799494906198
GO:0030005	cellular di-, tri-valent inorganic cation homeostasis	0.0164799494906198
GO:0055066	di-, tri-valent inorganic cation homeostasis	0.0164799494906198
GO:0004974	leukotriene receptor activity	0.0173368271137648
GO:0030003	cellular cation homeostasis	0.0173368271137648
GO:0055080	cation homeostasis	0.0173368271137648
GO:0043124	negative regulation of I-kappaB kinase/NF-kappaB cascade	0.0188533124660523
GO:0055082	cellular chemical homeostasis	0.0202857552107383
GO:0006873	cellular ion homeostasis	0.0202857552107383
GO:0050718	positive regulation of interleukin-1 beta secretion	0.0202857552107383
GO:0050706	regulation of interleukin-1 beta secretion	0.0202857552107383
GO:0043085	positive regulation of catalytic activity	0.0202857552107383
GO:0050716	positive regulation of interleukin-1 secretion	0.0202857552107383
GO:0050704	regulation of interleukin-1 secretion	0.0202857552107383
GO:0050801	ion homeostasis	0.0202857552107383
GO:0019932	second-messenger-mediated signaling	0.0202857552107383
GO:0050702	interleukin-1 beta secretion	0.0215913114519548
GO:0050672	negative regulation of lymphocyte proliferation	0.0217118145535234
GO:0032945	negative regulation of mononuclear cell proliferation	0.0217118145535234
GO:0050701	interleukin-1 secretion	0.0217118145535234
GO:0048878	chemical homeostasis	0.021812809706439
GO:0051336	regulation of hydrolase activity	0.021812809706439
GO:0016358	dendrite development	0.021812809706439
GO:0048523	negative regulation of cellular process	0.0222381094285401
GO:0050715	positive regulation of cytokine secretion	0.0222381094285401
GO:0007166	cell surface receptor linked signal transduction	0.0222381094285401
GO:0004985	opioid receptor activity	0.0224114206445887
GO:0008656	caspase activator activity	0.0224114206445887
GO:0048519	negative regulation of biological process	0.0224114206445887
GO:0005096	GTPase activator activity	0.0225427971115012
GO:0050707	regulation of cytokine secretion	0.0225427971115012
GO:0007202	phospholipase C activation	0.0225427971115012
GO:0050714	positive regulation of protein secretion	0.0225427971115012
GO:0016505	apoptotic protease activator activity	0.0225427971115012
GO:0019725	cellular homeostasis	0.0238912041264944
GO:0016504	protease activator activity	0.0238912041264944
GO:0007193	G-protein signaling, adenylate cyclase inhibiting pathway	0.0238912041264944
GO:0051250	negative regulation of lymphocyte activation	0.024739396424922
GO:0050663	cytokine secretion	0.0255558362491887
GO:0043028	caspase regulator activity	0.0258718582086354
GO:0051047	positive regulation of secretion	0.0258718582086354
GO:0006914	autophagy	0.0309068112179078
GO:0050708	regulation of protein secretion	0.0309068112179078
GO:0042127	regulation of cell proliferation	0.031677914247718
GO:0042592	homeostatic process	0.0325735113717887
GO:0007585	respiratory gaseous exchange	0.032764573503621
GO:0005834	heterotrimeric G-protein complex	0.0410853019415701
GO:0022603	regulation of anatomical structure morphogenesis	0.0431284191752502
GO:0022604	regulation of cell morphogenesis	0.0431284191752502
GO:0050670	regulation of lymphocyte proliferation	0.0431284191752502
GO:0032944	regulation of mononuclear cell proliferation	0.0431284191752502
GO:0008360	regulation of cell shape	0.0431284191752502
GO:0050790	regulation of catalytic activity	0.0442110780729895
GO:0004435	phosphoinositide phospholipase C activity	0.0442110780729895
GO:0004434	inositol or phosphatidylinositol phosphodiesterase activity	0.0442110780729895
GO:0019897	extrinsic to plasma membrane	0.0477272926776687
GO:0043280	positive regulation of caspase activity	0.0477272926776687
GO:0032943	mononuclear cell proliferation	0.048449248386039
GO:0046651	lymphocyte proliferation	0.048449248386039
GO:0065009	regulation of a molecular function	0.048449248386039
GO:0050794	regulation of cellular process	0.048449248386039
GO:0005624	membrane fraction	0.048449248386039
GO:0004629	phospholipase C activity	0.048449248386039
GO:0009306	protein secretion	0.048449248386039
GO:0005794	Golgi apparatus	0.048449248386039
GO:0030695	GTPase regulator activity	0.048449248386039
GO:0051046	regulation of secretion	0.048449248386039
GO:0004871	signal transducer activity	0.048449248386039
GO:0060089	molecular transducer activity	0.048449248386039
GO:0043281	regulation of caspase activity	0.048449248386039

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
hematopoietic stem cell	1.24e-84	168
angioblastic mesenchymal cell	1.24e-84	168
hematopoietic oligopotent progenitor cell	1.44e-80	161
hematopoietic multipotent progenitor cell	1.44e-80	161
hematopoietic cell	3.97e-77	177
leukocyte	7.03e-72	136
myeloid cell	4.77e-64	108
common myeloid progenitor	4.77e-64	108
hematopoietic lineage restricted progenitor cell	9.15e-61	120
nongranular leukocyte	3.25e-58	115
myeloid leukocyte	1.32e-53	72
granulocyte monocyte progenitor cell	1.01e-47	67
myeloid lineage restricted progenitor cell	1.13e-46	66
macrophage dendritic cell progenitor	2.11e-43	61
monopoietic cell	1.53e-42	59
monocyte	1.53e-42	59
monoblast	1.53e-42	59
promonocyte	1.53e-42	59
defensive cell	2.06e-37	48
phagocyte	2.06e-37	48
classical monocyte	1.08e-32	42
CD14-positive, CD16-negative classical monocyte	1.08e-32	42
nucleate cell	4.55e-15	55
lymphocyte	1.69e-14	53
common lymphoid progenitor	1.69e-14	53
lymphoid lineage restricted progenitor cell	3.08e-14	52
mesenchymal cell	6.84e-13	354
stuff accumulating cell	7.11e-12	87
connective tissue cell	8.47e-12	361
mature alpha-beta T cell	5.33e-10	18
alpha-beta T cell	5.33e-10	18
immature T cell	5.33e-10	18
mature T cell	5.33e-10	18
immature alpha-beta T cell	5.33e-10	18
intermediate monocyte	3.89e-09	9
CD14-positive, CD16-positive monocyte	3.89e-09	9
granulocyte	2.20e-08	8
motile cell	3.57e-08	386
lymphocyte of B lineage	2.46e-07	24
pro-B cell	2.46e-07	24
CD8-positive, alpha-beta T cell	4.22e-07	11
T cell	7.97e-07	25
pro-T cell	7.97e-07	25

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	5.85e-53	98
blood island	5.85e-53	98
hemolymphoid system	3.59e-49	108
bone marrow	5.23e-41	76
immune system	1.00e-40	93
bone element	8.88e-36	82
skeletal element	5.74e-30	90
skeletal system	7.99e-25	100
adult organism	1.67e-20	114
lateral plate mesoderm	5.10e-15	203
connective tissue	9.79e-11	371
blood	8.70e-09	15
haemolymphatic fluid	8.70e-09	15
organism substance	8.70e-09	15
musculoskeletal system	3.19e-07	167

Disease

Ontology term	p-value	n
myeloid leukemia	7.34e-11	31
leukemia	7.25e-09	39
hematologic cancer	6.93e-08	51
immune system cancer	6.93e-08	51

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
EGR1#1958	8	2.49408954740507	0.007106561314776	0.0296288286288978
ELF1#1997	12	3.19357346910565	1.93117413800973e-05	0.000435803577786514
MAX#4149	7	2.82299303519062	0.0067149521973491	0.0285442180202264
POLR2A#5430	15	2.01323735302319	9.45926752373161e-05	0.00137115397766968
SPI1#6688	13	6.66601285067472	5.10515875363416e-10	4.93226341416094e-08
ZEB1#6935	4	4.22210800438596	0.0125811231488872	0.0454956518315372

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.