Coexpression cluster:C2236

Full id: C2236_Eosinophils_Neutrophils_CD14CD16_CD14_Mast_Whole_CD19

Phase1 CAGE Peaks

Hg19::chr12:7060508..7060609,+	p1@PTPN6
Hg19::chr12:7060615..7060624,+	p8@PTPN6
Hg19::chr19:41848208..41848225,-	p18@TGFB1
Hg19::chr5:55711409..55711446,+	p@chr5:55711409..55711446 +

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
6.45030198789693e-06	0.00408304115833875	2	73	Leishmaniasis (KEGG):05140

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:0006470	protein amino acid dephosphorylation	0.00206049010094955
GO:0045066	regulatory T cell differentiation	0.00206049010094955
GO:0051280	negative regulation of release of sequestered calcium ion into cytosol	0.00206049010094955
GO:0009814	defense response, incompatible interaction	0.00206049010094955
GO:0009817	defense response to fungus, incompatible interaction	0.00206049010094955
GO:0050765	negative regulation of phagocytosis	0.00206049010094955
GO:0016311	dephosphorylation	0.00206049010094955
GO:0019049	evasion of host defenses by virus	0.00206049010094955
GO:0044415	evasion or tolerance of host defenses	0.00206049010094955
GO:0052173	response to defenses of other organism during symbiotic interaction	0.00206049010094955
GO:0048290	isotype switching to IgA isotypes	0.00206049010094955
GO:0035306	positive regulation of dephosphorylation	0.00206049010094955
GO:0044413	avoidance of host defenses	0.00206049010094955
GO:0051834	evasion or tolerance of defenses of other organism during symbiotic interaction	0.00206049010094955
GO:0048298	positive regulation of isotype switching to IgA isotypes	0.00206049010094955
GO:0051832	avoidance of defenses of other organism during symbiotic interaction	0.00206049010094955
GO:0035304	regulation of protein amino acid dephosphorylation	0.00206049010094955
GO:0052200	response to host defenses	0.00206049010094955
GO:0048296	regulation of isotype switching to IgA isotypes	0.00206049010094955
GO:0035307	positive regulation of protein amino acid dephosphorylation	0.00206049010094955
GO:0009611	response to wounding	0.00257793593993739
GO:0051279	regulation of release of sequestered calcium ion into cytosol	0.00268755622605763
GO:0007406	negative regulation of neuroblast proliferation	0.00268755622605763
GO:0007184	SMAD protein nuclear translocation	0.00316989145488023
GO:0045806	negative regulation of endocytosis	0.00316989145488023
GO:0031536	positive regulation of exit from mitosis	0.00316989145488023
GO:0035303	regulation of dephosphorylation	0.00355241227247147
GO:0001784	phosphotyrosine binding	0.00355241227247147
GO:0048535	lymph node development	0.00355241227247147
GO:0009605	response to external stimulus	0.00374612507344501
GO:0045830	positive regulation of isotype switching	0.00374612507344501
GO:0008354	germ cell migration	0.00374612507344501
GO:0045309	protein phosphorylated amino acid binding	0.00374612507344501
GO:0051283	negative regulation of sequestering of calcium ion	0.00405788400909243
GO:0051282	regulation of sequestering of calcium ion	0.00405788400909243
GO:0051209	release of sequestered calcium ion into cytosol	0.00405788400909243
GO:0030279	negative regulation of ossification	0.00405788400909243
GO:0050777	negative regulation of immune response	0.00405788400909243
GO:0045191	regulation of isotype switching	0.00405788400909243
GO:0002683	negative regulation of immune system process	0.00405788400909243
GO:0031575	G1/S transition checkpoint	0.00405788400909243
GO:0051208	sequestering of calcium ion	0.00405788400909243
GO:0051219	phosphoprotein binding	0.00405788400909243
GO:0050764	regulation of phagocytosis	0.00405788400909243
GO:0006915	apoptosis	0.00405788400909243
GO:0012501	programmed cell death	0.00405788400909243
GO:0002208	somatic diversification of immunoglobulins during immune response	0.00405788400909243
GO:0002381	immunoglobulin production during immune response	0.00405788400909243
GO:0051101	regulation of DNA binding	0.00405788400909243
GO:0002204	somatic recombination of immunoglobulin genes during immune response	0.00405788400909243
GO:0005160	transforming growth factor beta receptor binding	0.00405788400909243
GO:0001837	epithelial to mesenchymal transition	0.00405788400909243
GO:0019048	virus-host interaction	0.00405788400909243
GO:0045190	isotype switching	0.00405788400909243
GO:0046851	negative regulation of bone remodeling	0.00405788400909243
GO:0050768	negative regulation of neurogenesis	0.00405788400909243
GO:0050680	negative regulation of epithelial cell proliferation	0.00405788400909243
GO:0050832	defense response to fungus	0.00405788400909243
GO:0016265	death	0.00405788400909243
GO:0008219	cell death	0.00405788400909243
GO:0016447	somatic recombination of immunoglobulin gene segments	0.00405788400909243
GO:0045930	negative regulation of progression through mitotic cell cycle	0.00405788400909243
GO:0016202	regulation of striated muscle development	0.00405788400909243
GO:0010458	exit from mitosis	0.00405788400909243
GO:0007096	regulation of exit from mitosis	0.00405788400909243
GO:0051238	sequestering of metal ion	0.00405788400909243
GO:0016444	somatic cell DNA recombination	0.00447846922097053
GO:0016445	somatic diversification of immunoglobulins	0.00447846922097053
GO:0002562	somatic diversification of immune receptors via germline recombination within a single locus	0.00447846922097053
GO:0002200	somatic diversification of immune receptors	0.00470872117487484
GO:0007405	neuroblast proliferation	0.00493247861524983
GO:0050679	positive regulation of epithelial cell proliferation	0.00501082262934408
GO:0002377	immunoglobulin production	0.00501082262934408
GO:0050871	positive regulation of B cell activation	0.00501082262934408
GO:0009620	response to fungus	0.00508305403775861
GO:0017015	regulation of transforming growth factor beta receptor signaling pathway	0.00508305403775861
GO:0030278	regulation of ossification	0.00508305403775861
GO:0006950	response to stress	0.00552651683656853
GO:0042306	regulation of protein import into nucleus	0.00552651683656853
GO:0051701	interaction with host	0.00552651683656853
GO:0000060	protein import into nucleus, translocation	0.00552651683656853
GO:0033157	regulation of intracellular protein transport	0.00552651683656853
GO:0048468	cell development	0.00563188635386827
GO:0051092	activation of NF-kappaB transcription factor	0.00564007429432708
GO:0046850	regulation of bone remodeling	0.00565877078367979
GO:0014031	mesenchymal cell development	0.00565877078367979
GO:0048762	mesenchymal cell differentiation	0.00565877078367979
GO:0051241	negative regulation of multicellular organismal process	0.00565877078367979
GO:0045937	positive regulation of phosphate metabolic process	0.00565877078367979
GO:0050864	regulation of B cell activation	0.00565877078367979
GO:0032386	regulation of intracellular transport	0.00565877078367979
GO:0042552	myelination	0.005821067193276
GO:0007093	mitotic cell cycle checkpoint	0.00591625123079949
GO:0002440	production of molecular mediator of immune response	0.00591625123079949
GO:0051223	regulation of protein transport	0.00600746294850141
GO:0051098	regulation of binding	0.00600746294850141
GO:0046822	regulation of nucleocytoplasmic transport	0.0061577800398386
GO:0051091	positive regulation of transcription factor activity	0.00621760082049371
GO:0050678	regulation of epithelial cell proliferation	0.00621760082049371
GO:0051051	negative regulation of transport	0.00621760082049371
GO:0001763	morphogenesis of a branching structure	0.00621760082049371
GO:0044403	symbiosis, encompassing mutualism through parasitism	0.00621760082049371
GO:0007272	ensheathment of neurons	0.00621760082049371
GO:0008366	axon ensheathment	0.00621760082049371
GO:0044419	interspecies interaction between organisms	0.00621760082049371
GO:0007346	regulation of progression through mitotic cell cycle	0.00621760082049371
GO:0050673	epithelial cell proliferation	0.00635188300532194
GO:0030100	regulation of endocytosis	0.00642418962948427
GO:0030424	axon	0.00642418962948427
GO:0030141	secretory granule	0.00692716904027421
GO:0050767	regulation of neurogenesis	0.00705019239876943
GO:0047485	protein N-terminus binding	0.00717101349592748
GO:0001508	regulation of action potential	0.00727858622798703
GO:0051235	maintenance of localization	0.00727858622798703
GO:0006909	phagocytosis	0.00727858622798703
GO:0030217	T cell differentiation	0.00727858622798703
GO:0006793	phosphorus metabolic process	0.00739714753182425
GO:0006796	phosphate metabolic process	0.00739714753182425
GO:0001666	response to hypoxia	0.00820673422484349
GO:0048869	cellular developmental process	0.00820673422484349
GO:0030154	cell differentiation	0.00820673422484349
GO:0007179	transforming growth factor beta receptor signaling pathway	0.00843866546840953
GO:0016064	immunoglobulin mediated immune response	0.0084684843854286
GO:0051251	positive regulation of lymphocyte activation	0.0084684843854286
GO:0051090	regulation of transcription factor activity	0.00849735185625042
GO:0019724	B cell mediated immunity	0.00849735185625042
GO:0030308	negative regulation of cell growth	0.00859244092463929
GO:0045792	negative regulation of cell size	0.008686039487641
GO:0000075	cell cycle checkpoint	0.00893765386618177
GO:0022415	viral reproductive process	0.00902714296975374
GO:0042113	B cell activation	0.00951369295350302
GO:0045926	negative regulation of growth	0.00951369295350302
GO:0010033	response to organic substance	0.00959680958217342
GO:0042493	response to drug	0.009678681137634
GO:0030098	lymphocyte differentiation	0.00975933528817835
GO:0007088	regulation of mitosis	0.0101412323453735
GO:0051174	regulation of phosphorus metabolic process	0.0102921391075896
GO:0019220	regulation of phosphate metabolic process	0.0102921391075896
GO:0007204	elevation of cytosolic calcium ion concentration	0.0102921391075896
GO:0051480	cytosolic calcium ion homeostasis	0.0102921391075896
GO:0002449	lymphocyte mediated immunity	0.0105108110616537
GO:0043687	post-translational protein modification	0.0106637744193752
GO:0007178	transmembrane receptor protein serine/threonine kinase signaling pathway	0.0107141565090489
GO:0002250	adaptive immune response	0.0107141565090489
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0107141565090489
GO:0051249	regulation of lymphocyte activation	0.0107141565090489
GO:0051093	negative regulation of developmental process	0.0107811289564368
GO:0002443	leukocyte mediated immunity	0.0108471922724222
GO:0050865	regulation of cell activation	0.0110503331282197
GO:0043005	neuron projection	0.011113708774458
GO:0051247	positive regulation of protein metabolic process	0.0115846157013033
GO:0007166	cell surface receptor linked signal transduction	0.0116834586654113
GO:0014706	striated muscle development	0.0116834586654113
GO:0001503	ossification	0.0116834586654113
GO:0031214	biomineral formation	0.0116834586654113
GO:0002521	leukocyte differentiation	0.0118720457812149
GO:0046849	bone remodeling	0.012502112220223
GO:0006606	protein import into nucleus	0.012502112220223
GO:0051170	nuclear import	0.0125243917682088
GO:0042110	T cell activation	0.0125243917682088
GO:0050776	regulation of immune response	0.0125243917682088
GO:0002682	regulation of immune system process	0.0127007283478821
GO:0007050	cell cycle arrest	0.0127488499470269
GO:0048771	tissue remodeling	0.0131721626333633
GO:0006464	protein modification process	0.0134340631775533
GO:0002252	immune effector process	0.0135505160932149
GO:0051049	regulation of transport	0.0135505160932149
GO:0045087	innate immune response	0.0139588481081739
GO:0055074	calcium ion homeostasis	0.0140362234715278
GO:0006874	cellular calcium ion homeostasis	0.0140362234715278
GO:0043412	biopolymer modification	0.0140489859928888
GO:0017038	protein import	0.0145395928833342
GO:0006875	cellular metal ion homeostasis	0.0145395928833342
GO:0055065	metal ion homeostasis	0.0145395928833342
GO:0042060	wound healing	0.0153949540833138
GO:0006913	nucleocytoplasmic transport	0.017988952623837
GO:0046649	lymphocyte activation	0.0180032059714914
GO:0051169	nuclear transport	0.0180172957615725
GO:0030097	hemopoiesis	0.0184895278787589
GO:0001558	regulation of cell growth	0.0185007391088173
GO:0032502	developmental process	0.0187647019955975
GO:0007517	muscle development	0.0194240394070176
GO:0048534	hemopoietic or lymphoid organ development	0.0194299237665899
GO:0045321	leukocyte activation	0.0199954876014571
GO:0030005	cellular di-, tri-valent inorganic cation homeostasis	0.0199954876014571
GO:0002520	immune system development	0.0201083690822038
GO:0055066	di-, tri-valent inorganic cation homeostasis	0.0201104356201654
GO:0006310	DNA recombination	0.0213027112445465
GO:0010324	membrane invagination	0.0213027112445465
GO:0006897	endocytosis	0.0213027112445465
GO:0030003	cellular cation homeostasis	0.0213961365321492
GO:0016049	cell growth	0.0213961365321492
GO:0040008	regulation of growth	0.0213961365321492
GO:0055080	cation homeostasis	0.0214970119510755
GO:0008361	regulation of cell size	0.0215911465360642
GO:0051707	response to other organism	0.0215911465360642
GO:0001775	cell activation	0.0216833518416847
GO:0001501	skeletal development	0.0216833518416847
GO:0006917	induction of apoptosis	0.021876068821807
GO:0012502	induction of programmed cell death	0.021876068821807
GO:0004725	protein tyrosine phosphatase activity	0.0221662759483106
GO:0006605	protein targeting	0.0221662759483106
GO:0045893	positive regulation of transcription, DNA-dependent	0.0225409065093586
GO:0008285	negative regulation of cell proliferation	0.0225409065093586
GO:0045786	negative regulation of progression through cell cycle	0.0225409065093586
GO:0008284	positive regulation of cell proliferation	0.0231140999528246
GO:0016477	cell migration	0.0231140999528246
GO:0050793	regulation of developmental process	0.0231736693375057
GO:0006873	cellular ion homeostasis	0.0231736693375057
GO:0055082	cellular chemical homeostasis	0.0231736693375057
GO:0007067	mitosis	0.0232577860515655
GO:0048699	generation of neurons	0.0234376026025504
GO:0000087	M phase of mitotic cell cycle	0.0236157051062257
GO:0008083	growth factor activity	0.0242700046495253
GO:0043065	positive regulation of apoptosis	0.0244424856494988
GO:0043068	positive regulation of programmed cell death	0.0245186743594489
GO:0022008	neurogenesis	0.024782603119839
GO:0007276	gamete generation	0.0248564992906902
GO:0050801	ion homeostasis	0.0250230604966794
GO:0051239	regulation of multicellular organismal process	0.0258384340947735
GO:0045941	positive regulation of transcription	0.025906467296979
GO:0016044	membrane organization and biogenesis	0.0262500139072716
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0264182343048339
GO:0009607	response to biotic stimulus	0.0264182343048339
GO:0006954	inflammatory response	0.0264182343048339
GO:0016481	negative regulation of transcription	0.0264182343048339
GO:0007167	enzyme linked receptor protein signaling pathway	0.0271117065808389
GO:0048878	chemical homeostasis	0.0271719441412501
GO:0009888	tissue development	0.0271726741397441
GO:0022414	reproductive process	0.0271726741397441
GO:0000279	M phase	0.0271726741397441
GO:0016563	transcription activator activity	0.0273195892415244
GO:0042995	cell projection	0.0274350947975721
GO:0004721	phosphoprotein phosphatase activity	0.0274350947975721
GO:0019953	sexual reproduction	0.0274920948196355
GO:0045934	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0277215898472288
GO:0000278	mitotic cell cycle	0.0282074449957576
GO:0019226	transmission of nerve impulse	0.0284318936848912
GO:0051704	multi-organism process	0.0285690544056786
GO:0016023	cytoplasmic membrane-bound vesicle	0.0296399746567695
GO:0031988	membrane-bound vesicle	0.02990063306683
GO:0000074	regulation of progression through cell cycle	0.02990063306683
GO:0051726	regulation of cell cycle	0.0302810314848609
GO:0009887	organ morphogenesis	0.0304075868306677
GO:0031325	positive regulation of cellular metabolic process	0.0305330867900803
GO:0022403	cell cycle phase	0.0307403978631971
GO:0019725	cellular homeostasis	0.0311110003802775
GO:0031324	negative regulation of cellular metabolic process	0.0313896883456635
GO:0006928	cell motility	0.0313896883456635
GO:0051674	localization of cell	0.0313896883456635
GO:0009893	positive regulation of metabolic process	0.0318139601688625
GO:0007165	signal transduction	0.0318139601688625
GO:0005578	proteinaceous extracellular matrix	0.0340217146424188
GO:0051246	regulation of protein metabolic process	0.0340217146424188
GO:0031410	cytoplasmic vesicle	0.0341276918296541
GO:0031982	vesicle	0.0345507055252033
GO:0009892	negative regulation of metabolic process	0.0347328780898267
GO:0016791	phosphoric monoester hydrolase activity	0.0347559323918043
GO:0007154	cell communication	0.0361918096548299
GO:0044267	cellular protein metabolic process	0.0363645558128093
GO:0042127	regulation of cell proliferation	0.0367711650166377
GO:0044260	cellular macromolecule metabolic process	0.037023657213381
GO:0032989	cellular structure morphogenesis	0.0370459803513501
GO:0000902	cell morphogenesis	0.0370459803513501
GO:0042592	homeostatic process	0.0370595047182018
GO:0019538	protein metabolic process	0.0391184422583096
GO:0005615	extracellular space	0.0403561355709879
GO:0006886	intracellular protein transport	0.0403561355709879
GO:0042981	regulation of apoptosis	0.0432959286704676
GO:0042578	phosphoric ester hydrolase activity	0.0434249170822596
GO:0043067	regulation of programmed cell death	0.0434249170822596
GO:0006952	defense response	0.0438609639151437
GO:0042221	response to chemical stimulus	0.0440711758487935
GO:0016192	vesicle-mediated transport	0.0451662904214498
GO:0022402	cell cycle process	0.046399908682708
GO:0007267	cell-cell signaling	0.0473308073613599
GO:0065009	regulation of a molecular function	0.049421473323182

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	1.33e-82	172
angioblastic mesenchymal cell	1.33e-82	172
hematopoietic oligopotent progenitor cell	3.42e-78	165
hematopoietic multipotent progenitor cell	3.42e-78	165
leukocyte	7.16e-74	140
hematopoietic cell	8.55e-74	182
hematopoietic lineage restricted progenitor cell	8.95e-63	124
nongranular leukocyte	1.57e-59	119
myeloid cell	9.64e-49	112
common myeloid progenitor	9.64e-49	112
myeloid leukocyte	6.27e-41	76
granulocyte monocyte progenitor cell	3.54e-36	71
myeloid lineage restricted progenitor cell	4.10e-35	70
macrophage dendritic cell progenitor	3.54e-32	65
monopoietic cell	4.50e-31	63
monocyte	4.50e-31	63
monoblast	4.50e-31	63
promonocyte	4.50e-31	63
CD14-positive, CD16-negative classical monocyte	2.91e-30	42
classical monocyte	1.11e-26	45
lymphocyte	1.31e-24	53
common lymphoid progenitor	1.31e-24	53
lymphoid lineage restricted progenitor cell	3.81e-24	52
lymphocyte of B lineage	2.15e-13	24
pro-B cell	2.15e-13	24
mesenchymal cell	1.44e-11	358
T cell	5.49e-11	25
pro-T cell	5.49e-11	25
connective tissue cell	2.19e-10	365
B cell	4.50e-10	14
mature alpha-beta T cell	5.13e-10	18
alpha-beta T cell	5.13e-10	18
immature T cell	5.13e-10	18
mature T cell	5.13e-10	18
immature alpha-beta T cell	5.13e-10	18
intermediate monocyte	3.03e-08	9
CD14-positive, CD16-positive monocyte	3.03e-08	9
motile cell	5.53e-08	390
granulocyte	1.49e-07	8
CD8-positive, alpha-beta T cell	3.73e-07	11

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	5.39e-40	102
blood island	5.39e-40	102
hemolymphoid system	3.76e-35	112
bone marrow	1.55e-30	80
bone element	3.92e-26	86
immune system	8.71e-23	115
adult organism	8.97e-23	115
skeletal element	7.15e-19	101
skeletal system	7.15e-19	101
connective tissue	3.63e-09	375
lateral plate mesoderm	7.39e-07	216

Disease

Ontology term	p-value	n
hematologic cancer	4.34e-11	51
immune system cancer	4.34e-11	51
leukemia	2.36e-10	39
myeloid leukemia	1.34e-07	31

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
EBF1#1879	3	6.67985013492675	0.00518429411827891	0.0240395370696147
PBX3#5090	2	10.9572563433721	0.0117453018068803	0.0428245906789825
SPI1#6688	3	6.15324263139204	0.00658038711305903	0.0280922600433605

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.