Coexpression cluster:C2558

Full id: C2558_CD14_Monocytederived_Macrophage_spleen_dura_lymph_left

Phase1 CAGE Peaks

Hg19::chr1:206944507..206944524,-	p3@IL10
Hg19::chr3:9142472..9142491,+	p@chr3:9142472..9142491 +
Hg19::chr5:36680430..36680455,+	p6@SLC1A3
Hg19::chrX:5644225..5644242,-	p1@ENST00000422914

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:0030886	negative regulation of myeloid dendritic cell activation	0.00373837277758154
GO:0045355	negative regulation of interferon-alpha biosynthetic process	0.00373837277758154
GO:0005141	interleukin-10 receptor binding	0.00373837277758154
GO:0032695	negative regulation of interleukin-12 production	0.00373837277758154
GO:0030885	regulation of myeloid dendritic cell activation	0.00421703056648373
GO:0045347	negative regulation of MHC class II biosynthetic process	0.00421703056648373
GO:0032655	regulation of interleukin-12 production	0.00421703056648373
GO:0007253	cytoplasmic sequestering of NF-kappaB	0.00421703056648373
GO:0001773	myeloid dendritic cell activation	0.00421703056648373
GO:0042347	negative regulation of NF-kappaB import into nucleus	0.00421703056648373
GO:0045348	positive regulation of MHC class II biosynthetic process	0.00421703056648373
GO:0045354	regulation of interferon-alpha biosynthetic process	0.00421703056648373
GO:0032607	interferon-alpha production	0.00421703056648373
GO:0045349	interferon-alpha biosynthetic process	0.00421703056648373
GO:0045342	MHC class II biosynthetic process	0.00421703056648373
GO:0045346	regulation of MHC class II biosynthetic process	0.00421703056648373
GO:0032615	interleukin-12 production	0.00421703056648373
GO:0007267	cell-cell signaling	0.00421703056648373
GO:0001504	neurotransmitter uptake	0.00421703056648373
GO:0032606	interferon type I production	0.00421703056648373
GO:0042130	negative regulation of T cell proliferation	0.00421703056648373
GO:0005313	L-glutamate transmembrane transporter activity	0.00421703056648373
GO:0045351	interferon type I biosynthetic process	0.00421703056648373
GO:0045191	regulation of isotype switching	0.00421703056648373
GO:0015172	acidic amino acid transmembrane transporter activity	0.00421703056648373
GO:0042994	cytoplasmic sequestering of transcription factor	0.00421703056648373
GO:0002237	response to molecule of bacterial origin	0.00421703056648373
GO:0042092	T-helper 2 type immune response	0.00421703056648373
GO:0001818	negative regulation of cytokine production	0.00421703056648373
GO:0051220	cytoplasmic sequestering of protein	0.00421703056648373
GO:0042308	negative regulation of protein import into nucleus	0.00421703056648373
GO:0002208	somatic diversification of immunoglobulins during immune response	0.00421703056648373
GO:0002381	immunoglobulin production during immune response	0.00421703056648373
GO:0042992	negative regulation of transcription factor import into nucleus	0.00421703056648373
GO:0050672	negative regulation of lymphocyte proliferation	0.00421703056648373
GO:0002204	somatic recombination of immunoglobulin genes during immune response	0.00421703056648373
GO:0050868	negative regulation of T cell activation	0.00421703056648373
GO:0045190	isotype switching	0.00421703056648373
GO:0032945	negative regulation of mononuclear cell proliferation	0.00421703056648373
GO:0042345	regulation of NF-kappaB import into nucleus	0.00422524021915686
GO:0042348	NF-kappaB import into nucleus	0.00422524021915686
GO:0046823	negative regulation of nucleocytoplasmic transport	0.00422524021915686
GO:0015813	L-glutamate transport	0.00422524021915686
GO:0016447	somatic recombination of immunoglobulin gene segments	0.00422524021915686
GO:0051224	negative regulation of protein transport	0.00422524021915686
GO:0015800	acidic amino acid transport	0.00422524021915686
GO:0016444	somatic cell DNA recombination	0.00448512294667026
GO:0016445	somatic diversification of immunoglobulins	0.00448512294667026
GO:0002562	somatic diversification of immune receptors via germline recombination within a single locus	0.00448512294667026
GO:0017153	sodium:dicarboxylate symporter activity	0.00448512294667026
GO:0002200	somatic diversification of immune receptors	0.00460005837853158
GO:0042036	negative regulation of cytokine biosynthetic process	0.00460005837853158
GO:0006835	dicarboxylic acid transport	0.00470647192314367
GO:0005310	dicarboxylic acid transmembrane transporter activity	0.00470647192314367
GO:0002377	immunoglobulin production	0.00480527663985466
GO:0042100	B cell proliferation	0.00480527663985466
GO:0051250	negative regulation of lymphocyte activation	0.00498317648473598
GO:0042990	regulation of transcription factor import into nucleus	0.00532086228261171
GO:0042991	transcription factor import into nucleus	0.00532086228261171
GO:0042306	regulation of protein import into nucleus	0.00539139544131378
GO:0033157	regulation of intracellular protein transport	0.00539139544131378
GO:0030595	leukocyte chemotaxis	0.00554546659648675
GO:0032507	maintenance of cellular protein localization	0.0056622003417305
GO:0050864	regulation of B cell activation	0.0056622003417305
GO:0051651	maintenance of cellular localization	0.0056622003417305
GO:0032386	regulation of intracellular transport	0.0056622003417305
GO:0045185	maintenance of protein localization	0.00580071207558523
GO:0002440	production of molecular mediator of immune response	0.00584912688971298
GO:0002274	myeloid leukocyte activation	0.00584912688971298
GO:0051223	regulation of protein transport	0.00597901945045953
GO:0046822	regulation of nucleocytoplasmic transport	0.00602045177069617
GO:0030183	B cell differentiation	0.00602045177069617
GO:0051051	negative regulation of transport	0.00626153430883787
GO:0050900	leukocyte migration	0.00626153430883787
GO:0015179	L-amino acid transmembrane transporter activity	0.00637724512346562
GO:0042129	regulation of T cell proliferation	0.00668647045420683
GO:0005343	organic acid:sodium symporter activity	0.00737562614066439
GO:0015296	anion:cation symporter activity	0.00737797439175931
GO:0042098	T cell proliferation	0.00737797439175931
GO:0001817	regulation of cytokine production	0.00747223366902842
GO:0051235	maintenance of localization	0.00747223366902842
GO:0017148	negative regulation of translation	0.00747223366902842
GO:0050670	regulation of lymphocyte proliferation	0.00747223366902842
GO:0032944	regulation of mononuclear cell proliferation	0.00747223366902842
GO:0031327	negative regulation of cellular biosynthetic process	0.00791142726813731
GO:0009890	negative regulation of biosynthetic process	0.00870251049755147
GO:0016064	immunoglobulin mediated immune response	0.00870251049755147
GO:0019724	B cell mediated immunity	0.00870251049755147
GO:0032943	mononuclear cell proliferation	0.00870251049755147
GO:0045727	positive regulation of translation	0.00870251049755147
GO:0046651	lymphocyte proliferation	0.00870251049755147
GO:0005126	hematopoietin/interferon-class (D200-domain) cytokine receptor binding	0.00943610885175068
GO:0050863	regulation of T cell activation	0.00943610885175068
GO:0042035	regulation of cytokine biosynthetic process	0.00943610885175068
GO:0031328	positive regulation of cellular biosynthetic process	0.00943610885175068
GO:0042113	B cell activation	0.00949330646860266
GO:0015171	amino acid transmembrane transporter activity	0.0097031985626071
GO:0030098	lymphocyte differentiation	0.00975649000092232
GO:0042089	cytokine biosynthetic process	0.0101102086620081
GO:0042107	cytokine metabolic process	0.0101583465632025
GO:0006865	amino acid transport	0.0102517777777559
GO:0009891	positive regulation of biosynthetic process	0.0102517777777559
GO:0002449	lymphocyte mediated immunity	0.0104420024233583
GO:0002250	adaptive immune response	0.0106885360918715
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0106885360918715
GO:0051249	regulation of lymphocyte activation	0.0106885360918715
GO:0006836	neurotransmitter transport	0.0106885360918715
GO:0002443	leukocyte mediated immunity	0.0106885360918715
GO:0001505	regulation of neurotransmitter levels	0.0106885360918715
GO:0050865	regulation of cell activation	0.0108626209758598
GO:0015837	amine transport	0.0113023312774558
GO:0051247	positive regulation of protein metabolic process	0.0113346007808109
GO:0015370	solute:sodium symporter activity	0.0116302848965169
GO:0002521	leukocyte differentiation	0.0117899233592696
GO:0042742	defense response to bacterium	0.0121168876006111
GO:0006606	protein import into nucleus	0.0121168876006111
GO:0046943	carboxylic acid transmembrane transporter activity	0.0121168876006111
GO:0046942	carboxylic acid transport	0.0121168876006111
GO:0051170	nuclear import	0.0121168876006111
GO:0042110	T cell activation	0.0121168876006111
GO:0015849	organic acid transport	0.0121168876006111
GO:0005342	organic acid transmembrane transporter activity	0.0121168876006111
GO:0051248	negative regulation of protein metabolic process	0.0126244345520289
GO:0009617	response to bacterium	0.0127630680133989
GO:0002252	immune effector process	0.0130336914204533
GO:0051049	regulation of transport	0.0130336914204533
GO:0001816	cytokine production	0.0132831418191474
GO:0015294	solute:cation symporter activity	0.0132958028230356
GO:0017038	protein import	0.0141168753275877
GO:0007249	I-kappaB kinase/NF-kappaB cascade	0.0159562573805025
GO:0042330	taxis	0.0162785650400583
GO:0006935	chemotaxis	0.0162785650400583
GO:0006913	nucleocytoplasmic transport	0.0172401688036447
GO:0046649	lymphocyte activation	0.0172401688036447
GO:0051169	nuclear transport	0.0172401688036447
GO:0030097	hemopoiesis	0.0176606066078919
GO:0006916	anti-apoptosis	0.0185092718642826
GO:0048534	hemopoietic or lymphoid organ development	0.0186985862633258
GO:0045321	leukocyte activation	0.0192502490155955
GO:0007626	locomotory behavior	0.0192502490155955
GO:0002520	immune system development	0.0192502490155955
GO:0006417	regulation of translation	0.0193241649736255
GO:0006310	DNA recombination	0.0205408360571791
GO:0031326	regulation of cellular biosynthetic process	0.0206046712896671
GO:0051707	response to other organism	0.0211801702295847
GO:0001775	cell activation	0.0211953183833238
GO:0008509	anion transmembrane transporter activity	0.0211953183833238
GO:0032501	multicellular organismal process	0.021662995930589
GO:0009889	regulation of biosynthetic process	0.021662995930589
GO:0006605	protein targeting	0.021662995930589
GO:0008285	negative regulation of cell proliferation	0.0222082308787569
GO:0043066	negative regulation of apoptosis	0.0222575744863357
GO:0043069	negative regulation of programmed cell death	0.0224033379698629
GO:0016477	cell migration	0.0225471826960967
GO:0006810	transport	0.023112770376829
GO:0015293	symporter activity	0.0231147989916142
GO:0051234	establishment of localization	0.023855702942669
GO:0008083	growth factor activity	0.023855702942669
GO:0051239	regulation of multicellular organismal process	0.0259452236696486
GO:0009607	response to biotic stimulus	0.0267462490658675
GO:0007268	synaptic transmission	0.0267462490658675
GO:0006954	inflammatory response	0.0267462490658675
GO:0007610	behavior	0.0268550136245768
GO:0051179	localization	0.0269409793953437
GO:0005125	cytokine activity	0.0279666644296476
GO:0019226	transmission of nerve impulse	0.0295828715497254
GO:0051704	multi-organism process	0.029671736813535
GO:0015291	secondary active transmembrane transporter activity	0.0318738815999311
GO:0031325	positive regulation of cellular metabolic process	0.0321229753329957
GO:0007243	protein kinase cascade	0.0328910569679788
GO:0031324	negative regulation of cellular metabolic process	0.0329189960355018
GO:0006928	cell motility	0.0329189960355018
GO:0051674	localization of cell	0.0329189960355018
GO:0009893	positive regulation of metabolic process	0.0334095011152632
GO:0051246	regulation of protein metabolic process	0.0357161306587689
GO:0009611	response to wounding	0.0357161306587689
GO:0009892	negative regulation of metabolic process	0.0365987540911655
GO:0007154	cell communication	0.0382169243973137
GO:0042127	regulation of cell proliferation	0.0389099379666876
GO:0005615	extracellular space	0.0433642124796889
GO:0006886	intracellular protein transport	0.0433642124796889
GO:0050789	regulation of biological process	0.0455825782743777
GO:0042981	regulation of apoptosis	0.0461863797398652
GO:0043067	regulation of programmed cell death	0.0464147630813704
GO:0006952	defense response	0.0467994791501073
GO:0042221	response to chemical stimulus	0.0469429105331343

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
monopoietic cell	6.14e-56	59
monocyte	6.14e-56	59
monoblast	6.14e-56	59
promonocyte	6.14e-56	59
macrophage dendritic cell progenitor	1.28e-53	61
defensive cell	1.34e-53	48
phagocyte	1.34e-53	48
myeloid lineage restricted progenitor cell	1.94e-48	66
granulocyte monocyte progenitor cell	1.70e-47	67
myeloid leukocyte	2.68e-45	72
classical monocyte	3.82e-43	42
CD14-positive, CD16-negative classical monocyte	3.82e-43	42
myeloid cell	1.94e-26	108
common myeloid progenitor	1.94e-26	108
stuff accumulating cell	1.50e-23	87
nongranular leukocyte	9.13e-23	115
hematopoietic lineage restricted progenitor cell	3.92e-20	120
leukocyte	5.53e-19	136
hematopoietic oligopotent progenitor cell	4.41e-13	161
hematopoietic multipotent progenitor cell	4.41e-13	161
hematopoietic stem cell	1.05e-12	168
angioblastic mesenchymal cell	1.05e-12	168
macrophage	3.30e-12	6
hematopoietic cell	2.20e-11	177
adult endothelial progenitor cell	3.42e-07	3

Uber Anatomy

Ontology term	p-value	n
bone marrow	4.04e-40	76
immune system	4.59e-40	93
bone element	4.17e-36	82
hematopoietic system	1.64e-35	98
blood island	1.64e-35	98
hemolymphoid system	1.09e-33	108
skeletal element	1.35e-31	90
adult organism	1.85e-29	114
skeletal system	2.26e-28	100
organ	4.00e-16	503
lateral plate mesoderm	3.20e-14	203
neural tube	1.13e-12	56
neural rod	1.13e-12	56
future spinal cord	1.13e-12	56
neural keel	1.13e-12	56
musculoskeletal system	4.28e-12	167
telencephalon	3.48e-11	34
germ layer	5.55e-11	560
germ layer / neural crest	5.55e-11	560
embryonic tissue	5.55e-11	560
presumptive structure	5.55e-11	560
germ layer / neural crest derived structure	5.55e-11	560
epiblast (generic)	5.55e-11	560
anatomical system	8.00e-11	624
anatomical group	9.25e-11	625
embryonic structure	1.03e-10	564
developing anatomical structure	1.29e-10	581
regional part of nervous system	3.88e-10	53
regional part of brain	3.88e-10	53
embryo	6.52e-10	592
brain grey matter	1.18e-09	34
gray matter	1.18e-09	34
regional part of forebrain	1.36e-09	41
forebrain	1.36e-09	41
anterior neural tube	1.36e-09	41
future forebrain	1.36e-09	41
multi-cellular organism	1.65e-09	656
cerebral hemisphere	2.44e-09	32
regional part of telencephalon	2.67e-09	32
central nervous system	5.99e-09	81
regional part of cerebral cortex	2.12e-08	22
neural plate	5.05e-08	82
presumptive neural plate	5.05e-08	82
neocortex	6.61e-08	20
nervous system	2.22e-07	89
neurectoderm	2.40e-07	86
brain	2.61e-07	68
future brain	2.61e-07	68
mesoderm	3.06e-07	315
mesoderm-derived structure	3.06e-07	315
presumptive mesoderm	3.06e-07	315
cerebral cortex	4.21e-07	25
pallium	4.21e-07	25

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)
MA0003.1	0.0938548
MA0004.1	0.71247
MA0006.1	0.532262
MA0007.1	2.78189
MA0009.1	1.20602
MA0014.1	0.244769
MA0017.1	0.577281
MA0019.1	0.873355
MA0024.1	1.09684
MA0025.1	1.34373
MA0027.1	2.83281
MA0028.1	0.550763
MA0029.1	1.11704
MA0030.1	1.10506
MA0031.1	1.03735
MA0038.1	0.824639
MA0040.1	1.12314
MA0041.1	0.732902
MA0042.1	0.697662
MA0043.1	1.20635
MA0046.1	1.19471
MA0048.1	0.25531
MA0050.1	0.69864
MA0051.1	0.820063
MA0052.1	1.12718
MA0055.1	0.396851
MA0056.1	0
MA0057.1	0.248209
MA0058.1	0.605914
MA0059.1	0.604454
MA0060.1	0.393285
MA0061.1	0.360128
MA0063.1	0
MA0066.1	0.825101
MA0067.1	1.53181
MA0068.1	0.313194
MA0069.1	1.19071
MA0070.1	1.17908
MA0071.1	0.782546
MA0072.1	1.1744
MA0073.1	0.100363
MA0074.1	0.819248
MA0076.1	0.623864
MA0077.1	1.16637
MA0078.1	0.926725
MA0081.1	0.604638
MA0083.1	1.21381
MA0084.1	1.72172
MA0087.1	1.17185
MA0088.1	0.182167
MA0089.1	0
MA0090.1	0.640115
MA0091.1	0.715356
MA0092.1	0.673508
MA0093.1	0.535768
MA0095.1	0
MA0098.1	0
MA0100.1	0.83965
MA0101.1	0.539569
MA0103.1	0.521546
MA0105.1	0.232357
MA0106.1	0.869173
MA0107.1	0.453492
MA0108.2	1.03412
MA0109.1	0
MA0111.1	0.655276
MA0113.1	2.05499
MA0114.1	0.447443
MA0115.1	1.45393
MA0116.1	0.457606
MA0117.1	1.24497
MA0119.1	0.586221
MA0122.1	1.27173
MA0124.1	1.41151
MA0125.1	1.32534
MA0130.1	0
MA0131.1	0.94608
MA0132.1	0
MA0133.1	0
MA0135.1	1.23748
MA0136.1	0.832277
MA0139.1	0.344952
MA0140.1	0.779643
MA0141.1	0.602484
MA0142.1	1.00381
MA0143.1	0.887001
MA0144.1	0.430413
MA0145.1	0.195821
MA0146.1	0.061409
MA0147.1	0.46175
MA0148.1	0.739888
MA0149.1	0.769072
MA0062.2	0.353589
MA0035.2	0.778873
MA0039.2	0.10559
MA0138.2	0.928035
MA0002.2	0.379056
MA0137.2	0.558189
MA0104.2	0.392359
MA0047.2	0.856092
MA0112.2	0.551048
MA0065.2	0.199162
MA0150.1	0.633493
MA0151.1	0
MA0152.1	0.78681
MA0153.1	1.30799
MA0154.1	0.229241
MA0155.1	0.180766
MA0156.1	0.560797
MA0157.1	0.97481
MA0158.1	0
MA0159.1	0.462502
MA0160.1	0.756582
MA0161.1	0
MA0162.1	0.0928415
MA0163.1	0.0725493
MA0164.1	0.90014
MA0080.2	0.535868
MA0018.2	0.870662
MA0099.2	0.7872
MA0079.2	0.0270533
MA0102.2	1.75932
MA0258.1	0.418966
MA0259.1	0.471671
MA0442.1	0

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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No analysis results for this cluster

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.