Coexpression cluster:C687

Full id: C687_CD14_Macrophage_Monocytederived_Dendritic_Endothelial_Pericytes_schwannoma

Phase1 CAGE Peaks

Hg19::chr11:6640638..6640665,-	p1@TPP1
Hg19::chr16:81031957..81031962,-	p@chr16:81031957..81031962 -
Hg19::chr19:54887674..54887700,-	p@chr19:54887674..54887700 -
Hg19::chr19:55836684..55836695,-	p2@TMEM150B
Hg19::chr19:55836697..55836717,-	p1@TMEM150B
Hg19::chr1:156933510..156933528,-	p5@ARHGEF11
Hg19::chr1:206944527..206944552,-	p2@IL10
Hg19::chr2:113999360..113999386,-	p4@PAX8
Hg19::chr4:185314151..185314178,-	p@chr4:185314151..185314178 -
Hg19::chr4:185314188..185314207,-	p@chr4:185314188..185314207 -
Hg19::chr5:75698757..75698769,+	p16@IQGAP2
Hg19::chr5:75698771..75698784,+	p8@IQGAP2

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:0031325	positive regulation of cellular metabolic process	1.44708864309662e-05
GO:0009893	positive regulation of metabolic process	1.44708864309662e-05
GO:0048522	positive regulation of cellular process	0.000340399707680242
GO:0048518	positive regulation of biological process	0.00039129294247486
GO:0048856	anatomical structure development	0.00346825179540455
GO:0051247	positive regulation of protein metabolic process	0.00346825179540455
GO:0050794	regulation of cellular process	0.00414557086227873
GO:0030886	negative regulation of myeloid dendritic cell activation	0.00414557086227873
GO:0045355	negative regulation of interferon-alpha biosynthetic process	0.00414557086227873
GO:0005141	interleukin-10 receptor binding	0.00414557086227873
GO:0032695	negative regulation of interleukin-12 production	0.00414557086227873
GO:0019131	tripeptidyl-peptidase I activity	0.00414557086227873
GO:0050789	regulation of biological process	0.005007604007807
GO:0004996	thyroid-stimulating hormone receptor activity	0.00542547742072489
GO:0043171	peptide catabolic process	0.00542547742072489
GO:0045347	negative regulation of MHC class II biosynthetic process	0.00542547742072489
GO:0008240	tripeptidyl-peptidase activity	0.00542547742072489
GO:0030885	regulation of myeloid dendritic cell activation	0.00542547742072489
GO:0065007	biological regulation	0.00542547742072489
GO:0045893	positive regulation of transcription, DNA-dependent	0.00678286267540764
GO:0032502	developmental process	0.00678286267540764
GO:0032655	regulation of interleukin-12 production	0.00678286267540764
GO:0007253	cytoplasmic sequestering of NF-kappaB	0.00731399062475549
GO:0001773	myeloid dendritic cell activation	0.00731399062475549
GO:0045941	positive regulation of transcription	0.00731399062475549
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.00731399062475549
GO:0032501	multicellular organismal process	0.00731399062475549
GO:0042347	negative regulation of NF-kappaB import into nucleus	0.00731399062475549
GO:0030010	establishment of cell polarity	0.00731399062475549
GO:0045862	positive regulation of proteolysis	0.00731399062475549
GO:0045348	positive regulation of MHC class II biosynthetic process	0.00731399062475549
GO:0045354	regulation of interferon-alpha biosynthetic process	0.00731399062475549
GO:0032607	interferon-alpha production	0.00731399062475549
GO:0045349	interferon-alpha biosynthetic process	0.00731399062475549
GO:0031323	regulation of cellular metabolic process	0.00785245391915232
GO:0045342	MHC class II biosynthetic process	0.00785245391915232
GO:0045346	regulation of MHC class II biosynthetic process	0.00785245391915232
GO:0032615	interleukin-12 production	0.00785245391915232
GO:0019222	regulation of metabolic process	0.00866295884396289
GO:0005096	GTPase activator activity	0.00866295884396289
GO:0042130	negative regulation of T cell proliferation	0.00868084560304669
GO:0045351	interferon type I biosynthetic process	0.00868084560304669
GO:0032606	interferon type I production	0.00868084560304669
GO:0006928	cell motility	0.00868084560304669
GO:0051674	localization of cell	0.00868084560304669
GO:0005515	protein binding	0.00868084560304669
GO:0042994	cytoplasmic sequestering of transcription factor	0.00868084560304669
GO:0045191	regulation of isotype switching	0.00868084560304669
GO:0042092	T-helper 2 type immune response	0.00868084560304669
GO:0005095	GTPase inhibitor activity	0.00868084560304669
GO:0051220	cytoplasmic sequestering of protein	0.00868084560304669
GO:0002237	response to molecule of bacterial origin	0.00868084560304669
GO:0001818	negative regulation of cytokine production	0.00868084560304669
GO:0051246	regulation of protein metabolic process	0.00868084560304669
GO:0002208	somatic diversification of immunoglobulins during immune response	0.00868084560304669
GO:0002381	immunoglobulin production during immune response	0.00868084560304669
GO:0050868	negative regulation of T cell activation	0.00868084560304669
GO:0042308	negative regulation of protein import into nucleus	0.00868084560304669
GO:0042992	negative regulation of transcription factor import into nucleus	0.00868084560304669
GO:0050672	negative regulation of lymphocyte proliferation	0.00868084560304669
GO:0002204	somatic recombination of immunoglobulin genes during immune response	0.00868084560304669
GO:0045190	isotype switching	0.00868084560304669
GO:0032945	negative regulation of mononuclear cell proliferation	0.00868084560304669
GO:0008047	enzyme activator activity	0.00879225782841612
GO:0042348	NF-kappaB import into nucleus	0.00879225782841612
GO:0046823	negative regulation of nucleocytoplasmic transport	0.00879225782841612
GO:0042345	regulation of NF-kappaB import into nucleus	0.00879225782841612
GO:0007242	intracellular signaling cascade	0.00879225782841612
GO:0005083	small GTPase regulator activity	0.00885277140044013
GO:0051056	regulation of small GTPase mediated signal transduction	0.00885277140044013
GO:0016447	somatic recombination of immunoglobulin gene segments	0.00885277140044013
GO:0045453	bone resorption	0.00885277140044013
GO:0051224	negative regulation of protein transport	0.00885277140044013
GO:0016444	somatic cell DNA recombination	0.00981036771088836
GO:0016445	somatic diversification of immunoglobulins	0.00981036771088836
GO:0002562	somatic diversification of immune receptors via germline recombination within a single locus	0.00981036771088836
GO:0002200	somatic diversification of immune receptors	0.0101954741945606
GO:0042036	negative regulation of cytokine biosynthetic process	0.0101954741945606
GO:0030162	regulation of proteolysis	0.0106949389685248
GO:0002377	immunoglobulin production	0.0110437965500934
GO:0042100	B cell proliferation	0.0110437965500934
GO:0007275	multicellular organismal development	0.0111081060449981
GO:0048871	multicellular organismal homeostasis	0.0111081060449981
GO:0051250	negative regulation of lymphocyte activation	0.0111081060449981
GO:0001894	tissue homeostasis	0.0111081060449981
GO:0042990	regulation of transcription factor import into nucleus	0.0119937293804143
GO:0042991	transcription factor import into nucleus	0.0119937293804143
GO:0042306	regulation of protein import into nucleus	0.0121453156237049
GO:0016500	protein-hormone receptor activity	0.0121453156237049
GO:0033157	regulation of intracellular protein transport	0.0121453156237049
GO:0030595	leukocyte chemotaxis	0.0125571044995709
GO:0032507	maintenance of cellular protein localization	0.0129598778977745
GO:0051651	maintenance of cellular localization	0.0130727913479262
GO:0050864	regulation of B cell activation	0.0130727913479262
GO:0032386	regulation of intracellular transport	0.0130727913479262
GO:0045185	maintenance of protein localization	0.0134532890036535
GO:0002440	production of molecular mediator of immune response	0.0136848006735213
GO:0002274	myeloid leukocyte activation	0.0136848006735213
GO:0030695	GTPase regulator activity	0.0137693004310155
GO:0051223	regulation of protein transport	0.0137693004310155
GO:0006518	peptide metabolic process	0.0137693004310155
GO:0007163	establishment and/or maintenance of cell polarity	0.0138488690139391
GO:0046822	regulation of nucleocytoplasmic transport	0.0138488690139391
GO:0030183	B cell differentiation	0.0138488690139391
GO:0051051	negative regulation of transport	0.0145229331747046
GO:0050900	leukocyte migration	0.0145229331747046
GO:0000910	cytokinesis	0.0156306473236618
GO:0042129	regulation of T cell proliferation	0.0156306473236618
GO:0004289	subtilase activity	0.0159418155417927
GO:0009966	regulation of signal transduction	0.0162332840639816
GO:0006941	striated muscle contraction	0.0165471742413023
GO:0042098	T cell proliferation	0.0172838520684026
GO:0051235	maintenance of localization	0.0176941145288218
GO:0017148	negative regulation of translation	0.0176941145288218
GO:0001817	regulation of cytokine production	0.0176941145288218
GO:0032944	regulation of mononuclear cell proliferation	0.0178147887588494
GO:0050670	regulation of lymphocyte proliferation	0.0178147887588494
GO:0007264	small GTPase mediated signal transduction	0.0179841717525187
GO:0031327	negative regulation of cellular biosynthetic process	0.0187631647938454
GO:0065008	regulation of biological quality	0.0207346863543757
GO:0016064	immunoglobulin mediated immune response	0.0207346863543757
GO:0009890	negative regulation of biosynthetic process	0.0207346863543757
GO:0019724	B cell mediated immunity	0.0208612972281041
GO:0032943	mononuclear cell proliferation	0.0208612972281041
GO:0045727	positive regulation of translation	0.0208612972281041
GO:0046651	lymphocyte proliferation	0.0208612972281041
GO:0005126	hematopoietin/interferon-class (D200-domain) cytokine receptor binding	0.0228520209123766
GO:0050863	regulation of T cell activation	0.0228520209123766
GO:0042035	regulation of cytokine biosynthetic process	0.0228804678061735
GO:0031328	positive regulation of cellular biosynthetic process	0.0228804678061735
GO:0009653	anatomical structure morphogenesis	0.0229080085282027
GO:0042113	B cell activation	0.0229080085282027
GO:0030098	lymphocyte differentiation	0.0238497075266876
GO:0042089	cytokine biosynthetic process	0.024776960082457
GO:0042107	cytokine metabolic process	0.0249590236052958
GO:0009891	positive regulation of biosynthetic process	0.0255011896296816
GO:0002449	lymphocyte mediated immunity	0.0260352708378146
GO:0002250	adaptive immune response	0.0268864492015738
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0268864492015738
GO:0051249	regulation of lymphocyte activation	0.0268864492015738
GO:0002443	leukocyte mediated immunity	0.0273950593245228
GO:0050865	regulation of cell activation	0.027896342042255
GO:0010468	regulation of gene expression	0.0279530799537249
GO:0043283	biopolymer metabolic process	0.0279530799537249
GO:0004177	aminopeptidase activity	0.0279530799537249
GO:0048770	pigment granule	0.0279530799537249
GO:0042470	melanosome	0.0279530799537249
GO:0002521	leukocyte differentiation	0.0300933626416046
GO:0042742	defense response to bacterium	0.0314507346991382
GO:0046849	bone remodeling	0.0314507346991382
GO:0006606	protein import into nucleus	0.0314507346991382
GO:0051170	nuclear import	0.0316825417547719
GO:0042110	T cell activation	0.0316825417547719
GO:0051248	negative regulation of protein metabolic process	0.0333921647463723
GO:0048771	tissue remodeling	0.0334937664481431
GO:0009617	response to bacterium	0.0335940283593114
GO:0002252	immune effector process	0.0344123347683006
GO:0051049	regulation of transport	0.0344123347683006
GO:0001816	cytokine production	0.0351223165365737
GO:0017038	protein import	0.0376627093899688
GO:0048731	system development	0.0423386320615437
GO:0007249	I-kappaB kinase/NF-kappaB cascade	0.0423386320615437
GO:0005516	calmodulin binding	0.0426793116647242
GO:0042330	taxis	0.0430514455933189
GO:0006935	chemotaxis	0.0430514455933189
GO:0005089	Rho guanyl-nucleotide exchange factor activity	0.0451481686323264
GO:0006913	nucleocytoplasmic transport	0.0454629643846659
GO:0046649	lymphocyte activation	0.0454831304372573
GO:0051169	nuclear transport	0.0455030236474464
GO:0030097	hemopoiesis	0.0461895273061865
GO:0035023	regulation of Rho protein signal transduction	0.0461895273061865
GO:0001558	regulation of cell growth	0.0461895273061865
GO:0003012	muscle system process	0.0461895273061865
GO:0006936	muscle contraction	0.0461895273061865
GO:0005099	Ras GTPase activator activity	0.0461895273061865
GO:0005088	Ras guanyl-nucleotide exchange factor activity	0.0461895273061865
GO:0006916	anti-apoptosis	0.0473064165394246
GO:0048534	hemopoietic or lymphoid organ development	0.0478280163152249
GO:0048869	cellular developmental process	0.0478280163152249
GO:0030154	cell differentiation	0.0478280163152249
GO:0045321	leukocyte activation	0.0489505828554582
GO:0007626	locomotory behavior	0.0489505828554582
GO:0002520	immune system development	0.0489505828554582
GO:0006417	regulation of translation	0.0492137468793967
GO:0008238	exopeptidase activity	0.0494652716338911
GO:0007165	signal transduction	0.0494652716338911
GO:0007266	Rho protein signal transduction	0.0494652716338911

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	1.05e-73	59
monocyte	1.05e-73	59
monoblast	1.05e-73	59
promonocyte	1.05e-73	59
defensive cell	1.22e-71	48
phagocyte	1.22e-71	48
myeloid leukocyte	5.01e-71	72
macrophage dendritic cell progenitor	1.15e-70	61
myeloid lineage restricted progenitor cell	2.57e-68	66
granulocyte monocyte progenitor cell	5.27e-67	67
classical monocyte	4.07e-62	42
CD14-positive, CD16-negative classical monocyte	4.07e-62	42
myeloid cell	1.82e-43	108
common myeloid progenitor	1.82e-43	108
leukocyte	1.60e-40	136
nongranular leukocyte	1.88e-39	115
hematopoietic lineage restricted progenitor cell	4.83e-35	120
stuff accumulating cell	1.22e-31	87
hematopoietic stem cell	1.46e-29	168
angioblastic mesenchymal cell	1.46e-29	168
hematopoietic oligopotent progenitor cell	3.11e-27	161
hematopoietic multipotent progenitor cell	3.11e-27	161
hematopoietic cell	6.41e-27	177
intermediate monocyte	8.73e-13	9
CD14-positive, CD16-positive monocyte	8.73e-13	9
macrophage	1.42e-10	6

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	4.52e-62	98
blood island	4.52e-62	98
hemolymphoid system	8.08e-58	108
bone marrow	9.59e-57	76
immune system	9.86e-54	93
bone element	3.70e-51	82
skeletal element	7.11e-45	90
skeletal system	7.00e-40	100
lateral plate mesoderm	1.97e-25	203
adult organism	4.12e-22	114
musculoskeletal system	9.96e-19	167
mesoderm	3.14e-13	315
mesoderm-derived structure	3.14e-13	315
presumptive mesoderm	3.14e-13	315
germ layer	2.98e-09	560
germ layer / neural crest	2.98e-09	560
embryonic tissue	2.98e-09	560
presumptive structure	2.98e-09	560
germ layer / neural crest derived structure	2.98e-09	560
epiblast (generic)	2.98e-09	560
organ	3.64e-09	503
embryonic structure	5.64e-09	564
developing anatomical structure	1.04e-08	581
embryo	5.46e-08	592
anatomical system	6.44e-07	624
anatomical group	7.37e-07	625

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	0.00869098
MA0004.1	0.32225
MA0006.1	0.188769
MA0007.1	0.825205
MA0009.1	0.756202
MA0014.1	0.00958972
MA0017.1	0.220105
MA0019.1	1.15437
MA0024.1	0.654931
MA0025.1	0.886436
MA0027.1	2.35633
MA0028.1	0.583404
MA0029.1	0.673506
MA0030.1	0.662482
MA0031.1	0.600685
MA0038.1	0.414169
MA0040.1	0.67914
MA0041.1	0.89827
MA0042.1	0.310552
MA0043.1	0.756508
MA0046.1	0.745626
MA0048.1	0.155795
MA0050.1	2.30599
MA0051.1	0.410316
MA0052.1	0.682867
MA0055.1	0.0371476
MA0056.1	0
MA0057.1	0.617373
MA0058.1	0.676094
MA0059.1	0.673606
MA0060.1	0.103131
MA0061.1	0.28989
MA0063.1	0
MA0066.1	1.0654
MA0067.1	1.06751
MA0068.1	2.96303
MA0069.1	0.741884
MA0070.1	0.731026
MA0071.1	0.379038
MA0072.1	0.726666
MA0073.1	1.03026
MA0074.1	0.40963
MA0076.1	0.254045
MA0077.1	0.719193
MA0078.1	0.502027
MA0081.1	1.25193
MA0083.1	0.763502
MA0084.1	1.25286
MA0087.1	0.724294
MA0088.1	0.20556
MA0089.1	0
MA0090.1	0.266215
MA0091.1	0.324543
MA0092.1	0.291716
MA0093.1	0.558691
MA0095.1	0
MA0098.1	0
MA0100.1	0.426863
MA0101.1	0.19375
MA0103.1	0.535462
MA0105.1	0.0320473
MA0106.1	0.452066
MA0107.1	0.137948
MA0108.2	0.597764
MA0109.1	0
MA0111.1	0.761158
MA0113.1	1.17934
MA0114.1	0.418165
MA0115.1	0.992167
MA0116.1	0.433848
MA0117.1	0.792789
MA0119.1	0.226505
MA0122.1	0.818044
MA0124.1	0.951337
MA0125.1	0.868909
MA0130.1	0
MA0131.1	0.519055
MA0132.1	0
MA0133.1	0
MA0135.1	0.785738
MA0136.1	0.420617
MA0139.1	0.268952
MA0140.1	0.982486
MA0141.1	1.24597
MA0142.1	0.570448
MA0143.1	0.467429
MA0144.1	0.124153
MA0145.1	0.0932202
MA0146.1	0.00710499
MA0147.1	0.440281
MA0148.1	0.910784
MA0149.1	0.367947
MA0062.2	0.280813
MA0035.2	0.376007
MA0039.2	0.19592
MA0138.2	0.503176
MA0002.2	1.08633
MA0137.2	0.20663
MA0104.2	0.335786
MA0047.2	0.440861
MA0112.2	0.0192555
MA0065.2	0.23889
MA0150.1	0.723395
MA0151.1	0
MA0152.1	0.382565
MA0153.1	0.852412
MA0154.1	0.5526
MA0155.1	0.0793743
MA0156.1	0.600064
MA0157.1	0.544523
MA0158.1	0
MA0159.1	0.143477
MA0160.1	0.357736
MA0161.1	0
MA0162.1	0.138499
MA0163.1	0.00158421
MA0164.1	0.478818
MA0080.2	0.558855
MA0018.2	0.453345
MA0099.2	0.996203
MA0079.2	0.0295657
MA0102.2	1.28978
MA0258.1	0.117513
MA0259.1	0.149181
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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
SPI1#6688	6	4.10216175426136	0.00156889654803008	0.00994984130311594

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.