Coexpression cluster:C462

Full id: C462_CD14_Monocytederived_Macrophage_Hepatic_Dendritic_lung_adipose

Phase1 CAGE Peaks

Hg19::chr10:49860525..49860564,-	p7@ARHGAP22
Hg19::chr14:61448920..61448942,+	p4@SLC38A6
Hg19::chr14:93118883..93118894,+	p25@RIN3
Hg19::chr14:93214988..93215002,-	p2@LGMN
Hg19::chr17:29281231..29281262,+	p3@ADAP2
Hg19::chr17:29290132..29290136,+	p@chr17:29290132..29290136 +
Hg19::chr17:29297900..29297936,-	p2@AK092436
Hg19::chr17:7462347..7462356,+	p10@TNFSF13
Hg19::chr19:11688452..11688486,-	p1@ACP5
Hg19::chr19:12992244..12992272,-	p2@DNASE2
Hg19::chr19:40872251..40872269,+	p25@PLD3
Hg19::chr19:51645742..51645787,+	p1@SIGLEC7
Hg19::chr1:159796513..159796524,+	p7@SLAMF8
Hg19::chr1:206945673..206945712,-	p4@IL10
Hg19::chr1:22965767..22965778,+	p@chr1:22965767..22965778 +
Hg19::chr20:43990576..43990596,+	p4@SYS1
Hg19::chr20:48884002..48884088,+	p1@ENST00000425497 p1@ENST00000445003 p1@uc010zyr.1
Hg19::chr22:27014043..27014073,-	p2@CRYBB1
Hg19::chr22:47016102..47016117,+	p2@GRAMD4
Hg19::chr2:232106599..232106613,-	p@chr2:232106599..232106613 -
Hg19::chr5:76383909..76383944,+	p1@ENST00000514288

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
3.25661910109795e-05	0.02061439890995	3	121	Lysosome (KEGG):04142

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:0005764	lysosome	0.00929741119260226
GO:0000323	lytic vacuole	0.00929741119260226
GO:0005773	vacuole	0.00946609524320958
GO:0030886	negative regulation of myeloid dendritic cell activation	0.0179307328724496
GO:0045355	negative regulation of interferon-alpha biosynthetic process	0.0179307328724496
GO:0005141	interleukin-10 receptor binding	0.0179307328724496
GO:0032695	negative regulation of interleukin-12 production	0.0179307328724496
GO:0045347	negative regulation of MHC class II biosynthetic process	0.0228169020854112
GO:0016889	endodeoxyribonuclease activity, producing 3'-phosphomonoesters	0.0228169020854112
GO:0004531	deoxyribonuclease II activity	0.0228169020854112
GO:0030885	regulation of myeloid dendritic cell activation	0.0228169020854112
GO:0032655	regulation of interleukin-12 production	0.0313510836916462
GO:0007253	cytoplasmic sequestering of NF-kappaB	0.0313510836916462
GO:0001773	myeloid dendritic cell activation	0.0313510836916462
GO:0042347	negative regulation of NF-kappaB import into nucleus	0.0313510836916462
GO:0045348	positive regulation of MHC class II biosynthetic process	0.0313510836916462
GO:0045354	regulation of interferon-alpha biosynthetic process	0.0313510836916462
GO:0032607	interferon-alpha production	0.0313510836916462
GO:0045349	interferon-alpha biosynthetic process	0.0313510836916462
GO:0045342	MHC class II biosynthetic process	0.0313510836916462
GO:0045346	regulation of MHC class II biosynthetic process	0.0313510836916462
GO:0004630	phospholipase D activity	0.0313510836916462
GO:0032615	interleukin-12 production	0.0313510836916462
GO:0001509	legumain activity	0.0313510836916462
GO:0042130	negative regulation of T cell proliferation	0.0328150059188141
GO:0045351	interferon type I biosynthetic process	0.0328150059188141
GO:0032606	interferon type I production	0.0328150059188141
GO:0042994	cytoplasmic sequestering of transcription factor	0.0328150059188141
GO:0045191	regulation of isotype switching	0.0328150059188141
GO:0042092	T-helper 2 type immune response	0.0328150059188141
GO:0051220	cytoplasmic sequestering of protein	0.0328150059188141
GO:0002237	response to molecule of bacterial origin	0.0328150059188141
GO:0001818	negative regulation of cytokine production	0.0328150059188141
GO:0002208	somatic diversification of immunoglobulins during immune response	0.0328150059188141
GO:0002381	immunoglobulin production during immune response	0.0328150059188141
GO:0050868	negative regulation of T cell activation	0.0328150059188141
GO:0042308	negative regulation of protein import into nucleus	0.0328150059188141
GO:0042992	negative regulation of transcription factor import into nucleus	0.0328150059188141
GO:0050672	negative regulation of lymphocyte proliferation	0.0328150059188141
GO:0002204	somatic recombination of immunoglobulin genes during immune response	0.0328150059188141
GO:0045190	isotype switching	0.0328150059188141
GO:0032945	negative regulation of mononuclear cell proliferation	0.0328150059188141
GO:0042348	NF-kappaB import into nucleus	0.033405743502606
GO:0046823	negative regulation of nucleocytoplasmic transport	0.033405743502606
GO:0042345	regulation of NF-kappaB import into nucleus	0.033405743502606
GO:0016447	somatic recombination of immunoglobulin gene segments	0.0346434571716005
GO:0051224	negative regulation of protein transport	0.0346434571716005
GO:0016444	somatic cell DNA recombination	0.0375615612892389
GO:0016445	somatic diversification of immunoglobulins	0.0375615612892389
GO:0002562	somatic diversification of immune receptors via germline recombination within a single locus	0.0375615612892389
GO:0002200	somatic diversification of immune receptors	0.0385178777119114
GO:0042036	negative regulation of cytokine biosynthetic process	0.0385178777119114
GO:0002377	immunoglobulin production	0.0417129711359742
GO:0042100	B cell proliferation	0.0417129711359742
GO:0051250	negative regulation of lymphocyte activation	0.0432221762489413
GO:0005096	GTPase activator activity	0.0443656361163416
GO:0042990	regulation of transcription factor import into nucleus	0.0445173893930843
GO:0042991	transcription factor import into nucleus	0.0445173893930843
GO:0005212	structural constituent of eye lens	0.0445173893930843
GO:0042306	regulation of protein import into nucleus	0.0451002136213308
GO:0033157	regulation of intracellular protein transport	0.0451002136213308
GO:0016788	hydrolase activity, acting on ester bonds	0.0453904386158153
GO:0030595	leukocyte chemotaxis	0.0456453341420361
GO:0032507	maintenance of cellular protein localization	0.046635970718298
GO:0051651	maintenance of cellular localization	0.046635970718298
GO:0050864	regulation of B cell activation	0.046635970718298
GO:0032386	regulation of intracellular transport	0.046635970718298
GO:0045185	maintenance of protein localization	0.047779721085016
GO:0002440	production of molecular mediator of immune response	0.0481912578546151
GO:0002274	myeloid leukocyte activation	0.0481912578546151
GO:0051223	regulation of protein transport	0.0492635366268128
GO:0046822	regulation of nucleocytoplasmic transport	0.0496163041105543
GO:0030183	B cell differentiation	0.0496163041105543

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	3.26e-55	59
monocyte	3.26e-55	59
monoblast	3.26e-55	59
promonocyte	3.26e-55	59
macrophage dendritic cell progenitor	6.13e-53	61
defensive cell	6.44e-52	48
phagocyte	6.44e-52	48
myeloid lineage restricted progenitor cell	7.48e-48	66
myeloid leukocyte	3.17e-47	72
granulocyte monocyte progenitor cell	6.32e-47	67
classical monocyte	6.61e-41	42
CD14-positive, CD16-negative classical monocyte	6.61e-41	42
myeloid cell	1.38e-26	108
common myeloid progenitor	1.38e-26	108
nongranular leukocyte	7.06e-24	115
stuff accumulating cell	6.76e-23	87
leukocyte	3.09e-20	136
hematopoietic lineage restricted progenitor cell	4.80e-20	120
hematopoietic stem cell	1.03e-13	168
angioblastic mesenchymal cell	1.03e-13	168
hematopoietic oligopotent progenitor cell	2.64e-13	161
hematopoietic multipotent progenitor cell	2.64e-13	161
macrophage	4.36e-13	6
hematopoietic cell	2.45e-12	177
adult endothelial progenitor cell	2.47e-07	3

Uber Anatomy

Ontology term	p-value	n
immune system	3.85e-40	93
bone marrow	1.10e-39	76
hematopoietic system	4.36e-37	98
blood island	4.36e-37	98
bone element	9.63e-36	82
hemolymphoid system	2.20e-35	108
adult organism	1.42e-31	114
skeletal element	2.60e-31	90
skeletal system	8.75e-27	100
lateral plate mesoderm	1.16e-14	203
organ	3.20e-14	503
musculoskeletal system	3.57e-12	167
germ layer	1.61e-09	560
germ layer / neural crest	1.61e-09	560
embryonic tissue	1.61e-09	560
presumptive structure	1.61e-09	560
germ layer / neural crest derived structure	1.61e-09	560
epiblast (generic)	1.61e-09	560
anatomical system	1.71e-09	624
anatomical group	1.95e-09	625
embryonic structure	2.82e-09	564
developing anatomical structure	2.90e-09	581
multi-cellular organism	7.47e-09	656
embryo	1.27e-08	592
mesoderm	3.25e-08	315
mesoderm-derived structure	3.25e-08	315
presumptive mesoderm	3.25e-08	315
neural tube	2.08e-07	56
neural rod	2.08e-07	56
future spinal cord	2.08e-07	56
neural keel	2.08e-07	56

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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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.