Coexpression cluster:C821

Full id: C821_migratory_CD14_immature_CD14CD16_Dendritic_Macrophage_Monocytederived

Phase1 CAGE Peaks

Hg19::chr12:69719024..69719043,-	p@chr12:69719024..69719043 -
Hg19::chr17:4643087..4643113,+	p2@ZMYND15
Hg19::chr17:4643118..4643145,+	p1@ZMYND15
Hg19::chr18:56203944..56203982,-	p17@ALPK2
Hg19::chr3:121774202..121774222,+	p1@CD86
Hg19::chr3:121774295..121774306,+	p3@CD86
Hg19::chr3:121821281..121821283,+	p@chr3:121821281..121821283 +
Hg19::chr7:6414211..6414222,+	p2@RAC1
Hg19::chr8:39771339..39771352,+	p4@IDO1
Hg19::chr8:623777..623823,-	p2@ERICH1

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
0.000187878492077518	0.0396423618283563	2	102	Toll-like receptor signaling pathway (KEGG):04620
9.34899905302393e-05	0.0396423618283563	2	72	Viral myocarditis (KEGG):05416
0.000187878492077518	0.0396423618283563	2	102	Toll-like receptor signaling pathway (Wikipathways):WP75

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:0043016	regulation of lymphotoxin A biosynthetic process	0.00753461939402311
GO:0043017	positive regulation of lymphotoxin A biosynthetic process	0.00753461939402311
GO:0048261	negative regulation of receptor-mediated endocytosis	0.00753461939402311
GO:0045630	positive regulation of T-helper 2 cell differentiation	0.00753461939402311
GO:0035025	positive regulation of Rho protein signal transduction	0.00753461939402311
GO:0045404	positive regulation of interleukin-4 biosynthetic process	0.00753461939402311
GO:0045402	regulation of interleukin-4 biosynthetic process	0.00753461939402311
GO:0032641	lymphotoxin A production	0.00753461939402311
GO:0042109	lymphotoxin A biosynthetic process	0.00753461939402311
GO:0042097	interleukin-4 biosynthetic process	0.00753461939402311
GO:0045624	positive regulation of T-helper cell differentiation	0.00753461939402311
GO:0045628	regulation of T-helper 2 cell differentiation	0.00753461939402311
GO:0045806	negative regulation of endocytosis	0.00753461939402311
GO:0032633	interleukin-4 production	0.00753461939402311
GO:0045064	T-helper 2 cell differentiation	0.0082406260734007
GO:0031529	ruffle organization and biogenesis	0.0082406260734007
GO:0045622	regulation of T-helper cell differentiation	0.00852921161836958
GO:0048259	regulation of receptor-mediated endocytosis	0.00852921161836958
GO:0030032	lamellipodium biogenesis	0.00852921161836958
GO:0051057	positive regulation of small GTPase mediated signal transduction	0.00852921161836958
GO:0002294	CD4-positive, alpha-beta T cell differentiation during immune response	0.00852921161836958
GO:0002292	T cell differentiation during immune response	0.00852921161836958
GO:0042093	T-helper cell differentiation	0.00852921161836958
GO:0002366	leukocyte activation during immune response	0.00852921161836958
GO:0042092	T-helper 2 type immune response	0.00852921161836958
GO:0002285	lymphocyte activation during immune response	0.00852921161836958
GO:0002293	alpha-beta T cell differentiation during immune response	0.00852921161836958
GO:0002286	T cell activation during immune response	0.00852921161836958
GO:0002263	cell activation during immune response	0.00852921161836958
GO:0030742	GTP-dependent protein binding	0.00852921161836958
GO:0005041	low-density lipoprotein receptor activity	0.00852921161836958
GO:0043367	CD4-positive, alpha beta T cell differentiation	0.00852921161836958
GO:0045086	positive regulation of interleukin-2 biosynthetic process	0.00852921161836958
GO:0030228	lipoprotein receptor activity	0.00852921161836958
GO:0045076	regulation of interleukin-2 biosynthetic process	0.0110977673958521
GO:0015026	coreceptor activity	0.0110977673958521
GO:0042094	interleukin-2 biosynthetic process	0.0110977673958521
GO:0046632	alpha-beta T cell differentiation	0.0110977673958521
GO:0030169	low-density lipoprotein binding	0.0114885274969046
GO:0046631	alpha-beta T cell activation	0.0125180103570752
GO:0032623	interleukin-2 production	0.0134970475465134
GO:0008034	lipoprotein binding	0.0181885724770088
GO:0051051	negative regulation of transport	0.0185575468569413
GO:0030041	actin filament polymerization	0.0185575468569413
GO:0030100	regulation of endocytosis	0.0198985033483514
GO:0042108	positive regulation of cytokine biosynthetic process	0.0224885972698191
GO:0030217	T cell differentiation	0.0224885972698191
GO:0006898	receptor-mediated endocytosis	0.0224885972698191
GO:0030031	cell projection biogenesis	0.0268547456505492
GO:0045727	positive regulation of translation	0.0278930136771611
GO:0042035	regulation of cytokine biosynthetic process	0.0302754135134063
GO:0031328	positive regulation of cellular biosynthetic process	0.0302754135134063
GO:0008154	actin polymerization and/or depolymerization	0.0302754135134063
GO:0030098	lymphocyte differentiation	0.0311720084080662
GO:0042089	cytokine biosynthetic process	0.0319317503155234
GO:0042107	cytokine metabolic process	0.0319317503155234
GO:0009891	positive regulation of biosynthetic process	0.0322913838427321
GO:0005044	scavenger receptor activity	0.0326458682279682
GO:0002250	adaptive immune response	0.0326458682279682
GO:0008009	chemokine activity	0.0326458682279682
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0326458682279682
GO:0042379	chemokine receptor binding	0.0326458682279682
GO:0048770	pigment granule	0.0340809899234666
GO:0042470	melanosome	0.0340809899234666
GO:0051247	positive regulation of protein metabolic process	0.0343622254130415
GO:0002521	leukocyte differentiation	0.0358243535923532
GO:0051258	protein polymerization	0.0378480464406347
GO:0042110	T cell activation	0.0378480464406347
GO:0001664	G-protein-coupled receptor binding	0.0395726775772995
GO:0051049	regulation of transport	0.0412468429366429
GO:0001816	cytokine production	0.0417694350402286
GO:0044267	cellular protein metabolic process	0.0484331498350187
GO:0044260	cellular macromolecule metabolic process	0.0495517687458814

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
macrophage dendritic cell progenitor	1.40e-62	61
defensive cell	2.50e-62	48
phagocyte	2.50e-62	48
monopoietic cell	4.76e-60	59
monocyte	4.76e-60	59
monoblast	4.76e-60	59
promonocyte	4.76e-60	59
granulocyte monocyte progenitor cell	1.06e-58	67
classical monocyte	9.60e-56	42
CD14-positive, CD16-negative classical monocyte	9.60e-56	42
myeloid leukocyte	3.37e-55	72
myeloid lineage restricted progenitor cell	4.83e-55	66
leukocyte	1.76e-40	136
myeloid cell	6.89e-40	108
common myeloid progenitor	6.89e-40	108
nongranular leukocyte	1.88e-35	115
hematopoietic lineage restricted progenitor cell	7.73e-34	120
hematopoietic stem cell	1.46e-29	168
angioblastic mesenchymal cell	1.46e-29	168
hematopoietic oligopotent progenitor cell	1.48e-27	161
hematopoietic multipotent progenitor cell	1.48e-27	161
stuff accumulating cell	3.54e-27	87
hematopoietic cell	9.52e-27	177
intermediate monocyte	1.73e-12	9
CD14-positive, CD16-positive monocyte	1.73e-12	9
conventional dendritic cell	1.12e-09	8
dendritic cell	3.14e-09	10
Langerhans cell	3.78e-08	5
macrophage	8.40e-08	6

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	4.12e-58	98
blood island	4.12e-58	98
hemolymphoid system	9.40e-54	108
bone marrow	3.26e-49	76
immune system	1.09e-47	93
bone element	4.67e-44	82
skeletal element	2.85e-38	90
skeletal system	8.21e-35	100
adult organism	7.83e-31	114
lateral plate mesoderm	1.90e-20	203
musculoskeletal system	3.02e-14	167
neural tube	1.57e-10	56
neural rod	1.57e-10	56
future spinal cord	1.57e-10	56
neural keel	1.57e-10	56
regional part of nervous system	1.70e-09	53
regional part of brain	1.70e-09	53
organ	2.13e-09	503
mesoderm	2.77e-09	315
mesoderm-derived structure	2.77e-09	315
presumptive mesoderm	2.77e-09	315
germ layer	1.57e-08	560
germ layer / neural crest	1.57e-08	560
embryonic tissue	1.57e-08	560
presumptive structure	1.57e-08	560
germ layer / neural crest derived structure	1.57e-08	560
epiblast (generic)	1.57e-08	560
embryonic structure	3.11e-08	564
developing anatomical structure	1.04e-07	581
brain grey matter	1.68e-07	34
gray matter	1.68e-07	34
embryo	2.72e-07	592
brainstem	3.32e-07	6
neural nucleus	4.60e-07	9
nucleus of brain	4.60e-07	9
tissue	5.57e-07	773
regional part of forebrain	6.18e-07	41
forebrain	6.18e-07	41
anterior neural tube	6.18e-07	41
future forebrain	6.18e-07	41

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
BATF#10538	3	7.30734053769109	0.00667851738648644	0.0284147829603315
BDP1#55814	1	105.015340909091	0.0094819471733889	0.0357245700159294
IRF4#3662	3	6.57435380602324	0.00894914180685731	0.033936292115986
PAX5#5079	5	3.33478276558891	0.00985362449367583	0.0370314029685142
SPI1#6688	6	4.92259410511364	0.000443419790230525	0.00412931961407809

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.