Coexpression cluster:C392

Full id: C392_Monocytederived_CD14_Macrophage_CD14CD16_Dendritic_Eosinophils_migratory

Phase1 CAGE Peaks

Hg19::chr11:124932955..124932970,+	p3@SLC37A2
Hg19::chr12:8218926..8218980,-	p1@C3AR1
Hg19::chr13:44453688..44453795,+	p1@LACC1
Hg19::chr13:50018402..50018469,+	p1@SETDB2
Hg19::chr17:4642690..4642701,-	p9@CXCL16
Hg19::chr17:55055472..55055522,+	p1@SCPEP1
Hg19::chr18:74824549..74824569,+	p1@AK097116
Hg19::chr19:18284561..18284667,+	p1@IFI30
Hg19::chr19:54876531..54876549,-	p1@LAIR1
Hg19::chr19:7587555..7587570,+	p2@MCOLN1
Hg19::chr1:17944806..17944819,+	p10@ARHGEF10L
Hg19::chr1:17944832..17944849,+	p2@ARHGEF10L
Hg19::chr1:228870893..228870910,+	p3@RHOU
Hg19::chr3:46249843..46249846,-	p6@CCR1
Hg19::chr3:46249859..46249874,-	p4@CCR1
Hg19::chr3:46249878..46249905,-	p2@CCR1
Hg19::chr3:46412794..46412814,-	p@chr3:46412794..46412814 -
Hg19::chr3:46412829..46412861,-	p@chr3:46412829..46412861 -
Hg19::chr5:156536036..156536065,-	p2@HAVCR2
Hg19::chr5:156536071..156536082,-	p9@HAVCR2
Hg19::chr5:156536090..156536106,-	p8@HAVCR2
Hg19::chr5:180257951..180257966,+	p1@ENST00000501855
Hg19::chr5:180257974..180258065,+	p1@ENST00000502162 p1@ENST00000508309 p1@ENST00000509921
Hg19::chr5:77806227..77806251,-	p6@LHFPL2
Hg19::chr5:77806360..77806396,-	p9@LHFPL2
Hg19::chr8:17941575..17941642,-	p1@ASAH1
Hg19::chr9:115983665..115983682,-	p5@FKBP15

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:0042330	taxis	0.00405379739799262
GO:0006935	chemotaxis	0.00405379739799262
GO:0007626	locomotory behavior	0.00433475631325112
GO:0005764	lysosome	0.00433475631325112
GO:0000323	lytic vacuole	0.00433475631325112
GO:0042221	response to chemical stimulus	0.00433475631325112
GO:0005773	vacuole	0.0048306998448887
GO:0007610	behavior	0.00837779738250679
GO:0051480	cytosolic calcium ion homeostasis	0.00912516189803368
GO:0007204	elevation of cytosolic calcium ion concentration	0.00912516189803368
GO:0004943	C3a anaphylatoxin receptor activity	0.00912516189803368
GO:0004876	complement component C3a receptor activity	0.00912516189803368
GO:0006874	cellular calcium ion homeostasis	0.0193159095894078
GO:0055074	calcium ion homeostasis	0.0193159095894078
GO:0006875	cellular metal ion homeostasis	0.0193159095894078
GO:0055065	metal ion homeostasis	0.0193159095894078
GO:0004875	complement receptor activity	0.0193159095894078
GO:0004942	anaphylatoxin receptor activity	0.0225218536178917
GO:0048247	lymphocyte chemotaxis	0.0225218536178917
GO:0001653	peptide receptor activity	0.0225218536178917
GO:0008528	peptide receptor activity, G-protein coupled	0.0225218536178917
GO:0009605	response to external stimulus	0.0279409002264544
GO:0001848	complement binding	0.02853630822038
GO:0030005	cellular di-, tri-valent inorganic cation homeostasis	0.0287048152723536
GO:0055066	di-, tri-valent inorganic cation homeostasis	0.0287048152723536
GO:0030003	cellular cation homeostasis	0.0325569677870366
GO:0055080	cation homeostasis	0.0325569677870366
GO:0042277	peptide binding	0.0329217591962625
GO:0016021	integral to membrane	0.0329326172035117
GO:0031224	intrinsic to membrane	0.0329326172035117
GO:0055082	cellular chemical homeostasis	0.0343440629744898
GO:0006873	cellular ion homeostasis	0.0343440629744898
GO:0005041	low-density lipoprotein receptor activity	0.0343440629744898
GO:0030228	lipoprotein receptor activity	0.0343440629744898
GO:0004185	serine carboxypeptidase activity	0.0343440629744898
GO:0017040	ceramidase activity	0.0364180192480767
GO:0050801	ion homeostasis	0.0404833389821219
GO:0006954	inflammatory response	0.0465522445284474
GO:0030169	low-density lipoprotein binding	0.0475041394165519
GO:0048878	chemical homeostasis	0.0475041394165519

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
myeloid leukocyte	2.54e-60	72
granulocyte monocyte progenitor cell	4.67e-57	67
macrophage dendritic cell progenitor	5.44e-57	61
monopoietic cell	7.90e-56	59
monocyte	7.90e-56	59
monoblast	7.90e-56	59
promonocyte	7.90e-56	59
myeloid lineage restricted progenitor cell	1.23e-54	66
defensive cell	4.53e-54	48
phagocyte	4.53e-54	48
classical monocyte	7.48e-47	42
CD14-positive, CD16-negative classical monocyte	7.48e-47	42
myeloid cell	2.32e-38	108
common myeloid progenitor	2.32e-38	108
leukocyte	1.08e-33	136
hematopoietic lineage restricted progenitor cell	3.16e-29	120
nongranular leukocyte	5.24e-29	115
hematopoietic stem cell	1.03e-25	168
angioblastic mesenchymal cell	1.03e-25	168
hematopoietic oligopotent progenitor cell	1.36e-23	161
hematopoietic multipotent progenitor cell	1.36e-23	161
hematopoietic cell	5.88e-23	177
stuff accumulating cell	1.05e-22	87
intermediate monocyte	2.75e-10	9
CD14-positive, CD16-positive monocyte	2.75e-10	9
macrophage	2.01e-08	6

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	2.84e-63	98
blood island	2.84e-63	98
hemolymphoid system	9.92e-58	108
bone marrow	2.78e-55	76
immune system	5.94e-51	93
bone element	2.64e-49	82
adult organism	2.50e-46	114
skeletal element	1.32e-42	90
skeletal system	5.12e-37	100
lateral plate mesoderm	1.01e-24	203
neural tube	6.12e-15	56
neural rod	6.12e-15	56
future spinal cord	6.12e-15	56
neural keel	6.12e-15	56
musculoskeletal system	1.87e-14	167
regional part of nervous system	4.85e-13	53
regional part of brain	4.85e-13	53
organ	2.23e-12	503
regional part of forebrain	2.62e-11	41
forebrain	2.62e-11	41
anterior neural tube	2.62e-11	41
future forebrain	2.62e-11	41
mesoderm	3.56e-11	315
mesoderm-derived structure	3.56e-11	315
presumptive mesoderm	3.56e-11	315
germ layer	7.24e-11	560
germ layer / neural crest	7.24e-11	560
embryonic tissue	7.24e-11	560
presumptive structure	7.24e-11	560
germ layer / neural crest derived structure	7.24e-11	560
epiblast (generic)	7.24e-11	560
embryonic structure	1.78e-10	564
central nervous system	9.03e-10	81
developing anatomical structure	9.45e-10	581
brain grey matter	1.37e-09	34
gray matter	1.37e-09	34
telencephalon	1.65e-09	34
embryo	1.88e-09	592
neural plate	4.05e-09	82
presumptive neural plate	4.05e-09	82
brain	5.70e-09	68
future brain	5.70e-09	68
regional part of telencephalon	2.23e-08	32
anatomical system	2.28e-08	624
anatomical group	2.77e-08	625
cerebral hemisphere	3.20e-08	32
neurectoderm	3.42e-08	86
tissue	8.39e-08	773
nervous system	1.03e-07	89
neural nucleus	1.33e-07	9
nucleus of brain	1.33e-07	9
multi-cellular organism	1.55e-07	656
blood	3.94e-07	15
haemolymphatic fluid	3.94e-07	15
organism substance	3.94e-07	15
basal ganglion	4.81e-07	9
nuclear complex of neuraxis	4.81e-07	9
aggregate regional part of brain	4.81e-07	9
collection of basal ganglia	4.81e-07	9
cerebral subcortex	4.81e-07	9

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	5	4.51070403561178	0.00441220021019274	0.0209020129616402
BCL11A#53335	4	4.20288223757142	0.0141559221446243	0.0496667569073946
CTCF#10664	12	2.38233616581112	0.00186858308648917	0.0110212316580924
EBF1#1879	12	3.95842970958622	1.36112426091127e-05	0.00032974821778082
MEF2A#4205	6	4.16516242436535	0.00257954572908317	0.0142700978017754
POLR2A#5430	21	1.67024135954517	0.0009506830914421	0.00684511488363472
SPI1#6688	10	3.0386383364899	0.000844402612671174	0.00636694566924877
STAT1#6772	5	3.83455324022207	0.00869107245088687	0.0330236089535827
TBP#6908	15	2.05931704838688	0.00158410807947826	0.00998266238536352
USF2#7392	8	3.84953996594655	0.00071937991693606	0.00574662070864962
ZNF143#7702	7	3.50022725428131	0.00288584518373218	0.015613074240769
ZNF263#10127	8	2.43610122578094	0.0125167901394377	0.0452755531248133

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.