Coexpression cluster:C1003

Full id: C1003_CD14_Whole_Neutrophils_Macrophage_Eosinophils_blood_CD14CD16

Phase1 CAGE Peaks

Hg19::chr11:74173159..74173208,-	p1@KCNE3
Hg19::chr12:111136503..111136534,-	p@chr12:111136503..111136534 -
Hg19::chr17:73308205..73308208,-	p@chr17:73308205..73308208 -
Hg19::chr19:54327542..54327591,-	p1@NLRP12
Hg19::chr1:36273224..36273255,+	p@chr1:36273224..36273255 +
Hg19::chr2:32489922..32489962,-	p1@NLRC4
Hg19::chr9:132044730..132044797,+	p1@ENST00000455981
Hg19::chr9:134103465..134103477,+	p5@NUP214

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
1.14664594993182e-05	0.0072582688630684	2	40	NOD pathway (Wikipathways):WP1433

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:0050702	interleukin-1 beta secretion	7.57490059083126e-05
GO:0050701	interleukin-1 secretion	7.57490059083126e-05
GO:0050663	cytokine secretion	0.000174390626190338
GO:0006919	caspase activation	0.00067382201140424
GO:0043280	positive regulation of caspase activity	0.00067382201140424
GO:0009306	protein secretion	0.000695158306631893
GO:0043281	regulation of caspase activity	0.000695158306631893
GO:0051345	positive regulation of hydrolase activity	0.000978791776154371
GO:0008632	apoptotic program	0.00119485086613343
GO:0001816	cytokine production	0.0015767979984027
GO:0045184	establishment of protein localization	0.0015767979984027
GO:0008104	protein localization	0.0015767979984027
GO:0033036	macromolecule localization	0.0015767979984027
GO:0008592	regulation of Toll signaling pathway	0.0015767979984027
GO:0045381	regulation of interleukin-18 biosynthetic process	0.0015767979984027
GO:0050711	negative regulation of interleukin-1 secretion	0.0015767979984027
GO:0032621	interleukin-18 production	0.0015767979984027
GO:0042241	interleukin-18 biosynthetic process	0.0015767979984027
GO:0045751	negative regulation of Toll signaling pathway	0.0015767979984027
GO:0006913	nucleocytoplasmic transport	0.0015767979984027
GO:0051169	nuclear transport	0.0015767979984027
GO:0051649	establishment of cellular localization	0.00158324820883599
GO:0051641	cellular localization	0.0016323238568225
GO:0051234	establishment of localization	0.00230800641775064
GO:0031952	regulation of protein amino acid autophosphorylation	0.00230800641775064
GO:0008063	Toll signaling pathway	0.00230800641775064
GO:0031953	negative regulation of protein amino acid autophosphorylation	0.00230800641775064
GO:0006605	protein targeting	0.00230800641775064
GO:0051179	localization	0.00276285587215317
GO:0043085	positive regulation of catalytic activity	0.00296816009337106
GO:0045409	negative regulation of interleukin-6 biosynthetic process	0.00301929784466376
GO:0032940	secretion by cell	0.00365381566704111
GO:0050710	negative regulation of cytokine secretion	0.00365381566704111
GO:0008588	release of cytoplasmic sequestered NF-kappaB	0.00365381566704111
GO:0051336	regulation of hydrolase activity	0.00365381566704111
GO:0050709	negative regulation of protein secretion	0.00492557026173187
GO:0043124	negative regulation of I-kappaB kinase/NF-kappaB cascade	0.00492557026173187
GO:0042346	positive regulation of NF-kappaB import into nucleus	0.00492557026173187
GO:0046903	secretion	0.00511799569011294
GO:0042993	positive regulation of transcription factor import into nucleus	0.00530936569132165
GO:0033239	negative regulation of amine metabolic process	0.00530936569132165
GO:0050706	regulation of interleukin-1 beta secretion	0.00530936569132165
GO:0001933	negative regulation of protein amino acid phosphorylation	0.00530936569132165
GO:0045763	negative regulation of amino acid metabolic process	0.00530936569132165
GO:0050718	positive regulation of interleukin-1 beta secretion	0.00530936569132165
GO:0042307	positive regulation of protein import into nucleus	0.00530936569132165
GO:0016045	detection of bacterium	0.00530936569132165
GO:0050716	positive regulation of interleukin-1 secretion	0.00572898601354152
GO:0050704	regulation of interleukin-1 secretion	0.00572898601354152
GO:0046824	positive regulation of nucleocytoplasmic transport	0.00611564093431491
GO:0045408	regulation of interleukin-6 biosynthetic process	0.00611564093431491
GO:0050729	positive regulation of inflammatory response	0.00635319086322007
GO:0051222	positive regulation of protein transport	0.00635319086322007
GO:0031349	positive regulation of defense response	0.00635319086322007
GO:0042348	NF-kappaB import into nucleus	0.00649837821341494
GO:0042345	regulation of NF-kappaB import into nucleus	0.00649837821341494
GO:0042226	interleukin-6 biosynthetic process	0.00649837821341494
GO:0006886	intracellular protein transport	0.00649837821341494
GO:0050715	positive regulation of cytokine secretion	0.0068714115783419
GO:0008656	caspase activator activity	0.00693560630095651
GO:0006611	protein export from nucleus	0.00693560630095651
GO:0009595	detection of biotic stimulus	0.00693560630095651
GO:0042981	regulation of apoptosis	0.00693560630095651
GO:0043067	regulation of programmed cell death	0.00697019494470136
GO:0006952	defense response	0.0070268182643505
GO:0032635	interleukin-6 production	0.0070268182643505
GO:0050790	regulation of catalytic activity	0.0070268182643505
GO:0050707	regulation of cytokine secretion	0.0070268182643505
GO:0050714	positive regulation of protein secretion	0.0070268182643505
GO:0042036	negative regulation of cytokine biosynthetic process	0.0070268182643505
GO:0016505	apoptotic protease activator activity	0.0070268182643505
GO:0051048	negative regulation of secretion	0.00736197493058715
GO:0009605	response to external stimulus	0.00736462633673236
GO:0016504	protease activator activity	0.00758402081551587
GO:0065009	regulation of a molecular function	0.00804329113828006
GO:0042990	regulation of transcription factor import into nucleus	0.00828692481876517
GO:0042991	transcription factor import into nucleus	0.00828692481876517
GO:0043028	caspase regulator activity	0.00828692481876517
GO:0051047	positive regulation of secretion	0.00828692481876517
GO:0042306	regulation of protein import into nucleus	0.00846680735925782
GO:0033157	regulation of intracellular protein transport	0.00846680735925782
GO:0031347	regulation of defense response	0.00927652250642965
GO:0050727	regulation of inflammatory response	0.00927652250642965
GO:0032386	regulation of intracellular transport	0.00927652250642965
GO:0050708	regulation of protein secretion	0.00953366139556721
GO:0051223	regulation of protein transport	0.0101369460683548
GO:0016043	cellular component organization and biogenesis	0.0101369460683548
GO:0046822	regulation of nucleocytoplasmic transport	0.0102698260789929
GO:0006915	apoptosis	0.0109283285495152
GO:0012501	programmed cell death	0.0109602904579379
GO:0015031	protein transport	0.0109602904579379
GO:0048583	regulation of response to stimulus	0.0115730953542985
GO:0016265	death	0.0115730953542985
GO:0008219	cell death	0.0115730953542985
GO:0046907	intracellular transport	0.0115730953542985
GO:0051050	positive regulation of transport	0.0123306936518284
GO:0048522	positive regulation of cellular process	0.0124358428638279
GO:0017148	negative regulation of translation	0.0130309291760249
GO:0046777	protein amino acid autophosphorylation	0.0136423828183504
GO:0051168	nuclear export	0.0136423828183504
GO:0031327	negative regulation of cellular biosynthetic process	0.0136423828183504
GO:0001932	regulation of protein amino acid phosphorylation	0.0136423828183504
GO:0033238	regulation of amine metabolic process	0.0136423828183504
GO:0006521	regulation of amino acid metabolic process	0.0136423828183504
GO:0016540	protein autoprocessing	0.0136423828183504
GO:0048518	positive regulation of biological process	0.0140432120695036
GO:0009581	detection of external stimulus	0.014548934924582
GO:0009890	negative regulation of biosynthetic process	0.0147018576660075
GO:0006810	transport	0.0148343920872723
GO:0051046	regulation of secretion	0.0166928951268558
GO:0042035	regulation of cytokine biosynthetic process	0.0168221471566807
GO:0042325	regulation of phosphorylation	0.0177802710586506
GO:0048468	cell development	0.0178902917127125
GO:0042089	cytokine biosynthetic process	0.0181906239101521
GO:0042107	cytokine metabolic process	0.0181906239101521
GO:0051174	regulation of phosphorus metabolic process	0.0181906239101521
GO:0065002	intracellular protein transport across a membrane	0.0181906239101521
GO:0019220	regulation of phosphate metabolic process	0.0181906239101521
GO:0051606	detection of stimulus	0.0209031875249972
GO:0051028	mRNA transport	0.0212453421102523
GO:0005643	nuclear pore	0.022093649766506
GO:0051236	establishment of RNA localization	0.022807525363954
GO:0050657	nucleic acid transport	0.022807525363954
GO:0050658	RNA transport	0.022807525363954
GO:0006403	RNA localization	0.0228726818116536
GO:0042742	defense response to bacterium	0.0234279764019673
GO:0006606	protein import into nucleus	0.0234871350077813
GO:0046930	pore complex	0.0235453478534105
GO:0051170	nuclear import	0.023602636934532
GO:0016485	protein processing	0.0236590235700322
GO:0015931	nucleobase, nucleoside, nucleotide and nucleic acid transport	0.0242879433908741
GO:0051248	negative regulation of protein metabolic process	0.0242879433908741
GO:0009968	negative regulation of signal transduction	0.0242879433908741
GO:0009617	response to bacterium	0.0245681094106052
GO:0043122	regulation of I-kappaB kinase/NF-kappaB cascade	0.0248440436826517
GO:0051049	regulation of transport	0.0251158395639025
GO:0044453	nuclear membrane part	0.0251580599681375
GO:0017038	protein import	0.0274374923887226
GO:0008076	voltage-gated potassium channel complex	0.0274621664983352
GO:0048869	cellular developmental process	0.0297686566038937
GO:0030154	cell differentiation	0.0297686566038937
GO:0007249	I-kappaB kinase/NF-kappaB cascade	0.0303573541723488
GO:0030955	potassium ion binding	0.0307915959335931
GO:0031965	nuclear membrane	0.0325028642406793
GO:0042803	protein homodimerization activity	0.0336730421851064
GO:0007242	intracellular signaling cascade	0.0336730421851064
GO:0005249	voltage-gated potassium channel activity	0.0347700333977296
GO:0006417	regulation of translation	0.0384795459989576
GO:0005635	nuclear envelope	0.0402807316199666
GO:0031326	regulation of cellular biosynthetic process	0.0410343662885533
GO:0051707	response to other organism	0.0421834229628873
GO:0005267	potassium channel activity	0.0433164828787574
GO:0009889	regulation of biosynthetic process	0.0438337561294068
GO:0031420	alkali metal ion binding	0.0445427116193444

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	1.05e-58	72
monopoietic cell	7.10e-51	59
monocyte	7.10e-51	59
monoblast	7.10e-51	59
promonocyte	7.10e-51	59
macrophage dendritic cell progenitor	8.05e-50	61
granulocyte monocyte progenitor cell	1.81e-48	67
myeloid lineage restricted progenitor cell	3.20e-48	66
defensive cell	1.12e-45	48
phagocyte	1.12e-45	48
myeloid cell	2.87e-44	108
common myeloid progenitor	2.87e-44	108
classical monocyte	8.49e-40	42
CD14-positive, CD16-negative classical monocyte	8.49e-40	42
leukocyte	1.81e-33	136
hematopoietic stem cell	1.94e-31	168
angioblastic mesenchymal cell	1.94e-31	168
hematopoietic oligopotent progenitor cell	1.40e-29	161
hematopoietic multipotent progenitor cell	1.40e-29	161
nongranular leukocyte	1.51e-28	115
hematopoietic cell	4.70e-28	177
hematopoietic lineage restricted progenitor cell	9.03e-27	120
stuff accumulating cell	1.65e-17	87
intermediate monocyte	1.91e-09	9
CD14-positive, CD16-positive monocyte	1.91e-09	9
granulocyte	4.44e-09	8
macrophage	3.78e-07	6

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	2.79e-51	98
blood island	2.79e-51	98
hemolymphoid system	2.26e-48	108
bone marrow	5.03e-42	76
adult organism	1.10e-41	114
immune system	4.09e-39	93
bone element	4.92e-37	82
skeletal element	1.82e-31	90
skeletal system	6.05e-27	100
lateral plate mesoderm	2.82e-18	203
neural tube	1.66e-11	56
neural rod	1.66e-11	56
future spinal cord	1.66e-11	56
neural keel	1.66e-11	56
regional part of nervous system	5.02e-10	53
regional part of brain	5.02e-10	53
musculoskeletal system	6.30e-10	167
blood	1.08e-09	15
haemolymphatic fluid	1.08e-09	15
organism substance	1.08e-09	15
mesoderm	3.95e-09	315
mesoderm-derived structure	3.95e-09	315
presumptive mesoderm	3.95e-09	315
regional part of forebrain	3.94e-08	41
forebrain	3.94e-08	41
anterior neural tube	3.94e-08	41
future forebrain	3.94e-08	41
organ	1.13e-07	503
tissue	2.28e-07	773
germ layer	4.93e-07	560
germ layer / neural crest	4.93e-07	560
embryonic tissue	4.93e-07	560
presumptive structure	4.93e-07	560
germ layer / neural crest derived structure	4.93e-07	560
epiblast (generic)	4.93e-07	560
central nervous system	4.96e-07	81
embryonic structure	5.78e-07	564
neural plate	5.90e-07	82
presumptive neural plate	5.90e-07	82

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	0.0264723
MA0004.1	0.455723
MA0006.1	0.300178
MA0007.1	0.437331
MA0009.1	0.918715
MA0014.1	0.134069
MA0017.1	0.337901
MA0019.1	1.46622
MA0024.1	0.813542
MA0025.1	1.05265
MA0027.1	2.5321
MA0028.1	0.315574
MA0029.1	0.832916
MA0030.1	0.821423
MA0031.1	0.756713
MA0038.1	0.557409
MA0040.1	0.838784
MA0041.1	0.474018
MA0042.1	0.442535
MA0043.1	0.919032
MA0046.1	0.90778
MA0048.1	0.653157
MA0050.1	0.443405
MA0051.1	0.553205
MA0052.1	0.842664
MA0055.1	0.283474
MA0056.1	0
MA0057.1	0.632427
MA0058.1	0.362328
MA0059.1	0.361075
MA0060.1	0.190336
MA0061.1	0.497495
MA0063.1	0
MA0066.1	0.557833
MA0067.1	1.23721
MA0068.1	2.60013
MA0069.1	0.903908
MA0070.1	0.892666
MA0071.1	0.518907
MA0072.1	0.888148
MA0073.1	0.326687
MA0074.1	0.552456
MA0076.1	0.377799
MA0077.1	0.880402
MA0078.1	0.652193
MA0081.1	0.948525
MA0083.1	0.926258
MA0084.1	1.42483
MA0087.1	0.885691
MA0088.1	0.770971
MA0089.1	0
MA0090.1	0.391903
MA0091.1	0.458301
MA0092.1	0.421159
MA0093.1	0.303084
MA0095.1	0
MA0098.1	0
MA0100.1	0.571227
MA0101.1	0.30624
MA0103.1	0.291333
MA0105.1	0.279181
MA0106.1	0.59853
MA0107.1	0.236528
MA0108.2	0.753643
MA0109.1	0
MA0111.1	0.405141
MA0113.1	0.614917
MA0114.1	0.231781
MA0115.1	1.1606
MA0116.1	0.673701
MA0117.1	0.956472
MA0119.1	0.345493
MA0122.1	0.982472
MA0124.1	1.11898
MA0125.1	1.0347
MA0130.1	0
MA0131.1	0.670358
MA0132.1	0
MA0133.1	0
MA0135.1	0.949204
MA0136.1	1.38624
MA0139.1	0.470675
MA0140.1	0.516266
MA0141.1	0.359385
MA0142.1	0.724856
MA0143.1	0.615094
MA0144.1	0.623945
MA0145.1	0.480646
MA0146.1	0.0399277
MA0147.1	0.243042
MA0148.1	1.20731
MA0149.1	0.506665
MA0062.2	0.161302
MA0035.2	0.515566
MA0039.2	0.164269
MA0138.2	0.653421
MA0002.2	0.179788
MA0137.2	0.321796
MA0104.2	0.189646
MA0047.2	0.586412
MA0112.2	0.458158
MA0065.2	0.844872
MA0150.1	1.00335
MA0151.1	0
MA0152.1	0.52279
MA0153.1	1.01778
MA0154.1	0.0799828
MA0155.1	0.0535085
MA0156.1	0.323987
MA0157.1	0.697424
MA0158.1	0
MA0159.1	0.243637
MA0160.1	0.495355
MA0161.1	0
MA0162.1	0.0752715
MA0163.1	0.493198
MA0164.1	0.627336
MA0080.2	0.818924
MA0018.2	0.599912
MA0099.2	0.523145
MA0079.2	0.13841
MA0102.2	1.46209
MA0258.1	0.209744
MA0259.1	0.25092
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	4	4.10216175426136	0.0102780066240076	0.0381879374508069

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.