Coexpression cluster:C2383

Full id: C2383_Eosinophils_CD14_Monocytederived_Neutrophils_Alveolar_Mesenchymal_Melanocyte

Phase1 CAGE Peaks

Hg19::chr16:67514983..67515130,-	p1@ATP6V0D1
Hg19::chr19:48018203..48018358,-	p1@NAPA
Hg19::chr19:7587491..7587547,+	p1@MCOLN1
Hg19::chr1:44440575..44440646,+	p1@ATP6V0B

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
0.0001265553105429	0.0114442159390936	2	132	Oxidative phosphorylation (KEGG):00190
2.96233908517502e-07	0.000187516064091579	3	121	Lysosome (KEGG):04142
0.000176767794609482	0.0139867517484752	2	156	Phagosome (KEGG):04145
2.10227775867002e-05	0.00443580607079374	2	54	Vibrio cholerae infection (KEGG):05110
3.34441238781418e-05	0.00529253260371594	2	68	Epithelial cell signaling in Helicobacter pylori infection (KEGG):05120
0.000240529056385976	0.016917210299147	2	182	Tuberculosis (KEGG):05152
6.13871776917587e-05	0.00777161669577665	2	92	Rheumatoid arthritis (KEGG):05323
8.46702301374934e-05	0.00893270927950556	2	108	Signaling by Insulin receptor (Reactome):REACT_498
1.08913416837795e-05	0.00344710964291621	3	401	Transmembrane transport of small molecules (Reactome):REACT_15518

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:0005774	vacuolar membrane	2.12690639495335e-06
GO:0044437	vacuolar part	2.12690639495335e-06
GO:0005773	vacuole	7.05626795813025e-05
GO:0046933	hydrogen ion transporting ATP synthase activity, rotational mechanism	0.000654494485802874
GO:0046961	hydrogen ion transporting ATPase activity, rotational mechanism	0.000654494485802874
GO:0015985	energy coupled proton transport, down electrochemical gradient	0.000654494485802874
GO:0015986	ATP synthesis coupled proton transport	0.000654494485802874
GO:0006754	ATP biosynthetic process	0.000654494485802874
GO:0006753	nucleoside phosphate metabolic process	0.000654494485802874
GO:0046034	ATP metabolic process	0.000679327575874629
GO:0019829	cation-transporting ATPase activity	0.000679327575874629
GO:0016469	proton-transporting two-sector ATPase complex	0.000679327575874629
GO:0006812	cation transport	0.000679327575874629
GO:0008324	cation transmembrane transporter activity	0.000679327575874629
GO:0009145	purine nucleoside triphosphate biosynthetic process	0.000679327575874629
GO:0009206	purine ribonucleoside triphosphate biosynthetic process	0.000679327575874629
GO:0009201	ribonucleoside triphosphate biosynthetic process	0.000679327575874629
GO:0009142	nucleoside triphosphate biosynthetic process	0.000679327575874629
GO:0009205	purine ribonucleoside triphosphate metabolic process	0.000679327575874629
GO:0009144	purine nucleoside triphosphate metabolic process	0.000679327575874629
GO:0009199	ribonucleoside triphosphate metabolic process	0.000679327575874629
GO:0015992	proton transport	0.000679327575874629
GO:0006818	hydrogen transport	0.000679327575874629
GO:0006752	group transfer coenzyme metabolic process	0.000680308140524998
GO:0009141	nucleoside triphosphate metabolic process	0.00071262377934093
GO:0009152	purine ribonucleotide biosynthetic process	0.00071262377934093
GO:0009150	purine ribonucleotide metabolic process	0.000722588983265508
GO:0009260	ribonucleotide biosynthetic process	0.000722588983265508
GO:0006119	oxidative phosphorylation	0.000722588983265508
GO:0006164	purine nucleotide biosynthetic process	0.000722588983265508
GO:0006163	purine nucleotide metabolic process	0.000765303057262317
GO:0009259	ribonucleotide metabolic process	0.000765303057262317
GO:0009108	coenzyme biosynthetic process	0.000976243098870716
GO:0006810	transport	0.000976243098870716
GO:0015078	hydrogen ion transmembrane transporter activity	0.000992598112457579
GO:0051234	establishment of localization	0.000992598112457579
GO:0042625	ATPase activity, coupled to transmembrane movement of ions	0.000992598112457579
GO:0015075	ion transmembrane transporter activity	0.00100129924810985
GO:0015077	monovalent inorganic cation transmembrane transporter activity	0.00102071509263668
GO:0051188	cofactor biosynthetic process	0.00102071509263668
GO:0006811	ion transport	0.00102071509263668
GO:0051179	localization	0.0012022022451786
GO:0009165	nucleotide biosynthetic process	0.00125724219440041
GO:0044444	cytoplasmic part	0.00125724219440041
GO:0031090	organelle membrane	0.00125724219440041
GO:0022891	substrate-specific transmembrane transporter activity	0.00125724219440041
GO:0022890	inorganic cation transmembrane transporter activity	0.00134974205414562
GO:0042626	ATPase activity, coupled to transmembrane movement of substances	0.00134974205414562
GO:0043492	ATPase activity, coupled to movement of substances	0.00134974205414562
GO:0016820	hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances	0.00137805436761323
GO:0006732	coenzyme metabolic process	0.00137805436761323
GO:0022857	transmembrane transporter activity	0.00137805436761323
GO:0015399	primary active transmembrane transporter activity	0.0014539511882513
GO:0015405	P-P-bond-hydrolysis-driven transmembrane transporter activity	0.0014539511882513
GO:0022892	substrate-specific transporter activity	0.0016371179135362
GO:0009117	nucleotide metabolic process	0.00176300585492439
GO:0051186	cofactor metabolic process	0.00176300585492439
GO:0055086	nucleobase, nucleoside and nucleotide metabolic process	0.00198205606435121
GO:0033176	proton-transporting V-type ATPase complex	0.00229343837091778
GO:0016471	vacuolar proton-transporting V-type ATPase complex	0.00229343837091778
GO:0045176	apical protein localization	0.00257799018318488
GO:0008105	asymmetric protein localization	0.00317023212644919
GO:0042623	ATPase activity, coupled	0.00369739411654434
GO:0015672	monovalent inorganic cation transport	0.00369739411654434
GO:0006891	intra-Golgi vesicle-mediated transport	0.00506942459940437
GO:0016887	ATPase activity	0.00506942459940437
GO:0008553	hydrogen-exporting ATPase activity, phosphorylative mechanism	0.00527870060479556
GO:0019905	syntaxin binding	0.00547717104572753
GO:0022804	active transmembrane transporter activity	0.00547717104572753
GO:0005737	cytoplasm	0.00560961641398419
GO:0000149	SNARE binding	0.00581075732840653
GO:0031902	late endosome membrane	0.00791013438453246
GO:0006944	membrane fusion	0.00993720419036831
GO:0006091	generation of precursor metabolites and energy	0.00993720419036831
GO:0043231	intracellular membrane-bound organelle	0.0100104220092021
GO:0043227	membrane-bound organelle	0.0100104220092021
GO:0017111	nucleoside-triphosphatase activity	0.0108493781914646
GO:0016462	pyrophosphatase activity	0.0115653026832529
GO:0016818	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	0.0116131230087479
GO:0016817	hydrolase activity, acting on acid anhydrides	0.0116181970340841
GO:0005765	lysosomal membrane	0.0122026095197474
GO:0005770	late endosome	0.0122026095197474
GO:0044446	intracellular organelle part	0.012978169055937
GO:0044422	organelle part	0.012978169055937
GO:0016020	membrane	0.0133078004997655
GO:0016310	phosphorylation	0.0185497400184379
GO:0043229	intracellular organelle	0.0187225231232309
GO:0044440	endosomal part	0.0187225231232309
GO:0010008	endosome membrane	0.0187225231232309
GO:0043226	organelle	0.0187225231232309
GO:0048193	Golgi vesicle transport	0.0191564945824311
GO:0006793	phosphorus metabolic process	0.0251155195204847
GO:0006796	phosphate metabolic process	0.0251155195204847
GO:0007420	brain development	0.0288998111940217
GO:0015662	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism	0.0298220377738366
GO:0044249	cellular biosynthetic process	0.0314260659506957
GO:0044424	intracellular part	0.0364240838290581
GO:0006816	calcium ion transport	0.0364240838290581
GO:0005768	endosome	0.0380096433782001
GO:0005764	lysosome	0.0389788408700863
GO:0000323	lytic vacuole	0.0389788408700863
GO:0030182	neuron differentiation	0.040111091519398
GO:0007417	central nervous system development	0.0442719283451152
GO:0046872	metal ion binding	0.0442719283451152
GO:0045045	secretory pathway	0.0442719283451152
GO:0048699	generation of neurons	0.0442719283451152
GO:0009058	biosynthetic process	0.0442719283451152
GO:0015674	di-, tri-valent inorganic cation transport	0.0444844505046673
GO:0043167	ion binding	0.0445540920969773
GO:0022008	neurogenesis	0.0462972966958267
GO:0016044	membrane organization and biogenesis	0.0496843878099752

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	1.66e-31	72
macrophage dendritic cell progenitor	2.55e-30	61
defensive cell	1.23e-29	48
phagocyte	1.23e-29	48
monopoietic cell	1.73e-29	59
monocyte	1.73e-29	59
monoblast	1.73e-29	59
promonocyte	1.73e-29	59
myeloid lineage restricted progenitor cell	3.47e-28	66
granulocyte monocyte progenitor cell	5.85e-27	67
classical monocyte	1.09e-25	42
CD14-positive, CD16-negative classical monocyte	1.09e-25	42
stuff accumulating cell	1.96e-24	87
myeloid cell	2.00e-15	108
common myeloid progenitor	2.00e-15	108
somatic cell	8.62e-09	588
somatic stem cell	1.65e-08	433
multi fate stem cell	2.14e-08	427
smooth muscle cell	6.51e-08	43
smooth muscle myoblast	6.51e-08	43
vascular associated smooth muscle cell	1.08e-07	32
stem cell	1.94e-07	441
mesodermal cell	3.14e-07	121

Uber Anatomy

Ontology term	p-value	n
lateral plate mesoderm	7.02e-35	203
bone marrow	1.46e-26	76
mesoderm	2.42e-26	315
mesoderm-derived structure	2.42e-26	315
presumptive mesoderm	2.42e-26	315
hemolymphoid system	3.60e-26	108
hematopoietic system	4.59e-25	98
blood island	4.59e-25	98
immune system	1.41e-24	93
bone element	1.53e-23	82
skeletal element	1.90e-22	90
musculoskeletal system	2.76e-22	167
skeletal system	5.85e-20	100
multi-cellular organism	4.38e-19	656
developing anatomical structure	1.15e-18	581
embryonic structure	1.19e-18	564
germ layer	1.20e-18	560
germ layer / neural crest	1.20e-18	560
embryonic tissue	1.20e-18	560
presumptive structure	1.20e-18	560
germ layer / neural crest derived structure	1.20e-18	560
epiblast (generic)	1.20e-18	560
anatomical system	2.42e-18	624
anatomical group	4.66e-18	625
embryo	5.49e-16	592
circulatory system	8.11e-11	112
cardiovascular system	1.83e-10	109
tissue	1.23e-09	773
artery	2.25e-09	42
arterial blood vessel	2.25e-09	42
arterial system	2.25e-09	42
organ	2.34e-09	503
splanchnic layer of lateral plate mesoderm	2.40e-08	83
vasculature	5.47e-08	78
vascular system	5.47e-08	78
vessel	7.39e-08	68
tube	1.60e-07	192
systemic artery	1.74e-07	33
systemic arterial system	1.74e-07	33
epithelial tube open at both ends	5.74e-07	59
blood vessel	5.74e-07	59
blood vasculature	5.74e-07	59
vascular cord	5.74e-07	59

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
ATF3#467	4	22.4631745260087	3.92475754624726e-06	0.00012733698458295
CCNT2#905	4	6.33620157696263	0.000620310058721564	0.00511807254090863
E2F1#1869	4	4.90738921487932	0.00172402235736179	0.0106440748983511
E2F4#1874	4	12.6680603152844	3.88145892637771e-05	0.000726219435349269
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.0099641495067309
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0160780426463849
EP300#2033	3	5.0804562946674	0.0114429840539824	0.0418860862054488
ETS1#2113	4	9.72876092220234	0.000111595531741814	0.00154451706063918
FOS#2353	4	8.9979553088944	0.000152514771116863	0.0019477244045823
FOSL2#2355	3	12.6976504534213	0.00078756857297571	0.00616588262316418
GABPB1#2553	3	5.30076287713663	0.0101267882423427	0.0378536734875459
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0185862017995528
HMGN3#9324	4	8.17854772335059	0.000223457028444047	0.00248008805458745
IRF1#3659	4	7.6371637535639	0.000293885399618549	0.00307268968372826
MAX#4149	4	6.45255550900712	0.000576761319564549	0.00485190297656077
MXI1#4601	3	7.47117872156947	0.00374131473855096	0.018631469100683
MYC#4609	4	5.2222818716094	0.00134430939527274	0.00887025075391012
NANOG#79923	3	21.9335838607595	0.000155753581638277	0.00196482042670854
NFE2#4778	4	77.204260651629	2.80776035215453e-08	1.9165992380305e-06
NFKB1#4790	4	5.48806342419384	0.00110219956630198	0.00767570984230261
NR3C1#2908	3	11.2297674983798	0.00113167206806385	0.00775427759588773
NRF1#4899	4	12.2102794477109	4.49717228915276e-05	0.000793244682835375
PAX5#5079	4	6.66956553117783	0.000505277416948326	0.00443600102123959
POU2F2#5452	3	6.82959304330689	0.00486047377520374	0.0227552008520936
RXRA#6256	2	10.0373085695666	0.0139170380592011	0.048876237065872
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.00795635553052177
SIX5#147912	3	12.8150365165942	0.000766447113693038	0.006014951165238
SMARCB1#6598	3	13.6895368358681	0.000630578340937934	0.0051815083673656
SMARCC2#6601	2	47.0776872134488	0.000666928296709587	0.00545018187637344
SRF#6722	3	10.3478836966259	0.00143989377840126	0.00923659887736929
STAT1#6772	2	10.3532937485996	0.0131077747617126	0.0464890443284037
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0321887829203273
TBP#6908	4	3.70677068709639	0.00529637781478435	0.0243935615892689
THAP1#55145	4	31.3691446028513	1.03171810326891e-06	4.31697143378613e-05
USF1#7391	4	6.36149927720796	0.000610501139914083	0.00507644335601011
USF2#7392	4	12.9921973850696	3.50833029870167e-05	0.000681179602279426
YY1#7528	4	4.91117074985386	0.0017187183805544	0.0106737960960172
ZNF143#7702	3	10.1256574141709	0.00153486161068818	0.00976423291458021

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.