Coexpression cluster:C520

Full id: C520_Natural_CD14_CD8_Basophils_CD4_Peripheral_CD34

Phase1 CAGE Peaks

Hg19::chr10:11222326..11222339,-	p@chr10:11222326..11222339 -
Hg19::chr10:11222427..11222442,-	p@chr10:11222427..11222442 -
Hg19::chr10:17071741..17071777,+	p@chr10:17071741..17071777 +
Hg19::chr13:32889208..32889236,+	p3@BRCA2
Hg19::chr13:33002636..33002647,+	p@chr13:33002636..33002647 +
Hg19::chr15:65282401..65282422,+	p@chr15:65282401..65282422 +
Hg19::chr17:33569466..33569477,+	p@chr17:33569466..33569477 +
Hg19::chr17:65437348..65437360,-	p@chr17:65437348..65437360 -
Hg19::chr19:18597484..18597505,+	p@chr19:18597484..18597505 +
Hg19::chr1:160679034..160679048,+	p@chr1:160679034..160679048 +
Hg19::chr1:206751790..206751814,+	p@chr1:206751790..206751814 +
Hg19::chr1:221952092..221952101,+	p@chr1:221952092..221952101 +
Hg19::chr22:36553418..36553428,+	p@chr22:36553418..36553428 +
Hg19::chr4:40201863..40201881,-	p@chr4:40201863..40201881 -
Hg19::chr5:43018291..43018327,+	p2@ENST00000509036
Hg19::chr6:37016760..37016773,+	p@chr6:37016760..37016773 +
Hg19::chr6:37139954..37139971,-	p@chr6:37139954..37139971 -

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:0033593	BRCA2-MAGE-D1 complex	0.00150123631225715
GO:0033595	response to genistein	0.00150123631225715
GO:0033600	negative regulation of mammary gland epithelial cell proliferation	0.00150123631225715
GO:0033598	mammary gland epithelial cell proliferation	0.00150123631225715
GO:0042772	DNA damage response, signal transduction resulting in transcription	0.00150123631225715
GO:0033599	regulation of mammary gland epithelial cell proliferation	0.00150123631225715
GO:0006978	DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator	0.00150123631225715
GO:0048478	replication fork protection	0.00150123631225715
GO:0007141	male meiosis I	0.00150123631225715
GO:0001556	oocyte maturation	0.00150123631225715
GO:0010225	response to UV-C	0.00150123631225715
GO:0010332	response to gamma radiation	0.00150123631225715
GO:0033205	cytokinesis during cell cycle	0.0017156986425796
GO:0001833	inner cell mass cell proliferation	0.0017156986425796
GO:0031573	intra-S DNA damage checkpoint	0.00187654539032144
GO:0045931	positive regulation of progression through mitotic cell cycle	0.00187654539032144
GO:0001832	blastocyst growth	0.00191066439741819
GO:0048599	oocyte development	0.00191066439741819
GO:0009994	oocyte differentiation	0.00191066439741819
GO:0010165	response to X-ray	0.00191066439741819
GO:0007140	male meiosis	0.00191066439741819
GO:0051298	centrosome duplication	0.00191066439741819
GO:0043015	gamma-tubulin binding	0.00200164841634287
GO:0042771	DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis	0.00200164841634287
GO:0007090	regulation of S phase of mitotic cell cycle	0.0024726245143059
GO:0014070	response to organic cyclic substance	0.0024726245143059
GO:0000724	double-strand break repair via homologous recombination	0.0024726245143059
GO:0050680	negative regulation of epithelial cell proliferation	0.0024726245143059
GO:0000725	recombinational repair	0.0024726245143059
GO:0007569	cell aging	0.0024726245143059
GO:0010212	response to ionizing radiation	0.0024726245143059
GO:0030879	mammary gland development	0.0024726245143059
GO:0007098	centrosome cycle	0.0024726245143059
GO:0001824	blastocyst development	0.0024726245143059
GO:0033261	regulation of progression through S phase	0.00257354796386941
GO:0030330	DNA damage response, signal transduction by p53 class mediator	0.00259304453935326
GO:0008156	negative regulation of DNA replication	0.00259304453935326
GO:0048477	oogenesis	0.00259304453935326
GO:0000084	S phase of mitotic cell cycle	0.00259304453935326
GO:0051297	centrosome organization and biogenesis	0.00259304453935326
GO:0031023	microtubule organizing center organization and biogenesis	0.00259304453935326
GO:0051053	negative regulation of DNA metabolic process	0.00259304453935326
GO:0008630	DNA damage response, signal transduction resulting in induction of apoptosis	0.00259304453935326
GO:0007281	germ cell development	0.00259304453935326
GO:0051320	S phase	0.00280230778288002
GO:0043627	response to estrogen stimulus	0.00287193033649194
GO:0035264	multicellular organism growth	0.0030024726245143
GO:0045787	positive regulation of progression through cell cycle	0.0030024726245143
GO:0000077	DNA damage checkpoint	0.00306374757603501
GO:0007568	aging	0.00312257152949488
GO:0008585	female gonad development	0.00316624385857872
GO:0031570	DNA integrity checkpoint	0.00316624385857872
GO:0006275	regulation of DNA replication	0.00316624385857872
GO:0046545	development of primary female sexual characteristics	0.00316624385857872
GO:0046660	female sex differentiation	0.00316624385857872
GO:0050678	regulation of epithelial cell proliferation	0.00321693495483676
GO:0007346	regulation of progression through mitotic cell cycle	0.00335869819013464
GO:0009411	response to UV	0.00335869819013464
GO:0050673	epithelial cell proliferation	0.00335869819013464
GO:0000910	cytokinesis	0.00336640870021301
GO:0007292	female gamete generation	0.00336640870021301
GO:0006302	double-strand break repair	0.00336640870021301
GO:0008629	induction of apoptosis by intracellular signals	0.00336640870021301
GO:0048589	developmental growth	0.00336640870021301
GO:0030141	secretory granule	0.00336640870021301
GO:0048545	response to steroid hormone stimulus	0.00336640870021301
GO:0007584	response to nutrient	0.00374221225664102
GO:0006289	nucleotide-excision repair	0.00374221225664102
GO:0042770	DNA damage response, signal transduction	0.00374221225664102
GO:0048469	cell maturation	0.00386032194580411
GO:0048732	gland development	0.00389052790782135
GO:0051052	regulation of DNA metabolic process	0.00408669885003336
GO:0001701	in utero embryonic development	0.0041129761979648
GO:0008406	gonad development	0.00416342870599317
GO:0048608	reproductive structure development	0.00416342870599317
GO:0021700	developmental maturation	0.00418765918682259
GO:0000075	cell cycle checkpoint	0.00436723290838445
GO:0031667	response to nutrient levels	0.00456071791065464
GO:0045137	development of primary sexual characteristics	0.00456071791065464
GO:0003697	single-stranded DNA binding	0.00457877075238432
GO:0010033	response to organic substance	0.00459637784493548
GO:0009991	response to extracellular stimulus	0.00483324861507181
GO:0015631	tubulin binding	0.00484736544198695
GO:0051327	M phase of meiotic cell cycle	0.00487460261391734
GO:0007126	meiosis	0.00487460261391734
GO:0051321	meiotic cell cycle	0.00495757107768641
GO:0009725	response to hormone stimulus	0.005245699298002
GO:0009416	response to light stimulus	0.00546517488956537
GO:0007548	sex differentiation	0.00546517488956537
GO:0051329	interphase of mitotic cell cycle	0.00567133717963813
GO:0003006	reproductive developmental process	0.00574099161170867
GO:0051325	interphase	0.00587440296100625
GO:0009792	embryonic development ending in birth or egg hatching	0.00606882764529487
GO:0043009	chordate embryonic development	0.00606882764529487
GO:0009314	response to radiation	0.00638420494896726
GO:0005813	centrosome	0.00806914517838219
GO:0007420	brain development	0.00860502463520594
GO:0005815	microtubule organizing center	0.00900741787354291
GO:0043566	structure-specific DNA binding	0.00964430600601564
GO:0006261	DNA-dependent DNA replication	0.00981005907019525
GO:0009628	response to abiotic stimulus	0.00981005907019525
GO:0006310	DNA recombination	0.0115977864123396
GO:0007283	spermatogenesis	0.0120665409249349
GO:0006917	induction of apoptosis	0.0120665409249349
GO:0048232	male gamete generation	0.0120665409249349
GO:0012502	induction of programmed cell death	0.0120665409249349
GO:0008285	negative regulation of cell proliferation	0.0126272213180508
GO:0007417	central nervous system development	0.0129464415919424
GO:0009790	embryonic development	0.0129464415919424
GO:0051301	cell division	0.0133746507819274
GO:0043065	positive regulation of apoptosis	0.013832820305798
GO:0043068	positive regulation of programmed cell death	0.013832820305798
GO:0007276	gamete generation	0.0140292526171996
GO:0022414	reproductive process	0.015978376053937
GO:0000279	M phase	0.015978376053937
GO:0016563	transcription activator activity	0.0159959317409469
GO:0019953	sexual reproduction	0.0161671602858463
GO:0045934	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0162337079189841
GO:0000278	mitotic cell cycle	0.0164505222788515
GO:0016023	cytoplasmic membrane-bound vesicle	0.0173313460439444
GO:0031988	membrane-bound vesicle	0.0173313460439444
GO:0000074	regulation of progression through cell cycle	0.0173313460439444
GO:0006260	DNA replication	0.0173313460439444
GO:0051726	regulation of cell cycle	0.0173852850354941
GO:0022403	cell cycle phase	0.0177265983751325
GO:0031324	negative regulation of cellular metabolic process	0.0181578106339675
GO:0006281	DNA repair	0.0185349491151119
GO:0031410	cytoplasmic vesicle	0.0199382947721653
GO:0031982	vesicle	0.0201095840897702
GO:0009892	negative regulation of metabolic process	0.0201396625275113
GO:0006974	response to DNA damage stimulus	0.0205359959661436
GO:0042127	regulation of cell proliferation	0.0213357524378365
GO:0015630	microtubule cytoskeleton	0.0233425315319383
GO:0009719	response to endogenous stimulus	0.0237060898263891
GO:0042981	regulation of apoptosis	0.0253542132736764
GO:0043067	regulation of programmed cell death	0.0254327092900035
GO:0042221	response to chemical stimulus	0.0258168813991084
GO:0008092	cytoskeletal protein binding	0.0262389998924946
GO:0022402	cell cycle process	0.0270006530981502
GO:0009605	response to external stimulus	0.0271509310188222
GO:0007399	nervous system development	0.0304931971510956
GO:0008283	cell proliferation	0.0315048183839881
GO:0007049	cell cycle	0.0352318116359091
GO:0006915	apoptosis	0.0356543624161074
GO:0012501	programmed cell death	0.0356983641700873
GO:0008219	cell death	0.0370917706538638
GO:0016265	death	0.0370917706538638
GO:0044430	cytoskeletal part	0.0372468901257315
GO:0048522	positive regulation of cellular process	0.0384477702521698
GO:0048518	positive regulation of biological process	0.0425150123631226
GO:0048523	negative regulation of cellular process	0.0450765955864582
GO:0048513	organ development	0.0450765955864582
GO:0048519	negative regulation of biological process	0.0463911456493583
GO:0006950	response to stress	0.0476496304825517
GO:0048468	cell development	0.0480780552310047
GO:0006259	DNA metabolic process	0.0480780552310047

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
hematopoietic stem cell	5.21e-54	172
angioblastic mesenchymal cell	5.21e-54	172
hematopoietic cell	1.67e-52	182
leukocyte	1.05e-51	140
hematopoietic oligopotent progenitor cell	8.18e-50	165
hematopoietic multipotent progenitor cell	8.18e-50	165
hematopoietic lineage restricted progenitor cell	1.90e-43	124
nongranular leukocyte	1.51e-40	119
myeloid cell	1.14e-30	112
common myeloid progenitor	1.14e-30	112
myeloid leukocyte	2.36e-28	76
CD14-positive, CD16-negative classical monocyte	3.78e-26	42
granulocyte monocyte progenitor cell	3.27e-25	71
classical monocyte	6.33e-25	45
myeloid lineage restricted progenitor cell	8.54e-24	70
macrophage dendritic cell progenitor	2.88e-22	65
monopoietic cell	2.73e-21	63
monocyte	2.73e-21	63
monoblast	2.73e-21	63
promonocyte	2.73e-21	63
mesenchymal cell	9.98e-20	358
connective tissue cell	8.05e-19	365
lymphoid lineage restricted progenitor cell	1.44e-17	52
lymphocyte	9.02e-17	53
common lymphoid progenitor	9.02e-17	53
motile cell	2.26e-15	390
multi fate stem cell	9.19e-15	430
stem cell	1.20e-13	444
somatic stem cell	1.89e-13	436
T cell	6.85e-11	25
pro-T cell	6.85e-11	25
mature alpha-beta T cell	1.69e-10	18
alpha-beta T cell	1.69e-10	18
immature T cell	1.69e-10	18
mature T cell	1.69e-10	18
immature alpha-beta T cell	1.69e-10	18
native cell	7.38e-07	722
CD8-positive, alpha-beta T cell	9.55e-07	11

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	2.10e-31	112
hematopoietic system	8.69e-30	102
blood island	8.69e-30	102
bone element	3.84e-23	86
bone marrow	4.39e-23	80
immune system	1.95e-19	115
connective tissue	7.95e-18	375
skeletal element	3.08e-17	101
skeletal system	3.08e-17	101
lateral plate mesoderm	5.56e-12	216

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
EBF1#1879	6	3.14345888702435	0.0082556798385042	0.0325327301306848
FOS#2353	6	3.17574893255097	0.00785510561119647	0.0322577608889489
FOSL2#2355	6	5.97536491925707	0.000297459514596548	0.00310446429948525
MEF2A#4205	4	4.41017197873978	0.0110070197206115	0.040493223875478
NFKB1#4790	8	2.58261808197357	0.00612962073262582	0.0271029407152713
POLR2A#5430	15	1.89481162637477	0.00045412137082633	0.00422032228579205
SPI1#6688	6	2.89564359124332	0.0122532128785811	0.0444190662903897
STAT1#6772	5	6.09017279329388	0.000995541757041492	0.00714348234721102
WRNIP1#56897	2	12.919995805809	0.0102923120972492	0.0382329284412098
YY1#7528	8	2.31113917640181	0.0121921825045688	0.0442054972607069

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.