Coexpression cluster:C297

Full id: C297_Eosinophils_CD4_Basophils_Natural_Neutrophils_CD8_Peripheral

Phase1 CAGE Peaks

Hg19::chr10:35416142..35416169,+	p3@CREM
Hg19::chr10:35416172..35416184,+	p13@CREM
Hg19::chr11:3862855..3862867,+	p@chr11:3862855..3862867 +
Hg19::chr12:106697097..106697117,-	p@chr12:106697097..106697117 -
Hg19::chr14:52314051..52314062,-	p@chr14:52314051..52314062 -
Hg19::chr17:38497640..38497647,+	p27@RARA
Hg19::chr17:62097904..62097915,-	p4@ICAM2
Hg19::chr17:76837188..76837205,+	p@chr17:76837188..76837205 +
Hg19::chr19:41769066..41769091,+	p@chr19:41769066..41769091 +
Hg19::chr19:59085102..59085126,+	p@chr19:59085102..59085126 +
Hg19::chr1:185536411..185536432,+	p@chr1:185536411..185536432 +
Hg19::chr1:198650975..198650986,-	p@chr1:198650975..198650986 -
Hg19::chr1:198651031..198651051,-	p@chr1:198651031..198651051 -
Hg19::chr1:198651180..198651193,+	p@chr1:198651180..198651193 +
Hg19::chr1:198651195..198651213,+	p@chr1:198651195..198651213 +
Hg19::chr1:45273151..45273188,+	p@chr1:45273151..45273188 +
Hg19::chr20:34356239..34356262,+	p@chr20:34356239..34356262 +
Hg19::chr20:42839727..42839752,+	p1@LOC100505783
Hg19::chr20:43150543..43150551,-	p@chr20:43150543..43150551 -
Hg19::chr20:43150846..43150896,+	p@chr20:43150846..43150896 +
Hg19::chr20:43150918..43150934,+	p@chr20:43150918..43150934 +
Hg19::chr20:5590658..5590681,+	p@chr20:5590658..5590681 +
Hg19::chr22:39097139..39097148,+	p@chr22:39097139..39097148 +
Hg19::chr22:47158371..47158384,-	p@chr22:47158371..47158384 -
Hg19::chr2:170441202..170441230,-	p@chr2:170441202..170441230 -
Hg19::chr2:197034975..197035000,-	p@chr2:197034975..197035000 -
Hg19::chr2:197035024..197035040,-	p@chr2:197035024..197035040 -
Hg19::chr2:55845186..55845202,+	p@chr2:55845186..55845202 +
Hg19::chr2:97204412..97204438,-	p@chr2:97204412..97204438 -
Hg19::chr4:152020461..152020473,-	p@chr4:152020461..152020473 -
Hg19::chr6:108145154..108145165,-	p@chr6:108145154..108145165 -
Hg19::chr7:36816762..36816783,-	p@chr7:36816762..36816783 -
Hg19::chr7:66146955..66146980,-	p@chr7:66146955..66146980 -
Hg19::chr7:66309834..66309894,-	p1@LOC729156
Hg19::chr7:75796016..75796041,+	p@chr7:75796016..75796041 +
Hg19::chr8:118532766..118532792,-	p@chr8:118532766..118532792 -
Hg19::chr8:64080945..64080978,-	p@chr8:64080945..64080978 -
Hg19::chr9:100684655..100684671,+	p@chr9:100684655..100684671 +
Hg19::chr9:132650707..132650725,-	p8@FNBP1
Hg19::chr9:132650755..132650788,-	p4@FNBP1
Hg19::chr9:132650792..132650809,-	p12@FNBP1
Hg19::chr9:33159824..33159848,+	p@chr9:33159824..33159848 +

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
6.41827216562196e-05	0.040627662808387	2	73	Notch up reg. targets (Netpath):NetPath_3

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:0003713	transcription coactivator activity	0.0112437650335631
GO:0008140	cAMP response element binding protein binding	0.0112437650335631
GO:0003712	transcription cofactor activity	0.0112437650335631
GO:0016563	transcription activator activity	0.0112437650335631
GO:0008134	transcription factor binding	0.0175123136485932
GO:0003708	retinoic acid receptor activity	0.0378801066558398

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
leukocyte	2.77e-92	136
hematopoietic stem cell	5.88e-76	168
angioblastic mesenchymal cell	5.88e-76	168
nongranular leukocyte	7.76e-72	115
hematopoietic lineage restricted progenitor cell	1.36e-71	120
hematopoietic cell	1.32e-70	177
hematopoietic oligopotent progenitor cell	1.85e-67	161
hematopoietic multipotent progenitor cell	1.85e-67	161
classical monocyte	5.30e-51	42
CD14-positive, CD16-negative classical monocyte	5.30e-51	42
myeloid leukocyte	7.92e-47	72
defensive cell	6.82e-43	48
phagocyte	6.82e-43	48
granulocyte monocyte progenitor cell	6.76e-37	67
macrophage dendritic cell progenitor	1.69e-35	61
myeloid lineage restricted progenitor cell	5.02e-34	66
monopoietic cell	2.36e-33	59
monocyte	2.36e-33	59
monoblast	2.36e-33	59
promonocyte	2.36e-33	59
myeloid cell	3.20e-33	108
common myeloid progenitor	3.20e-33	108
lymphoid lineage restricted progenitor cell	1.24e-32	52
lymphocyte	8.83e-32	53
common lymphoid progenitor	8.83e-32	53
nucleate cell	3.58e-30	55
mature alpha-beta T cell	3.14e-23	18
alpha-beta T cell	3.14e-23	18
immature T cell	3.14e-23	18
mature T cell	3.14e-23	18
immature alpha-beta T cell	3.14e-23	18
mesenchymal cell	6.09e-21	354
connective tissue cell	5.34e-20	361
T cell	8.52e-19	25
pro-T cell	8.52e-19	25
stuff accumulating cell	7.50e-18	87
motile cell	1.05e-16	386
CD8-positive, alpha-beta T cell	2.32e-15	11
intermediate monocyte	2.95e-14	9
CD14-positive, CD16-positive monocyte	2.95e-14	9
granulocyte	3.23e-14	8
multi fate stem cell	9.53e-13	427
stem cell	1.07e-12	441
somatic stem cell	3.29e-12	433
CD4-positive, alpha-beta T cell	2.83e-11	6
lymphocyte of B lineage	2.91e-11	24
pro-B cell	2.91e-11	24
B cell	6.37e-11	14
blood cell	8.86e-10	11

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	1.01e-38	98
blood island	1.01e-38	98
hemolymphoid system	1.03e-34	108
bone marrow	1.65e-32	76
immune system	9.55e-32	93
bone element	4.67e-29	82
skeletal element	3.46e-25	90
skeletal system	3.01e-21	100
connective tissue	1.02e-18	371
lateral plate mesoderm	1.37e-10	203
musculoskeletal system	1.21e-07	167

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	8	4.27869990971595	0.000466323120705573	0.00429170958788943
BATF#10538	10	5.79947661721515	5.93965793861152e-06	0.00017815391598238
BCL11A#53335	11	7.43009538427804	1.60966870389735e-07	8.91368980733483e-06
BCL3#602	5	4.11275033377837	0.00708303449987804	0.0295389945347108
BCLAF1#9774	14	7.21754920337395	3.07699218625634e-09	2.57292223331005e-07
BRCA1#672	17	8.16980764130486	4.96860992546389e-12	6.49457637053221e-10
BRF2#55290	4	102.340531561462	7.88423726816163e-08	4.71874989140133e-06
CCNT2#905	17	2.56465301924678	0.000108545912570439	0.00151071782555226
CEBPB#1051	20	3.7957845837261	2.93067916697899e-08	1.99269011406327e-06
CHD2#1106	13	3.20172135341712	0.000109665437997956	0.0015250797175857
CTCF#10664	17	2.16962757957799	0.00084429401635489	0.00636658648188364
CTCFL#140690	10	4.70154151404151	3.63874760731806e-05	0.000704145194294406
E2F4#1874	9	2.71458435327524	0.00482466198888748	0.0226382816720918
E2F6#1876	19	2.26966568814882	0.000182456816216191	0.00221011452433342
EBF1#1879	17	3.60499848551603	1.11799004160593e-06	4.60417042410418e-05
EGR1#1958	25	2.96915422310127	2.39834497378206e-08	1.68673906206616e-06
ELF1#1997	27	2.73734868780485	2.16864782773001e-08	1.53657673324488e-06
ELK4#2005	12	4.63876618813372	5.72957160997209e-06	0.000172397213878961
EP300#2033	18	2.90311788266709	1.07598646932828e-05	0.000279053764266642
ETS1#2113	15	3.47455747221512	9.80106808828958e-06	0.000257189384440421
FOS#2353	13	2.78508140513398	0.000440522037928036	0.00410416423899787
FOSL2#2355	13	5.24030018712624	5.30749507015305e-07	2.47459588228444e-05
FOXA1#3169	13	3.42996325576216	5.39654083920658e-05	0.000914950208938143
GABPB1#2553	21	3.53384191809109	3.76526773060242e-08	2.4951827190126e-06
GATA1#2623	9	2.90578031652867	0.00306982966126973	0.0161826135671992
GTF2B#2959	8	6.08453903510938	4.18112365998534e-05	0.000757585659134645
GTF2F1#2962	14	4.24655362558588	2.13268969595545e-06	7.75813232866217e-05
HEY1#23462	28	2.69340736207047	1.22115425605082e-08	9.09024442962877e-07
HMGN3#9324	16	3.11563722794308	1.76253764855585e-05	0.000402443527497866
IRF1#3659	15	2.72755848341568	0.000168604496076662	0.00206120624672252
IRF4#3662	13	6.7830634506589	2.69676201628614e-08	1.85538292634327e-06
JUND#3727	18	2.99771311794473	6.81826711745991e-06	0.000198188978424825
MAX#4149	20	3.07264548047958	9.91561689780469e-07	4.20282919314052e-05
MEF2A#4205	12	5.35520883132687	1.29637386153801e-06	5.15190219654369e-05
MEF2C#4208	9	8.8524331055623	6.12772843712137e-07	2.81183580951019e-05
MXI1#4601	19	4.50642526062921	4.80064081371731e-09	3.87161487215306e-07
MYC#4609	25	3.10850111405322	9.1160011331437e-09	6.96463820295826e-07
NFKB1#4790	28	3.65870894946256	6.95021977783518e-12	8.85212199240645e-10
NFYB#4801	8	3.19234157210218	0.00304182160910167	0.0160471186054943
NRF1#4899	9	2.61648845308091	0.00613129345830464	0.0271091891745429
PAX5#5079	26	4.1287786621577	5.12966171779913e-12	6.68000922874343e-10
PBX3#5090	9	4.69596700430231	9.65983251816607e-05	0.00137503509385954
POLR2A#5430	40	2.04519350148388	1.34958418921476e-11	1.66213706529953e-09
POU2F2#5452	21	4.55306202887126	3.75602121697042e-10	3.73595333218261e-08
RAD21#5885	12	2.95858111298752	0.000453596917153148	0.0042173247067175
REST#5978	11	2.52738847327162	0.00298698446343545	0.0158797490647358
RFX5#5993	23	6.59766545298779	1.26053327826328e-14	2.1688440699924e-12
RXRA#6256	9	4.30170367267141	0.000187267503512739	0.0022647094487456
SIN3A#25942	30	3.86348909058224	1.04916321365618e-13	1.64032270765026e-11
SIX5#147912	7	2.8477858925765	0.0103808524444159	0.0385440076949073
SMC3#9126	11	3.94033955462527	6.90500969681743e-05	0.00110099588965789
SP1#6667	28	3.7989209187606	2.70412291122094e-12	3.63469617406698e-10
SP2#6668	7	4.3589217489741	0.000989717214774768	0.00710412894803175
SPI1#6688	22	4.29750279017857	3.34981793693828e-10	3.3639580338067e-08
SRF#6722	20	6.57008488674658	1.69092484396929e-12	2.32366447078038e-10
STAT1#6772	7	3.45109791619987	0.00371632043915319	0.0187411294227291
STAT3#6774	13	3.25602488007155	9.23444819976633e-05	0.00134378784385592
TAF1#6872	34	2.70627556465095	1.14184188233196e-11	1.42306472970009e-09
TAF7#6879	11	2.99437532033722	0.000754794306590111	0.00593554420495178
TBP#6908	34	3.00071912764946	4.66216504574772e-13	6.82905827788002e-11
TCF12#6938	21	5.31723245109321	2.04337792876457e-11	2.45296951152003e-09
TCF7L2#6934	12	3.07719330375353	0.00031605275343791	0.00323832370414029
USF1#7391	14	2.12049975906932	0.00370799143482147	0.0187018359714743
USF2#7392	10	3.09338032977847	0.00107996321696611	0.00762354027825098
YY1#7528	22	2.57251801182821	4.28712985869587e-06	0.000135638762590833
ZEB1#6935	8	3.21684419381788	0.00290189666263321	0.0156820441658258
ZNF263#10127	12	2.34909761057448	0.00341082501017724	0.0173826747298053

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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