Coexpression cluster:C176

Full id: C176_Eosinophils_Neutrophils_Mast_CD14_CD4_Basophils_CD19

Phase1 CAGE Peaks

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Hg19::chr10:124768300..124768334,-	p1@IKZF5
Hg19::chr10:28821674..28821715,+	p2@WAC
Hg19::chr10:32636106..32636150,-	p3@EPC1
Hg19::chr10:69644404..69644425,+	p1@SIRT1
Hg19::chr10:76586348..76586366,+	p1@KAT6B
Hg19::chr10:98592009..98592061,+	p1@C10orf12 p1@LCOR
Hg19::chr11:118661828..118661886,-	p1@DDX6
Hg19::chr11:13299319..13299424,+	p1@ARNTL
Hg19::chr11:65265141..65265306,+	p4@MALAT1
Hg19::chr11:9482551..9482580,+	p1@ZNF143
Id	Short description

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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

p.value	FDR	nGenes	nPathway	Name
8.89e-5	1.41e-2	5	162	TNF alpha/NF-kB down reg. targets (Netpath)
2.34e-4	2.96e-2	4	108	{HDAC1,108} (Static Module)
3.35e-4	3.54e-2	2	10	{TIA1,10} (Static Module)
4.47e-4	4.04e-2	4	128	Cell cycle (KEGG)
1.52e-5	4.81e-3	5	112	{EP300,115} (Static Module)
8.63e-7	5.46e-4	6	116	Androgen Receptor Signaling Pathway (Wikipathways)
4.49e-5	9.47e-3	3	25	{BCLAF1,25} (Static Module)

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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 ID	GO name	FDR corrected p-value
GO:0000123	histone acetyltransferase complex	1.97e-3
GO:0000184	mRNA catabolic process, nonsense-mediated decay	4.67e-3
GO:0000375	RNA splicing, via transesterification reactions	2.89e-2
GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	2.89e-2
GO:0000398	nuclear mRNA splicing, via spliceosome	2.89e-2
GO:0001666	response to hypoxia	1.65e-2
GO:0003002	regionalization	3.93e-2
GO:0003676	nucleic acid binding	1.00e-7
GO:0003677	DNA binding	2.93e-8
GO:0003682	chromatin binding	8.46e-3

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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

Ontology term	p-value	n
T cell	1.02e-07	25
pro-T cell	1.02e-07	25
hematopoietic cell	1.04e-39	177
leukocyte	1.10e-46	136
hematopoietic stem cell	1.21e-44	168
angioblastic mesenchymal cell	1.21e-44	168
myeloid leukocyte	1.51e-27	72
myeloid cell	2.44e-26	108
common myeloid progenitor	2.44e-26	108
lymphoid lineage restricted progenitor cell	2.85e-13	52
lymphocyte	3.59e-13	53
common lymphoid progenitor	3.59e-13	53
myeloid lineage restricted progenitor cell	3.74e-23	66
granulocyte monocyte progenitor cell	3.95e-24	67
hematopoietic oligopotent progenitor cell	4.62e-41	161
hematopoietic multipotent progenitor cell	4.62e-41	161
defensive cell	5.78e-20	48
phagocyte	5.78e-20	48
macrophage dendritic cell progenitor	6.17e-21	61
nongranular leukocyte	6.28e-35	115
mature alpha-beta T cell	6.39e-10	18
alpha-beta T cell	6.39e-10	18
immature T cell	6.39e-10	18
mature T cell	6.39e-10	18
immature alpha-beta T cell	6.39e-10	18
monopoietic cell	6.62e-20	59
monocyte	6.62e-20	59
monoblast	6.62e-20	59
promonocyte	6.62e-20	59
CD8-positive, alpha-beta T cell	7.98e-07	11
hematopoietic lineage restricted progenitor cell	8.21e-38	120
nucleate cell	8.64e-14	55
classical monocyte	9.83e-23	42
CD14-positive, CD16-negative classical monocyte	9.83e-23	42

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Uber Anatomy

Ontology term	p-value	n

Ontology term	p-value	n
immune system	1.20e-17	93
adult organism	1.20e-24	114
skeletal element	1.63e-14	90
central nervous system	1.86e-07	81
bone element	1.90e-18	82
nervous system	2.43e-07	89
hemolymphoid system	2.47e-23	108
skeletal system	2.52e-12	100
regional part of nervous system	2.83e-09	53
regional part of brain	2.83e-09	53
blood	3.94e-07	15
haemolymphatic fluid	3.94e-07	15
organism substance	3.94e-07	15
telencephalon	4.05e-07	34
brain grey matter	4.11e-07	34
gray matter	4.11e-07	34
regional part of forebrain	4.17e-09	41
forebrain	4.17e-09	41
anterior neural tube	4.17e-09	41
future forebrain	4.17e-09	41
hematopoietic system	4.21e-27	98
blood island	4.21e-27	98
bone marrow	4.66e-19	76
brain	5.05e-07	68
future brain	5.05e-07	68
neural tube	7.68e-10	56
neural rod	7.68e-10	56
future spinal cord	7.68e-10	56
neural keel	7.68e-10	56

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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

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Motifs	-log10(p-value)

Motifs	-log10(p-value)
motif23_CGCNAT	9.04
motif65_TNGCGA	7.66
motif160_AGCCGGTAACG	6.89
motif86_CGCACAGACCGCGC	6.13
motif109_TCNMTMGC	5.85
motif38_TCGNCA	4.80
motif106_KCGCANTC	4.27
motif169_GCCTGGCC	4.07
motif95_AGCGAGCTAGC	3.71
motif117_SKSNGCGCTSN	3.70

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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	28	6.41804986457393	1.6703669379992e-15	3.08763632987077e-13
BCL3#602	10	3.52521457181003	0.000565467227653071	0.00482332830683266
BCLAF1#9774	25	5.52363459441884	1.98946434955337e-12	2.71250218280685e-10
BHLHE40#8553	14	6.41025907813963	4.12477158197312e-08	2.71961502051572e-06
BRCA1#672	42	8.65038456138161	8.41940743150004e-29	3.18592207513925e-26
CCNT2#905	71	4.5905133873913	1.17047810954241e-35	5.84897431973681e-33
CEBPB#1051	41	3.33486788427365	4.42490965794855e-13	6.49063398548439e-11
CHD2#1106	60	6.33307520456134	5.92161677601478e-36	2.98767021483192e-33
CTCF#10664	37	2.02377026330384	7.43593228313639e-06	0.000212942509382638
CTCFL#140690	21	4.23138736263736	1.7517413286226e-08	1.26521516334727e-06
E2F1#1869	72	3.60542881093175	1.9471004105034e-29	7.58780670793152e-27
E2F4#1874	43	5.55843462813501	5.47244369254552e-22	1.5240974581487e-19
E2F6#1876	72	3.68607359879808	4.55928480911686e-30	1.83141210068983e-27
EBF1#1879	22	1.99941092473998	0.00111439344640342	0.00765496824183942
EGR1#1958	68	3.46118549435805	6.51761727185527e-26	2.14729788724067e-23
ELF1#1997	90	3.91049812543549	4.17145374789434e-47	2.79270806395088e-44
ELK4#2005	37	6.1297981771767	4.87193863613021e-20	1.2410253639483e-17
EP300#2033	36	2.48838675657179	6.86346032735989e-08	4.16509548593341e-06
ETS1#2113	53	5.26147274364004	6.29766179707759e-27	2.17788576299664e-24
FAM48A#55578	2	23.5748724489796	0.00335169998841279	0.017288891939045
FOS#2353	30	2.75447611496768	1.53138272428548e-07	8.59871399686295e-06
FOSL1#8061	7	2.83668426545522	0.0121108099384669	0.0439196110685628
FOSL2#2355	25	4.31892872565349	3.65094048626798e-10	3.63836425043265e-08
FOXA1#3169	26	2.939968504939	3.90609694567911e-07	1.89743655306874e-05
GABPB1#2553	65	4.68774948318205	5.52345738383487e-32	2.40360152379304e-29
GATA1#2623	31	4.28948522916136	1.72589674405777e-12	2.36860617677595e-10
GATA3#2625	19	5.28054908966239	2.81172131235106e-09	2.36626399791001e-07
GTF2B#2959	13	4.2374468280226	1.22632919077175e-05	0.000305089553013364
GTF2F1#2962	38	4.93986850323256	1.80130492470792e-17	3.80053505114283e-15
HDAC2#3066	20	2.73788168094413	3.20280711595823e-05	0.000642770892358882
HDAC8#55869	2	15.8486537472132	0.00723490186487388	0.0299427745538167
HEY1#23462	90	3.71030605999504	4.1609239846454e-45	2.71601712520238e-42
HMGN3#9324	60	5.0072741163371	2.73654242372022e-30	1.1034816764128e-27
HNF4A#3172	17	4.01274424663482	1.01493047995734e-06	4.27930255939704e-05
HNF4G#3174	12	3.52082724813634	0.000157066064565252	0.00198042046566828
IRF1#3659	63	4.90960527014822	8.25138354938216e-32	3.54636315437829e-29
IRF3#3661	12	5.75289210752934	1.27180261288656e-06	5.08911084625516e-05
IRF4#3662	10	2.23617476395348	0.0141290041740246	0.0495773104062273
JUN#3725	26	3.31973019388515	3.57705126804954e-08	2.38559168188905e-06
JUNB#3726	12	3.74824073385565	8.77420472340428e-05	0.00129522143760794
JUND#3727	47	3.35458372722386	2.10680643089929e-15	3.83332328983782e-13
MAX#4149	52	3.42380496396296	8.31352282543196e-18	1.80510605065549e-15
MEF2A#4205	17	3.25137679044846	1.63684044987878e-05	0.000378124263978965
MEF2C#4208	10	4.21544433598205	0.000138129092722616	0.00180461149798064
MXI1#4601	36	3.6593528432177	1.57729933432822e-12	2.17323964614651e-10
MYC#4609	63	3.35718120317747	1.78622064781502e-22	5.08313619174802e-20
NANOG#79923	13	3.87940939033841	3.06903784187106e-05	0.000626029771810882
NFE2#4778	8	6.30238862462278	4.39169911094187e-05	0.000778717594987534
NFKB1#4790	78	4.36805048048081	1.28609391933949e-39	7.38012982647788e-37
NFYA#4800	21	3.94833872139226	5.6858364174278e-08	3.56009034532219e-06
NFYB#4801	22	3.76240256712043	6.01278299330073e-08	3.73568734703947e-06
NR2C2#7182	12	3.99362582513153	4.81291931224098e-05	0.000836784551441878
NR3C1#2908	24	3.66686285661381	2.13598876113865e-08	1.5154927325038e-06
NRF1#4899	35	4.36081408846818	2.24727625957165e-14	3.77944098668927e-12
PAX5#5079	60	4.08340746806806	1.74039086987352e-25	5.62738953742168e-23
PBX3#5090	14	3.13064466953488	0.000147459701684741	0.00190271111740211
POLR2A#5430	98	2.14745317655807	2.87511288600786e-33	1.31123980219116e-30
POU2F2#5452	56	5.20349946156716	1.40381579124456e-28	5.23618276506397e-26
RAD21#5885	18	1.90194500120626	0.00570551270883114	0.0257220945263582
RDBP#7936	7	10.9741717135732	4.0215919736412e-06	0.000129873544877895
REST#5978	47	4.62807499651038	5.18680252218766e-21	1.37488443810852e-18
RFX5#5993	47	5.7780796824303	4.67581579046352e-25	1.48883391872018e-22
RXRA#6256	17	3.48233154454353	6.73788686337537e-06	0.000196618654966208
SETDB1#9869	11	4.5257172240624	3.33593832103034e-05	0.000662613279402981
SIN3A#25942	74	4.08425989575837	1.94975475531037e-34	9.29819346529042e-32
SIX5#147912	35	6.10239834123536	7.9758994485173e-19	1.87189879214314e-16
SMARCB1#6598	25	4.65630504621363	7.61792959830484e-11	8.36602470365257e-09
SP1#6667	58	3.37251142787931	3.62829933446048e-20	9.3104657049562e-18
SP2#6668	21	5.60432796296671	1.22359805870121e-10	1.31337469324455e-08
SPI1#6688	37	3.09755071240144	9.29923923855307e-11	1.01272497063112e-08
SREBF1#6720	13	6.23546982373824	1.79067098469578e-07	9.80681106295978e-06
SRF#6722	38	5.34992626492221	1.26503668495048e-18	2.90371794152843e-16
STAT1#6772	17	3.5919590556366	4.48381955876548e-06	0.000140247268912222
STAT2#6773	7	4.66169794188862	0.000809835252259833	0.00618082314460426
STAT3#6774	26	2.79087846863276	1.05329098027572e-06	4.39140346063937e-05
TAF1#6872	94	3.20659541693936	4.52450544989909e-44	2.88130990659763e-41
TAF7#6879	58	6.76651046413864	5.26953738907919e-36	2.67157871542738e-33
TBP#6908	92	3.47982554298844	6.92551135599247e-45	4.46477457104011e-42
TCF12#6938	31	3.36396338742632	7.84046337193137e-10	7.41040863439946e-08
TCF7L2#6934	33	3.62669210799523	2.45988660044192e-11	2.90949146844342e-09
TFAP2A#7020	20	3.37114987204999	1.48572570856753e-06	5.73209114433264e-05
TFAP2C#7022	35	3.8604387892358	7.93136945585133e-13	1.13316592968489e-10
THAP1#55145	15	4.8013996841099	5.26632433244004e-07	2.45869310217124e-05
TRIM28#10155	21	3.98368393827054	4.89181192718202e-08	3.15367867816644e-06
USF1#7391	46	2.9860098648119	3.91121687526651e-13	5.76140450262283e-11
USF2#7392	30	3.97720328114375	2.87850176152008e-11	3.35897034046253e-09
WRNIP1#56897	4	4.48244752446433	0.0125932712562831	0.0455380048727565
YY1#7528	83	4.15946094120276	2.52330133653372e-42	1.51454636946118e-39
ZBTB33#10009	25	8.07773597703601	4.22079339190957e-16	8.20885365098032e-14
ZBTB7A#51341	51	3.8259936194048	1.78898290656159e-19	4.31500198102509e-17
ZEB1#6935	18	3.10195690118153	1.67325741842288e-05	0.000385683803846099
ZNF143#7702	35	4.82174162579568	1.11394479873663e-15	2.08867649614462e-13
ZNF263#10127	40	3.35585372939211	8.15364124798729e-13	1.16016095136041e-10

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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