Coexpression cluster:C246

Full id: C246_Neutrophils_Eosinophils_Whole_CD14_CD14CD16_Basophils_migratory

Phase1 CAGE Peaks

Hg19::chr10:11207438..11207455,+	p1@CELF2
Hg19::chr10:12391685..12391734,+	p2@CAMK1D
Hg19::chr11:61722670..61722712,+	p2@BEST1
Hg19::chr11:65408273..65408341,+	p3@SIPA1
Hg19::chr12:51717949..51717976,-	p4@BIN2
Hg19::chr12:53835508..53835533,+	p1@PRR13 p2@PCBP2
Hg19::chr13:46753825..46753846,-	p@chr13:46753825..46753846 -
Hg19::chr13:46756271..46756348,-	p1@LCP1
Hg19::chr13:50699661..50699695,-	p1@DLEU2
Hg19::chr14:93118543..93118570,+	p4@RIN3
Hg19::chr14:93155682..93155685,+	p@chr14:93155682..93155685 +
Hg19::chr15:69958901..69958913,-	p@chr15:69958901..69958913 -
Hg19::chr15:85259768..85259799,+	p@chr15:85259768..85259799 +
Hg19::chr16:69796212..69796275,+	p1@WWP2
Hg19::chr17:61699766..61699826,+	p1@MAP3K3
Hg19::chr17:73840423..73840499,-	p1@UNC13D
Hg19::chr18:74208364..74208381,-	p@chr18:74208364..74208381 -
Hg19::chr18:74844727..74844747,-	p2@MBP
Hg19::chr19:1067043..1067054,+	p9@HMHA1
Hg19::chr19:14492247..14492264,+	p1@CD97
Hg19::chr19:2085323..2085357,-	p2@MOB3A
Hg19::chr19:38916839..38916871,-	p1@RASGRP4
Hg19::chr1:161039597..161039625,-	p2@ARHGAP30
Hg19::chr1:198608152..198608247,+	p1@PTPRC
Hg19::chr1:26869597..26869637,+	p3@RPS6KA1
Hg19::chr21:30671189..30671207,+	p4@BACH1
Hg19::chr22:17565841..17565896,+	p1@IL17RA
Hg19::chr22:17565903..17565929,+	p2@IL17RA
Hg19::chr22:37678505..37678563,+	p1@CYTH4
Hg19::chr22:51021397..51021434,-	p2@CHKB-CPT1B p2@CHKB
Hg19::chr2:175499294..175499339,-	p4@WIPF1
Hg19::chr2:231084659..231084721,-	p1@SP110
Hg19::chr2:32289003..32289089,+	p1@AB384105
Hg19::chr3:121379739..121379771,-	p1@HCLS1
Hg19::chr3:122512619..122512690,-	p1@HSPBAP1
Hg19::chr3:129158715..129158766,-	p2@MBD4
Hg19::chr4:88312301..88312375,-	p1@HSD17B11
Hg19::chr5:100238920..100238949,-	p2@ST8SIA4
Hg19::chr5:100238956..100238994,-	p1@ST8SIA4
Hg19::chr5:100239086..100239122,+	p1@AK055485
Hg19::chr5:154238052..154238091,+	p2@CNOT8
Hg19::chr5:175085039..175085106,+	p1@HRH2
Hg19::chr5:176853702..176853742,+	p2@GRK6
Hg19::chr5:95157986..95158004,-	p2@GLRX
Hg19::chr6:33266687..33266728,-	p1@RGL2
Hg19::chr7:106505696..106505798,+	p1@PIK3CG
Hg19::chr7:26332645..26332661,+	p8@SNX10
Hg19::chr7:36763985..36764000,-	p4@AOAH
Hg19::chr8:103251611..103251667,+	p2@ENST00000520820
Hg19::chr8:67579326..67579368,-	p2@VCPIP1
Hg19::chr9:115095883..115095932,-	p1@PTBP3
Hg19::chr9:95726554..95726616,+	p1@FGD3
Hg19::chrX:48542169..48542241,+	p1@WAS
Hg19::chrX:71321022..71321043,+	p@chrX:71321022..71321043 +

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
0.000322629172590525	0.0340373777083004	3	95	Fc gamma R-mediated phagocytosis (KEGG):04666
0.000136358655931522	0.0215787573011634	3	71	Bacterial invasion of epithelial cells (KEGG):05100
0.000125242807661058	0.0215787573011634	3	69	IL-5 Signaling Pathway (Wikipathways):WP127
3.00804519216102e-06	0.00190409260663793	5	161	B Cell Receptor Signaling Pathway (Wikipathways):WP23
9.08047147404293e-06	0.00287396922153459	3	29	MAPK Cascade (Wikipathways):WP422
0.000256925614176628	0.0325267827547611	2	17	{HCLS1,17} (Static Module):NA

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:0007154	cell communication	0.000219800609395661
GO:0009966	regulation of signal transduction	0.000585506406463515
GO:0007165	signal transduction	0.00112135234340188
GO:0030695	GTPase regulator activity	0.00139879786256928
GO:0005515	protein binding	0.00821279443007198
GO:0030048	actin filament-based movement	0.0113800714176354
GO:0030036	actin cytoskeleton organization and biogenesis	0.0113800714176354
GO:0065007	biological regulation	0.0113800714176354
GO:0030029	actin filament-based process	0.0113800714176354
GO:0007242	intracellular signaling cascade	0.0113800714176354
GO:0005737	cytoplasm	0.0113800714176354
GO:0006464	protein modification process	0.0239540251157988
GO:0043687	post-translational protein modification	0.0244979746616004
GO:0043412	biopolymer modification	0.0282238563994342
GO:0007010	cytoskeleton organization and biogenesis	0.0315329711302865
GO:0001726	ruffle	0.0315329711302865
GO:0001891	phagocytic cup	0.0315329711302865
GO:0050528	acyloxyacyl hydrolase activity	0.0315329711302865
GO:0002378	immunoglobulin biosynthetic process	0.0315329711302865
GO:0019975	interleukin-17 binding	0.0315329711302865
GO:0030368	interleukin-17 receptor activity	0.0315329711302865
GO:0006468	protein amino acid phosphorylation	0.0418521866255157
GO:0005083	small GTPase regulator activity	0.0434877302590047
GO:0051056	regulation of small GTPase mediated signal transduction	0.0434877302590047
GO:0008154	actin polymerization and/or depolymerization	0.0456442428978856
GO:0006793	phosphorus metabolic process	0.0456442428978856
GO:0006796	phosphate metabolic process	0.0456442428978856
GO:0043209	myelin sheath	0.0456442428978856
GO:0006710	androgen catabolic process	0.0456442428978856

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
hematopoietic stem cell	9.67e-79	168
angioblastic mesenchymal cell	9.67e-79	168
hematopoietic oligopotent progenitor cell	1.50e-74	161
hematopoietic multipotent progenitor cell	1.50e-74	161
hematopoietic cell	7.68e-74	177
leukocyte	7.30e-72	136
hematopoietic lineage restricted progenitor cell	1.36e-60	120
nongranular leukocyte	6.87e-59	115
myeloid cell	3.44e-52	108
common myeloid progenitor	3.44e-52	108
myeloid leukocyte	8.13e-47	72
granulocyte monocyte progenitor cell	9.86e-42	67
myeloid lineage restricted progenitor cell	2.03e-40	66
macrophage dendritic cell progenitor	2.47e-38	61
monopoietic cell	1.09e-37	59
monocyte	1.09e-37	59
monoblast	1.09e-37	59
promonocyte	1.09e-37	59
defensive cell	2.21e-34	48
phagocyte	2.21e-34	48
classical monocyte	4.41e-31	42
CD14-positive, CD16-negative classical monocyte	4.41e-31	42
nucleate cell	7.20e-19	55
lymphocyte	1.32e-18	53
common lymphoid progenitor	1.32e-18	53
lymphoid lineage restricted progenitor cell	1.90e-18	52
mesenchymal cell	2.22e-11	354
connective tissue cell	2.21e-10	361
T cell	4.19e-10	25
pro-T cell	4.19e-10	25
mature alpha-beta T cell	1.26e-09	18
alpha-beta T cell	1.26e-09	18
immature T cell	1.26e-09	18
mature T cell	1.26e-09	18
immature alpha-beta T cell	1.26e-09	18
stuff accumulating cell	2.98e-09	87
lymphocyte of B lineage	3.47e-08	24
pro-B cell	3.47e-08	24
intermediate monocyte	5.15e-08	9
CD14-positive, CD16-positive monocyte	5.15e-08	9
granulocyte	1.46e-07	8
B cell	3.68e-07	14
CD8-positive, alpha-beta T cell	7.96e-07	11

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	5.75e-48	98
blood island	5.75e-48	98
hemolymphoid system	2.11e-43	108
bone marrow	1.47e-35	76
immune system	2.58e-34	93
bone element	9.46e-31	82
skeletal element	1.06e-25	90
adult organism	3.89e-24	114
skeletal system	1.17e-20	100
lateral plate mesoderm	6.62e-13	203
blood	8.68e-10	15
haemolymphatic fluid	8.68e-10	15
organism substance	8.68e-10	15
connective tissue	3.44e-09	371

Disease

Ontology term	p-value	n
hematologic cancer	1.18e-08	51
immune system cancer	1.18e-08	51
leukemia	3.46e-08	39
myeloid leukemia	6.86e-07	31

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
E2F1#1869	21	1.90842913911974	0.00138657961336456	0.0090243028753151
EBF1#1879	20	3.29869142465519	7.07426279704601e-07	3.16957928897764e-05
EGR1#1958	25	2.30934217352321	1.24908008657656e-05	0.000308398759248156
ELF1#1997	45	3.54841496567295	2.42527982603946e-20	6.28520594917456e-18
ETS1#2113	15	2.70243358950065	0.000260382288536763	0.00279113885173878
GABPB1#2553	22	2.87942674807422	1.5732290254349e-06	5.99221247948196e-05
GATA1#2623	12	3.01340180973343	0.00047265730468022	0.00433853544063082
HEY1#23462	29	2.1696892638901	4.86121192221296e-06	0.000150474247760521
IRF1#3659	16	2.2628633343893	0.00112461923298725	0.00771151651723164
MAX#4149	16	1.91186829896507	0.00637462235121672	0.0277538429105687
MYC#4609	25	2.41772308870806	5.37755905274527e-06	0.000164314479201189
NFKB1#4790	33	3.35381653700734	3.46966644243456e-12	4.59858494392668e-10
NRF1#4899	11	2.48727914675593	0.00389062338111856	0.0189671295010335
PBX3#5090	8	3.24659447211024	0.00298223188688548	0.0158754939616919
POLR2A#5430	48	1.90884726805162	7.80036710520287e-11	8.55737962290213e-09
POU2F2#5452	19	3.20400661290941	2.34324371142833e-06	8.32401462509739e-05
PRDM1#639	3	7.32394198763671	0.00810331862424713	0.0320047836401976
RFX5#5993	11	2.45420405739159	0.00430741532808852	0.0204510683025066
SIN3A#25942	28	2.80460689538563	3.40948872317986e-08	2.27966448630078e-06
SP2#6668	7	3.3902724714243	0.00436542157703896	0.0206935486603292
SPI1#6688	28	4.25409367108586	1.84045789291855e-12	2.51591075757226e-10
SREBF1#6720	5	4.35239346671188	0.00579421312096576	0.0260488926064544
TAF1#6872	39	2.41442231748271	1.78566113836129e-10	1.86866396422159e-08
TBP#6908	34	2.33389265483847	3.37944588907238e-08	2.26247403338994e-06
YY1#7528	21	1.90989973605428	0.00137249188942719	0.00902939719306368
ZBTB7A#51341	17	2.31448996729426	0.000572144509156753	0.0048313551416415
ZEB1#6935	14	4.37848237491878	2.19157431595235e-06	7.8573920351441e-05
ZNF263#10127	13	1.97933224594701	0.0112697345025402	0.0413664570242432

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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