Coexpression cluster:C509

Full id: C509_Neutrophils_Eosinophils_CD14_Whole_CD34_CD19_Peripheral

Phase1 CAGE Peaks

Hg19::chr10:99894399..99894453,+	p1@C10orf28
Hg19::chr11:95522907..95522989,-	p1@FAM76B
Hg19::chr12:105501487..105501562,+	p1@KIAA1033
Hg19::chr12:118810688..118810744,-	p1@TAOK3
Hg19::chr16:50775971..50776014,+	p1@CYLD
Hg19::chr17:62502968..62503006,-	p2@DDX5
Hg19::chr18:9137005..9137035,+	p@chr18:9137005..9137035 +
Hg19::chr21:34697258..34697336,+	p1@IFNAR1
Hg19::chr22:30279148..30279192,+	p1@MTMR3
Hg19::chr2:128145498..128145563,-	p1@MAP3K2
Hg19::chr2:24583314..24583433,-	p1@ITSN2
Hg19::chr2:64751475..64751556,+	p1@AFTPH
Hg19::chr5:147763539..147763586,+	p1@FBXO38
Hg19::chr7:106809432..106809455,+	p1@HBP1
Hg19::chr8:96145974..96146041,+	p1@PLEKHF2
Hg19::chrX:100663186..100663241,+	p1@HNRNPH2
Hg19::chrX:44732415..44732450,+	p1@KDM6A
Hg19::chrX:54070731..54070781,-	p1@PHF8

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:0030133	transport vesicle	0.0188889352968199
GO:0007254	JNK cascade	0.0188889352968199
GO:0031098	stress-activated protein kinase signaling pathway	0.0188889352968199
GO:0007243	protein kinase cascade	0.0188889352968199
GO:0043687	post-translational protein modification	0.0277494551879854
GO:0019962	interferon-alpha/beta binding	0.0277494551879854
GO:0004905	interferon-alpha/beta receptor activity	0.0277494551879854
GO:0046329	negative regulation of JNK cascade	0.0322552606000145
GO:0005737	cytoplasm	0.0322552606000145
GO:0000165	MAPKKK cascade	0.0322552606000145
GO:0006464	protein modification process	0.0322552606000145
GO:0030121	AP-1 adaptor complex	0.0322552606000145
GO:0019961	interferon binding	0.0322552606000145
GO:0004904	interferon receptor activity	0.0322552606000145
GO:0044424	intracellular part	0.0322552606000145
GO:0043412	biopolymer modification	0.0322552606000145
GO:0045786	negative regulation of progression through cell cycle	0.0408542297560198
GO:0045351	interferon type I biosynthetic process	0.0408542297560198
GO:0032606	interferon type I production	0.0408542297560198

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	3.70e-47	136
hematopoietic lineage restricted progenitor cell	3.06e-39	120
hematopoietic stem cell	1.17e-38	168
angioblastic mesenchymal cell	1.17e-38	168
nongranular leukocyte	1.19e-36	115
hematopoietic oligopotent progenitor cell	3.91e-36	161
hematopoietic multipotent progenitor cell	3.91e-36	161
myeloid leukocyte	5.15e-35	72
hematopoietic cell	5.78e-34	177
granulocyte monocyte progenitor cell	2.68e-31	67
myeloid lineage restricted progenitor cell	4.31e-30	66
macrophage dendritic cell progenitor	2.04e-28	61
defensive cell	9.80e-28	48
phagocyte	9.80e-28	48
monopoietic cell	1.63e-27	59
monocyte	1.63e-27	59
monoblast	1.63e-27	59
promonocyte	1.63e-27	59
classical monocyte	8.41e-27	42
CD14-positive, CD16-negative classical monocyte	8.41e-27	42
myeloid cell	3.82e-26	108
common myeloid progenitor	3.82e-26	108
lymphoid lineage restricted progenitor cell	1.44e-09	52
nucleate cell	1.55e-09	55
lymphocyte	3.08e-09	53
common lymphoid progenitor	3.08e-09	53
stuff accumulating cell	2.45e-08	87
mature alpha-beta T cell	3.37e-08	18
alpha-beta T cell	3.37e-08	18
immature T cell	3.37e-08	18
mature T cell	3.37e-08	18
immature alpha-beta T cell	3.37e-08	18
mesenchymal cell	1.02e-07	354

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	1.74e-33	98
blood island	1.74e-33	98
hemolymphoid system	1.73e-30	108
bone marrow	2.78e-26	76
bone element	8.26e-25	82
immune system	8.61e-25	93
adult organism	8.26e-24	114
skeletal element	1.12e-21	90
skeletal system	9.41e-20	100
neural tube	1.09e-07	56
neural rod	1.09e-07	56
future spinal cord	1.09e-07	56
neural keel	1.09e-07	56
regional part of forebrain	4.70e-07	41
forebrain	4.70e-07	41
anterior neural tube	4.70e-07	41
future forebrain	4.70e-07	41
regional part of nervous system	5.36e-07	53
regional part of brain	5.36e-07	53

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	7	8.73567898233674	7.11832414395998e-06	0.000205197531126425
BHLHE40#8553	4	9.97151412155054	0.000586789015255046	0.00491567000595346
BRCA1#672	5	5.60673073422882	0.0014835168212706	0.00948903805099707
CCNT2#905	14	4.92815678208205	9.60784791139458e-09	7.30833232351157e-07
CHD2#1106	11	6.32134728751586	1.14456586357404e-07	6.64096190143384e-06
E2F1#1869	14	3.81685827823947	2.80080033108096e-07	1.41927601056654e-05
E2F4#1874	8	5.63024902901531	3.19335818496187e-05	0.000640997761828238
EBF1#1879	6	2.96882228218967	0.0112240115262793	0.0412131118304356
EGR1#1958	13	3.60257379069621	2.58786130943899e-06	9.08788323122052e-05
ELF1#1997	15	3.54841496567295	1.40980687262883e-07	7.9847516252973e-06
ELK4#2005	7	6.31387620051534	5.82725740562361e-05	0.000969097032143192
EP300#2033	8	3.01064076721031	0.00244970224095202	0.0137891803569466
ETS1#2113	9	4.86438046110117	2.6061409457402e-05	0.000562826208089662
FOS#2353	7	3.49920484234782	0.00218479461911982	0.0126009368912224
FOSL2#2355	6	5.64340020152056	0.000423899735635967	0.00396237935112188
FOXA1#3169	7	4.3094410136499	0.000631250780954892	0.00518417868303436
GABPB1#2553	9	3.53384191809109	0.000326663425749213	0.00333005383326716
GATA1#2623	6	4.52010271460015	0.00137177948024089	0.009025278892332
GTF2B#2959	4	7.09862887429427	0.00206412753922727	0.0119710915187337
GTF2F1#2962	6	4.24655362558588	0.00189537348763769	0.011164744031325
HEY1#23462	16	3.59120981609396	1.78396865355315e-08	1.28760125921519e-06
HMGN3#9324	8	3.63491009926693	0.00069736051048815	0.00560933721155822
HNF4A#3172	4	5.14050896954526	0.00655862767354443	0.0280325973234011
HNF4G#3174	5	7.98706181290189	0.000297670211889214	0.00310604248771082
IRF1#3659	16	6.78859000316791	8.74521507392966e-13	1.23759013158013e-10
IRF3#3661	4	10.4404338247755	0.00049377390688625	0.00436694496242637
JUN#3725	5	3.47578588676009	0.0115349971237048	0.0421844514532742
JUND#3727	10	3.88592441215057	5.14688713080812e-05	0.000876036090375602
MAX#4149	13	4.66017897872737	1.17151458807717e-07	6.76350536562697e-06
MXI1#4601	9	4.98078581437965	2.15158679768434e-05	0.000473970836455082
MYC#4609	12	3.4815212477396	1.40881703397654e-05	0.000338943658630444
NFE2#4778	4	17.1565023670287	7.43078141794464e-05	0.00115142934793579
NFKB1#4790	16	4.87827859928341	1.5468342524303e-10	1.63181638878352e-08
NFYA#4800	9	9.21279034991526	1.26299161532635e-07	7.22770308564758e-06
NFYB#4801	8	7.44879700157176	4.07516661513521e-06	0.000129521097418779
PAX5#5079	12	4.44637702078522	9.8090335066856e-07	4.16272104999893e-05
PBX3#5090	5	6.0873646352067	0.0010268889150663	0.00727543934608296
POLR2A#5430	18	2.14745317655807	1.059158074972e-06	4.41234185049864e-05
POU2F2#5452	8	4.04716624788557	0.000333364930271925	0.00339472503438666
SIN3A#25942	16	4.80789753494679	1.94005847662396e-10	2.01609718646896e-08
SIX5#147912	8	7.59409571353733	3.52877746851906e-06	0.000116553444033732
SP1#6667	10	3.1657674323005	0.000304228420343878	0.00313841485502709
SP2#6668	5	7.26486958162351	0.000460265115228254	0.00424081414815382
SPI1#6688	7	3.19057025331439	0.00372569755106236	0.0185749535294731
SREBF1#6720	3	7.83430824008138	0.00618041242352939	0.0273205829637258
TAF1#6872	17	3.15732149209278	1.58473138591732e-08	1.16064348677292e-06
TAF7#6879	9	5.71653470246196	6.97179630487212e-06	0.000201362675410547
TBP#6908	16	3.29490727741901	6.69614874550662e-08	4.07302899727412e-06
TCF12#6938	6	3.54482163406214	0.00473211634105121	0.0222911685780095
TCF7L2#6934	7	4.18840199677563	0.000750178742713626	0.00590591871779499
TFAP2C#7022	7	4.20358890383453	0.000733940461332141	0.00584416040264314
USF1#7391	15	5.3012493976733	4.46175296849933e-10	4.35089652919796e-08
USF2#7392	9	6.4960986925348	2.41613336419054e-06	8.55095060734312e-05
YY1#7528	14	3.81979947210855	2.77275053238948e-07	1.40642687155039e-05
ZEB1#6935	5	4.6912311159844	0.00324854487916675	0.0168282713474181
ZNF143#7702	8	6.00038957876796	2.00891846238146e-05	0.000445833904149294
ZNF263#10127	10	4.56768979833926	1.21695898680601e-05	0.000302974921628207

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.