Coexpression cluster:C646

Full id: C646_CD14_Mast_vagina_thymus_MCF7_immature_Eosinophils

Phase1 CAGE Peaks

Hg19::chr10:126847417..126847439,+	p@chr10:126847417..126847439 +
Hg19::chr11:63953135..63953159,-	p@chr11:63953135..63953159 -
Hg19::chr12:1704640..1704649,+	p@chr12:1704640..1704649 +
Hg19::chr12:1704650..1704671,+	p@chr12:1704650..1704671 +
Hg19::chr13:31191642..31191749,-	p2@HMGB1
Hg19::chr6:31782588..31782612,+	p@chr6:31782588..31782612 +
Hg19::chr6:31782632..31782654,+	p@chr6:31782632..31782654 +
Hg19::chr6:31790025..31790063,+	p@chr6:31790025..31790063 +
Hg19::chr6:44215668..44215690,+	p13@HSP90AB1
Hg19::chr7:157129414..157129491,-	p@chr7:157129414..157129491 -
Hg19::chr7:641637..641649,+	p@chr7:641637..641649 +
Hg19::chr9:33025026..33025046,-	p5@APTX
Hg19::chrX:118740549..118740569,+	p@chrX:118740549..118740569 +

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:0006950	response to stress	0.00546884366603595
GO:0033699	DNA 5'-adenosine monophosphate hydrolase activity	0.00546884366603595
GO:0017055	negative regulation of transcriptional preinitiation complex assembly	0.00546884366603595
GO:0035312	5'-3' exodeoxyribonuclease activity	0.00546884366603595
GO:0030911	TPR domain binding	0.00546884366603595
GO:0006288	base-excision repair, DNA ligation	0.00546884366603595
GO:0000785	chromatin	0.00546884366603595
GO:0008409	5'-3' exonuclease activity	0.00546884366603595
GO:0030235	nitric-oxide synthase regulator activity	0.00546884366603595
GO:0008967	phosphoglycolate phosphatase activity	0.00546884366603595
GO:0006281	DNA repair	0.00546884366603595
GO:0000012	single strand break repair	0.00546884366603595
GO:0051103	DNA ligation during DNA repair	0.00546884366603595
GO:0006974	response to DNA damage stimulus	0.00546884366603595
GO:0051123	transcriptional preinitiation complex assembly	0.00546884366603595
GO:0045898	regulation of transcriptional preinitiation complex assembly	0.00546884366603595
GO:0044427	chromosomal part	0.00546884366603595
GO:0016895	exodeoxyribonuclease activity, producing 5'-phosphomonoesters	0.00561185847523729
GO:0004529	exodeoxyribonuclease activity	0.00561185847523729
GO:0045429	positive regulation of nitric oxide biosynthetic process	0.00561185847523729
GO:0009719	response to endogenous stimulus	0.00561185847523729
GO:0005694	chromosome	0.00561185847523729
GO:0006266	DNA ligation	0.00580392531463132
GO:0045428	regulation of nitric oxide biosynthetic process	0.00598028115587165
GO:0042221	response to chemical stimulus	0.00598028115587165
GO:0008301	DNA bending activity	0.00627481473872941
GO:0006268	DNA unwinding during replication	0.00878767242417505
GO:0032392	DNA geometric change	0.00920378733858085
GO:0032508	DNA duplex unwinding	0.00920378733858085
GO:0042542	response to hydrogen peroxide	0.00959366799323775
GO:0031647	regulation of protein stability	0.00959366799323775
GO:0046209	nitric oxide metabolic process	0.00959366799323775
GO:0016796	exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	0.00959366799323775
GO:0006809	nitric oxide biosynthetic process	0.00959366799323775
GO:0008219	cell death	0.00981296665538481
GO:0016265	death	0.00981296665538481
GO:0000302	response to reactive oxygen species	0.0108178019051623
GO:0006284	base-excision repair	0.0136508321545364
GO:0047485	protein N-terminus binding	0.0148191578271127
GO:0048468	cell development	0.0161969686070464
GO:0006259	DNA metabolic process	0.0161969686070464
GO:0003684	damaged DNA binding	0.0172259976547266
GO:0004536	deoxyribonuclease activity	0.0172259976547266
GO:0000793	condensed chromosome	0.0174464800683915
GO:0003725	double-stranded RNA binding	0.0174464800683915
GO:0051789	response to protein stimulus	0.0185918184031567
GO:0006986	response to unfolded protein	0.0185918184031567
GO:0009891	positive regulation of biosynthetic process	0.0215915490740713
GO:0004527	exonuclease activity	0.0217539351273584
GO:0048770	pigment granule	0.0240862170172025
GO:0042470	melanosome	0.0240862170172025
GO:0065007	biological regulation	0.0251203755349182
GO:0048869	cellular developmental process	0.0255408107288152
GO:0030154	cell differentiation	0.0255408107288152
GO:0003690	double-stranded DNA binding	0.0290403494790685
GO:0003682	chromatin binding	0.0311238690921357
GO:0006979	response to oxidative stress	0.0311238690921357
GO:0019904	protein domain specific binding	0.0318162727159351
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	0.0318162727159351
GO:0044271	nitrogen compound biosynthetic process	0.0361915885977443
GO:0043566	structure-specific DNA binding	0.0384906468708542
GO:0006261	DNA-dependent DNA replication	0.0386682473302357
GO:0005730	nucleolus	0.0386682473302357
GO:0006916	anti-apoptosis	0.0392117309418119
GO:0006310	DNA recombination	0.0433794383969251
GO:0043231	intracellular membrane-bound organelle	0.0433794383969251
GO:0043227	membrane-bound organelle	0.0433794383969251
GO:0051082	unfolded protein binding	0.0433794383969251
GO:0045892	negative regulation of transcription, DNA-dependent	0.0433881727652442
GO:0005515	protein binding	0.0446881835055404
GO:0009889	regulation of biosynthetic process	0.0450553585491057
GO:0043066	negative regulation of apoptosis	0.0464283747168019
GO:0043069	negative regulation of programmed cell death	0.0464283747168019
GO:0043232	intracellular non-membrane-bound organelle	0.0467892241541275
GO:0043228	non-membrane-bound organelle	0.0467892241541275
GO:0004518	nuclease activity	0.0476754711706606

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
classical monocyte	1.25e-21	45
myeloid leukocyte	1.70e-21	76
CD14-positive, CD16-negative classical monocyte	1.98e-21	42
leukocyte	5.60e-19	140
granulocyte monocyte progenitor cell	7.72e-19	71
myeloid lineage restricted progenitor cell	3.99e-18	70
hematopoietic cell	1.40e-17	182
myeloid cell	1.74e-17	112
common myeloid progenitor	1.74e-17	112
hematopoietic stem cell	5.39e-17	172
angioblastic mesenchymal cell	5.39e-17	172
macrophage dendritic cell progenitor	5.58e-17	65
hematopoietic oligopotent progenitor cell	4.72e-16	165
hematopoietic multipotent progenitor cell	4.72e-16	165
monopoietic cell	5.10e-16	63
monocyte	5.10e-16	63
monoblast	5.10e-16	63
promonocyte	5.10e-16	63
hematopoietic lineage restricted progenitor cell	1.87e-15	124
nongranular leukocyte	2.85e-13	119

Uber Anatomy

Ontology term	p-value	n
neural tube	9.15e-18	57
neural rod	9.15e-18	57
future spinal cord	9.15e-18	57
neural keel	9.15e-18	57
bone marrow	1.04e-15	80
adult organism	5.10e-15	115
bone element	6.05e-15	86
central nervous system	2.30e-13	82
hematopoietic system	7.45e-13	102
blood island	7.45e-13	102
hemolymphoid system	1.11e-12	112
regional part of brain	1.17e-12	59
anterior neural tube	1.42e-12	42
regional part of forebrain	4.64e-12	41
forebrain	4.64e-12	41
future forebrain	4.64e-12	41
brain	8.52e-12	69
future brain	8.52e-12	69
immune system	3.39e-11	115
regional part of nervous system	1.03e-10	94
nervous system	1.03e-10	94
neurectoderm	2.10e-09	90
gray matter	3.17e-09	34
brain grey matter	3.17e-09	34
skeletal element	3.62e-09	101
skeletal system	3.62e-09	101
telencephalon	4.20e-09	34
regional part of telencephalon	7.64e-09	33
neural plate	1.13e-08	86
presumptive neural plate	1.13e-08	86
cerebral hemisphere	3.68e-08	32
lateral plate mesoderm	4.43e-07	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
CCNT2#905	10	4.87400121304818	1.72226346360207e-06	6.49824688855263e-05
CHD2#1106	5	3.97847032081418	0.00558368656684048	0.0252524419241438
E2F6#1876	8	3.08748045027531	0.00121584853405667	0.00818288471764043
EGR1#1958	8	3.06964867372932	0.00126568416933679	0.00849202036241582
ELF1#1997	8	2.62036797465079	0.00372565735117579	0.0185765266924209
ELK4#2005	4	4.9955943564517	0.006554850858591	0.0280176012450022
EP300#2033	6	3.12643464287225	0.00695371655281501	0.029409540903031
ETS1#2113	6	4.49019734870877	0.00106508682285967	0.00752412085312775
GTF2B#2959	4	9.82887074902284	0.000546622148132622	0.00472041264501595
GTF2F1#2962	7	6.8598173951772	2.05623134739606e-05	0.000455269759785239
HEY1#23462	9	2.79699995291934	0.000914123114219825	0.00665296891470413
HSF1#3297	7	88.4642051282051	5.05042282057528e-13	7.35650082228817e-11
IRF1#3659	7	4.11231894422672	0.000547579966104684	0.00472751129040317
JUNB#3726	3	7.06399215226642	0.007792750127433	0.0320167989991729
NFKB1#4790	7	2.95511107456591	0.0040713240829685	0.0194726605560152
PBX3#5090	4	6.74292698053666	0.00222199559447697	0.0127752820199054
POLR2A#5430	13	2.14745317655807	4.83928878402115e-05	0.000840529654605662
PPARGC1A#10891	4	107.708041958042	4.61292015241441e-08	3.01482332789743e-06
SIN3A#25942	8	3.32854444727085	0.000719146205919868	0.00574519319208025
SRF#6722	5	5.3066070239107	0.00156826497609789	0.00994704395959477
STAT2#6773	3	15.060870273794	0.00091606785034798	0.00666572913136576
TAF1#6872	9	2.31441665936213	0.00394222869196859	0.0189515499360418
TAF7#6879	6	5.27680126381104	0.000446292320197271	0.00415347742194642
TBP#6908	8	2.28108965359778	0.00928530908545583	0.0350760804273853
THAP1#55145	3	7.23903336988877	0.00728433784323498	0.0301378188016329
WRNIP1#56897	3	25.3430686960099	0.000201329398099232	0.00239319838471269
YY1#7528	7	2.64447655761361	0.00776069714688224	0.0319177541672534

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.