Coexpression cluster:C269

Full id: C269_Basophils_Mast_Eosinophils_mature_CD14_chorionic_CD4

Phase1 CAGE Peaks

Hg19::chr14:75745523..75745537,+	p1@FOS
Hg19::chr14:75745802..75745826,-	p@chr14:75745802..75745826 -
Hg19::chr14:75746579..75746605,+	p9@FOS
Hg19::chr14:75746613..75746623,+	p11@FOS
Hg19::chr14:75746687..75746702,+	p10@FOS
Hg19::chr14:75746705..75746720,+	p8@FOS
Hg19::chr14:75746722..75746777,+	p2@FOS
Hg19::chr14:75746781..75746799,+	p6@FOS
Hg19::chr14:75747250..75747267,+	p5@FOS
Hg19::chr14:75747296..75747329,+	p4@FOS
Hg19::chr14:75747492..75747516,+	p@chr14:75747492..75747516 +
Hg19::chr14:75747550..75747561,+	p@chr14:75747550..75747561 +
Hg19::chr14:75747573..75747583,+	p@chr14:75747573..75747583 +
Hg19::chr14:75747611..75747620,+	p@chr14:75747611..75747620 +
Hg19::chr14:75747625..75747645,+	p@chr14:75747625..75747645 +
Hg19::chr14:75747656..75747717,+	p@chr14:75747656..75747717 +
Hg19::chr14:75747782..75747798,+	p@chr14:75747782..75747798 +
Hg19::chr14:75747827..75747836,+	p@chr14:75747827..75747836 +
Hg19::chr14:75747960..75747972,+	p@chr14:75747960..75747972 +
Hg19::chr14:75748018..75748039,+	p@chr14:75748018..75748039 +
Hg19::chr14:75748187..75748202,+	p@chr14:75748187..75748202 +
Hg19::chr14:75748263..75748319,+	p@chr14:75748263..75748319 +
Hg19::chr14:75748371..75748442,+	p1@S65140
Hg19::chr14:75748616..75748661,+	p2@S65140
Hg19::chr19:45972203..45972226,+	p5@FOSB
Hg19::chr19:45973899..45973920,+	p@chr19:45973899..45973920 +
Hg19::chr19:45973962..45973979,+	p@chr19:45973962..45973979 +
Hg19::chr19:45974005..45974026,+	p11@FOSB
Hg19::chr19:45974032..45974054,+	p9@FOSB
Hg19::chr19:45974146..45974170,+	p7@FOSB
Hg19::chr19:45974438..45974449,+	p26@FOSB
Hg19::chr19:45975749..45975760,+	p@chr19:45975749..45975760 +
Hg19::chr19:45975995..45976038,+	p2@AF432216
Hg19::chr19:45976177..45976190,+	p6@AF432216
Hg19::chr19:45976666..45976678,+	p3@AF432216
Hg19::chr19:45977115..45977124,+	p@chr19:45977115..45977124 +
Hg19::chr19:45977207..45977222,+	p@chr19:45977207..45977222 +
Hg19::chr19:45977304..45977312,+	p@chr19:45977304..45977312 +
Hg19::chr19:45977321..45977334,+	p@chr19:45977321..45977334 +
Hg19::chr19:45977344..45977355,+	p@chr19:45977344..45977355 +
Hg19::chr19:45977475..45977486,+	p@chr19:45977475..45977486 +
Hg19::chr19:45977515..45977522,+	p@chr19:45977515..45977522 +
Hg19::chr19:45977611..45977627,+	p@chr19:45977611..45977627 +
Hg19::chr19:45977632..45977642,+	p@chr19:45977632..45977642 +
Hg19::chr19:45977697..45977713,+	p4@FOSB
Hg19::chr19:45977759..45977770,+	p10@FOSB
Hg19::chr19:45977916..45977932,+	p13@FOSB
Hg19::chr19:45977993..45978005,+	p6@FOSB
Hg19::chr19:45978061..45978070,+	p24@FOSB

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
1.99497924496294e-05	0.00618101169771345	2	128	Osteoclast differentiation (KEGG):04380
2.92938943019595e-05	0.00618101169771345	2	155	TGF-beta Receptor Signaling Pathway (Wikipathways):WP366
8.97102502502407e-06	0.00567865884084024	2	86	{JUN,88} (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:0046983	protein dimerization activity	0.00711510319422719
GO:0006357	regulation of transcription from RNA polymerase II promoter	0.00711510319422719
GO:0006366	transcription from RNA polymerase II promoter	0.0108672074601084
GO:0043565	sequence-specific DNA binding	0.0151367636305051
GO:0006306	DNA methylation	0.0207554734031237
GO:0006305	DNA alkylation	0.0207554734031237
GO:0006304	DNA modification	0.0210525571751405
GO:0003700	transcription factor activity	0.0210525571751405
GO:0004289	subtilase activity	0.0210525571751405
GO:0003704	specific RNA polymerase II transcription factor activity	0.0211114637320105
GO:0043414	biopolymer methylation	0.0221429353030901
GO:0040029	regulation of gene expression, epigenetic	0.0293102504025579
GO:0032259	methylation	0.0299662068333565
GO:0007275	multicellular organismal development	0.0300828750979383
GO:0046982	protein heterodimerization activity	0.0365019430155593
GO:0003690	double-stranded DNA binding	0.0365019430155593
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	0.0377712194593578
GO:0006730	one-carbon compound metabolic process	0.0377712194593578
GO:0043566	structure-specific DNA binding	0.0377712194593578
GO:0032502	developmental process	0.0377712194593578
GO:0006355	regulation of transcription, DNA-dependent	0.0377712194593578
GO:0006351	transcription, DNA-dependent	0.0377712194593578
GO:0032774	RNA biosynthetic process	0.0377712194593578
GO:0003677	DNA binding	0.0377712194593578
GO:0045449	regulation of transcription	0.0377712194593578
GO:0045892	negative regulation of transcription, DNA-dependent	0.0377712194593578
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0377712194593578
GO:0005667	transcription factor complex	0.0377712194593578
GO:0006350	transcription	0.0377712194593578
GO:0032501	multicellular organismal process	0.0377712194593578
GO:0010468	regulation of gene expression	0.0377712194593578
GO:0031323	regulation of cellular metabolic process	0.0385252847918647
GO:0019222	regulation of metabolic process	0.0404684885098427
GO:0016070	RNA metabolic process	0.0404684885098427
GO:0003702	RNA polymerase II transcription factor activity	0.0417237654697631
GO:0006954	inflammatory response	0.0417237654697631
GO:0016481	negative regulation of transcription	0.0417237654697631
GO:0007610	behavior	0.0417237654697631
GO:0045934	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0440945903855701
GO:0004252	serine-type endopeptidase activity	0.0448697405908615
GO:0008236	serine-type peptidase activity	0.0477218639162913
GO:0017171	serine hydrolase activity	0.0477218639162913
GO:0031324	negative regulation of cellular metabolic process	0.0477218639162913

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	7.85e-41	42
CD14-positive, CD16-negative classical monocyte	7.85e-41	42
myeloid leukocyte	3.21e-34	72
defensive cell	8.09e-34	48
phagocyte	8.09e-34	48
leukocyte	6.28e-30	136
granulocyte monocyte progenitor cell	6.32e-29	67
macrophage dendritic cell progenitor	1.44e-27	61
myeloid lineage restricted progenitor cell	3.09e-26	66
monopoietic cell	1.66e-25	59
monocyte	1.66e-25	59
monoblast	1.66e-25	59
promonocyte	1.66e-25	59
hematopoietic lineage restricted progenitor cell	6.25e-24	120
nongranular leukocyte	6.09e-23	115
hematopoietic stem cell	8.88e-20	168
angioblastic mesenchymal cell	8.88e-20	168
myeloid cell	3.31e-19	108
common myeloid progenitor	3.31e-19	108
hematopoietic oligopotent progenitor cell	6.59e-19	161
hematopoietic multipotent progenitor cell	6.59e-19	161
hematopoietic cell	1.21e-17	177
stuff accumulating cell	1.08e-16	87
intermediate monocyte	1.81e-10	9
CD14-positive, CD16-positive monocyte	1.81e-10	9
connective tissue cell	8.86e-09	361
granulocyte	1.92e-08	8
mesenchymal cell	2.92e-08	354
CD4-positive, alpha-beta T cell	9.09e-08	6

Uber Anatomy

Ontology term	p-value	n
bone marrow	5.43e-25	76
bone element	2.11e-23	82
skeletal element	4.97e-23	90
skeletal system	4.19e-20	100
hematopoietic system	5.14e-20	98
blood island	5.14e-20	98
immune system	1.39e-18	93
hemolymphoid system	1.20e-16	108
connective tissue	5.44e-09	371

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
KAT2A#2648	8	100.58612244898	1.86712808033721e-14	3.16560048023276e-12
POLR2A#5430	49	2.14745317655807	5.40215358511943e-17	1.10410081854459e-14
TAF1#6872	23	1.5691849912682	0.00885441928633549	0.0336075990640206
TAF7#6879	21	4.89988688782453	2.03765091642971e-10	2.10494781464889e-08
ZBTB7A#51341	15	2.25058448200283	0.00162443201781854	0.0101674490895931

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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