Coexpression cluster:C189

Full id: C189_b_splenic_tonsil_CD19_lymph_appendix_spleen

Phase1 CAGE Peaks

Hg19::chr10:267221..267230,+	p@chr10:267221..267230 +
Hg19::chr10:37455757..37455787,+	p@chr10:37455757..37455787 +
Hg19::chr10:79970622..79970624,+	p@chr10:79970622..79970624 +
Hg19::chr12:123416933..123416944,-	p@chr12:123416933..123416944 -
Hg19::chr12:68835921..68835926,-	p2@ENST00000546086
Hg19::chr13:100375524..100375531,+	p@chr13:100375524..100375531 +
Hg19::chr13:100377188..100377194,+	p@chr13:100377188..100377194 +
Hg19::chr13:100377368..100377389,+	p@chr13:100377368..100377389 +
Hg19::chr14:101036119..101036130,-	p20@BEGAIN
Hg19::chr14:106161355..106161362,-	p@chr14:106161355..106161362 -
Hg19::chr14:106327961..106327980,-	p2@DQ431661
Hg19::chr14:106351913..106351948,-	p1@IGHD3-22
Hg19::chr14:106877761..106877767,-	p1@AF460681 p1@AF460715 p1@AF460721 p1@AF460739 p1@AF460749 p1@AF460752 p1@AF460755 p1@AF460757 p1@AF460765 p1@AF460795 p1@AF460799 p1@AF460809 p1@AF460810 p1@AF460812 p1@AF460813 p1@AF460814 p1@AF460816 p1@AF460819 p1@AF460820 p1@AF460831 p1@AF460842
Hg19::chr14:106878083..106878099,-	p1@IGHV4-39
Hg19::chr14:75981521..75981530,+	p@chr14:75981521..75981530 +
Hg19::chr15:45028719..45028738,+	p6@TRIM69
Hg19::chr15:45671019..45671033,-	p7@GATM
Hg19::chr15:52404161..52404166,+	p@chr15:52404161..52404166 +
Hg19::chr15:52404181..52404187,+	p@chr15:52404181..52404187 +
Hg19::chr15:57506462..57506496,+	p36@TCF12
Hg19::chr15:78177670..78177678,+	p@chr15:78177670..78177678 +
Hg19::chr16:4975293..4975294,+	p@chr16:4975293..4975294 +
Hg19::chr16:53412335..53412342,+	p@chr16:53412335..53412342 +
Hg19::chr16:53412381..53412387,+	p@chr16:53412381..53412387 +
Hg19::chr16:76613424..76613434,+	p@chr16:76613424..76613434 +
Hg19::chr16:76613646..76613671,+	p@chr16:76613646..76613671 +
Hg19::chr17:48994960..48994968,+	p@chr17:48994960..48994968 +
Hg19::chr17:55334804..55334824,+	p@chr17:55334804..55334824 +
Hg19::chr17:70420105..70420110,+	p@chr17:70420105..70420110 +
Hg19::chr17:70420494..70420517,+	p@chr17:70420494..70420517 +
Hg19::chr17:78371475..78371480,+	p@chr17:78371475..78371480 +
Hg19::chr17:80328570..80328583,+	p@chr17:80328570..80328583 +
Hg19::chr17:80328744..80328754,+	p@chr17:80328744..80328754 +
Hg19::chr18:74240756..74240772,+	p2@LOC284276
Hg19::chr1:173379658..173379666,-	p@chr1:173379658..173379666 -
Hg19::chr1:207105167..207105184,-	p5@PIGR
Hg19::chr1:207105188..207105210,-	p3@PIGR
Hg19::chr1:207105216..207105252,-	p4@PIGR
Hg19::chr1:22502943..22502969,+	p@chr1:22502943..22502969 +
Hg19::chr1:25799245..25799271,+	p@chr1:25799245..25799271 +
Hg19::chr1:31896395..31896404,+	p@chr1:31896395..31896404 +
Hg19::chr1:31896446..31896458,+	p@chr1:31896446..31896458 +
Hg19::chr21:43704482..43704491,+	p9@ABCG1
Hg19::chr21:43706764..43706775,+	p@chr21:43706764..43706775 +
Hg19::chr22:22930643..22930649,+	p1@IGLV2-33
Hg19::chr22:23040132..23040138,+	p1@IGLV2-23
Hg19::chr22:23040389..23040405,+	p1@ENST00000385095
Hg19::chr22:23040696..23040701,+	p1@AJ408281
Hg19::chr22:34616800..34616810,+	p@chr22:34616800..34616810 +
Hg19::chr22:34653635..34653640,+	p@chr22:34653635..34653640 +
Hg19::chr22:37484895..37484906,-	p@chr22:37484895..37484906 -
Hg19::chr22:37484928..37484953,-	p@chr22:37484928..37484953 -
Hg19::chr2:111538269..111538279,+	p@chr2:111538269..111538279 +
Hg19::chr2:160779191..160779202,-	p@chr2:160779191..160779202 -
Hg19::chr2:170998413..170998419,-	p@chr2:170998413..170998419 -
Hg19::chr2:170998667..170998714,+	p@chr2:170998667..170998714 +
Hg19::chr2:54810455..54810472,-	p@chr2:54810455..54810472 -
Hg19::chr3:108014582..108014611,+	p@chr3:108014582..108014611 +
Hg19::chr3:118484990..118484992,-	p@chr3:118484990..118484992 -
Hg19::chr3:119299336..119299359,+	p12@ADPRH
Hg19::chr3:166801172..166801180,-	p@chr3:166801172..166801180 -
Hg19::chr3:171076173..171076182,-	p@chr3:171076173..171076182 -
Hg19::chr3:31431437..31431441,+	p@chr3:31431437..31431441 +
Hg19::chr3:61896640..61896646,+	p@chr3:61896640..61896646 +
Hg19::chr3:96533659..96533667,+	p11@EPHA6
Hg19::chr3:96533671..96533680,+	p10@EPHA6
Hg19::chr3:96533682..96533687,+	p13@EPHA6
Hg19::chr5:169494477..169494513,+	p@chr5:169494477..169494513 +
Hg19::chr5:26877471..26877484,+	p@chr5:26877471..26877484 +
Hg19::chr5:26877490..26877500,+	p@chr5:26877490..26877500 +
Hg19::chr5:26877504..26877517,+	p@chr5:26877504..26877517 +
Hg19::chr5:26877541..26877549,+	p@chr5:26877541..26877549 +
Hg19::chr5:63461151..63461183,+	p4@RNF180
Hg19::chr5:63461191..63461205,+	p5@RNF180
Hg19::chr5:80255013..80255020,+	p@chr5:80255013..80255020 +
Hg19::chr6:113971101..113971111,-	p@chr6:113971101..113971111 -
Hg19::chr6:113971125..113971136,-	p@chr6:113971125..113971136 -
Hg19::chr6:149353791..149353807,-	p3@ENST00000433442
Hg19::chr6:149353870..149353873,-	p8@ENST00000433442
Hg19::chr7:30803690..30803693,-	p@chr7:30803690..30803693 -
Hg19::chr8:72753886..72753911,+	p@chr8:72753886..72753911 +
Hg19::chr8:87719795..87719814,+	p1@ENST00000519041
Hg19::chr8:87719833..87719844,+	p2@ENST00000519041
Hg19::chr9:128397835..128397850,-	p@chr9:128397835..128397850 -
Hg19::chr9:5580708..5580720,-	p@chr9:5580708..5580720 -
Hg19::chrX:114701086..114701089,+	p@chrX:114701086..114701089 +
Hg19::chrX:11682523..11682558,-	p26@ARHGAP6
Hg19::chrX:48792308..48792316,-	p20@OTUD5
Hg19::chrX:48792324..48792350,-	p14@OTUD5

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:0009720	detection of hormone stimulus	0.0238912751849613
GO:0019534	toxin transporter activity	0.0238912751849613
GO:0015068	glycine amidinotransferase activity	0.0238912751849613
GO:0015067	amidinotransferase activity	0.0238912751849613
GO:0006600	creatine metabolic process	0.0238912751849613
GO:0033700	phospholipid efflux	0.0238912751849613
GO:0006601	creatine biosynthetic process	0.0238912751849613
GO:0009726	detection of endogenous stimulus	0.0238912751849613
GO:0055091	phospholipid homeostasis	0.0238912751849613
GO:0006599	phosphagen metabolic process	0.0243383958235739
GO:0042396	phosphagen biosynthetic process	0.0243383958235739
GO:0051725	protein amino acid de-ADP-ribosylation	0.0243383958235739
GO:0003875	ADP-ribosylarginine hydrolase activity	0.0243383958235739
GO:0032365	intracellular lipid transport	0.0243383958235739
GO:0032366	intracellular sterol transport	0.0243383958235739
GO:0032367	intracellular cholesterol transport	0.0243383958235739
GO:0008565	protein transporter activity	0.0243383958235739
GO:0005515	protein binding	0.0243383958235739
GO:0033344	cholesterol efflux	0.0339267824801768
GO:0044446	intracellular organelle part	0.0341777671594579
GO:0044422	organelle part	0.0341777671594579
GO:0005885	Arp2/3 protein complex	0.0341777671594579
GO:0042987	amyloid precursor protein catabolic process	0.0373554338073769
GO:0043531	ADP binding	0.0402667158160958
GO:0017127	cholesterol transporter activity	0.0472295975431517

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	1.41e-19	140
nongranular leukocyte	1.56e-17	119
lymphocyte	1.75e-16	53
common lymphoid progenitor	1.75e-16	53
lymphocyte of B lineage	2.88e-16	24
pro-B cell	2.88e-16	24
lymphoid lineage restricted progenitor cell	6.63e-16	52
hematopoietic lineage restricted progenitor cell	9.53e-15	124
hematopoietic stem cell	3.40e-12	172
angioblastic mesenchymal cell	3.40e-12	172
hematopoietic cell	1.40e-11	182
hematopoietic oligopotent progenitor cell	5.68e-11	165
hematopoietic multipotent progenitor cell	5.68e-11	165
B cell	3.16e-10	14

Uber Anatomy

Ontology term	p-value	n
adult organism	1.91e-33	115
blood	3.56e-09	15
haemolymphatic fluid	3.56e-09	15
organism substance	3.56e-09	15
hematopoietic system	4.01e-08	102
blood island	4.01e-08	102
central nervous system	6.45e-08	82
neural tube	7.77e-08	57
neural rod	7.77e-08	57
future spinal cord	7.77e-08	57
neural keel	7.77e-08	57
anterior neural tube	3.45e-07	42
hemolymphoid system	7.97e-07	112
regional part of forebrain	8.67e-07	41
forebrain	8.67e-07	41
future forebrain	8.67e-07	41

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)
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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
BATF#10538	10	2.73683166205659	0.00357413267895909	0.0181062690559667
EBF1#1879	20	2.00145322394809	0.00180493635857967	0.010918375230449

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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