Coexpression cluster:C359

Full id: C359_xeroderma_tonsil_acute_colon_lymph_trachea_bladder

Phase1 CAGE Peaks

Hg19::chr11:131056606..131056628,-	p@chr11:131056606..131056628 -
Hg19::chr11:32154200..32154208,+	p1@ENST00000525133
Hg19::chr11:33676379..33676397,+	p@chr11:33676379..33676397 +
Hg19::chr11:57182176..57182224,-	p@chr11:57182176..57182224 -
Hg19::chr11:77150035..77150044,-	p@chr11:77150035..77150044 -
Hg19::chr14:106329430..106329463,-	p1@uc001yrw.1 p1@uc001ysj.2 p1@uc001ysk.1 p1@uc001ysl.1
Hg19::chr14:107170409..107170434,-	p1@IGHV1-69
Hg19::chr14:75802600..75802617,+	p@chr14:75802600..75802617 +
Hg19::chr14:75802635..75802649,+	p@chr14:75802635..75802649 +
Hg19::chr15:55611565..55611576,+	p7@PIGB
Hg19::chr17:76130076..76130100,-	p@chr17:76130076..76130100 -
Hg19::chr17:9955844..9955857,-	p@chr17:9955844..9955857 -
Hg19::chr17:9955874..9955881,-	p@chr17:9955874..9955881 -
Hg19::chr18:56203145..56203154,+	p@chr18:56203145..56203154 +
Hg19::chr18:67613122..67613129,-	p@chr18:67613122..67613129 -
Hg19::chr19:7766976..7766982,-	p9@FCER2
Hg19::chr1:101837029..101837058,+	p@chr1:101837029..101837058 +
Hg19::chr1:101914223..101914228,-	p@chr1:101914223..101914228 -
Hg19::chr1:111682499..111682513,+	p5@CEPT1
Hg19::chr1:111772329..111772341,+	p7@CHI3L2
Hg19::chr1:111772350..111772370,+	p3@CHI3L2
Hg19::chr1:111772381..111772415,+	p2@CHI3L2
Hg19::chr1:111772435..111772463,+	p4@CHI3L2
Hg19::chr1:152880744..152880747,+	p3@IVL
Hg19::chr1:152880760..152880771,+	p2@IVL
Hg19::chr22:23055620..23055631,+	p1@DQ234400
Hg19::chr22:23055632..23055638,+	p3@DQ234400
Hg19::chr22:26346329..26346352,+	p@chr22:26346329..26346352 +
Hg19::chr4:5364767..5364769,+	p@chr4:5364767..5364769 +
Hg19::chr7:55583740..55583751,-	p5@VOPP1
Hg19::chr7:70241758..70241770,+	p47@AUTS2

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:0008654	phospholipid biosynthetic process	0.010737464781943
GO:0046467	membrane lipid biosynthetic process	0.010737464781943
GO:0018153	isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine	0.010737464781943
GO:0018262	isopeptide cross-linking	0.010737464781943
GO:0018199	peptidyl-glutamine modification	0.010737464781943
GO:0004307	ethanolaminephosphotransferase activity	0.0111736804937354
GO:0004142	diacylglycerol cholinephosphotransferase activity	0.0111736804937354
GO:0006644	phospholipid metabolic process	0.0111736804937354
GO:0019863	IgE binding	0.0142568348656904
GO:0006643	membrane lipid metabolic process	0.0142568348656904
GO:0010224	response to UV-B	0.0146376878124516
GO:0008610	lipid biosynthetic process	0.0165118839613148
GO:0017169	CDP-alcohol phosphatidyltransferase activity	0.0165118839613148
GO:0018205	peptidyl-lysine modification	0.0172477522886803
GO:0006032	chitin catabolic process	0.0186546222107435
GO:0006046	N-acetylglucosamine catabolic process	0.0186546222107435
GO:0005789	endoplasmic reticulum membrane	0.0186546222107435
GO:0006043	glucosamine catabolic process	0.0186546222107435
GO:0046348	amino sugar catabolic process	0.0186546222107435
GO:0006030	chitin metabolic process	0.0186546222107435
GO:0004568	chitinase activity	0.0186546222107435
GO:0042175	nuclear envelope-endoplasmic reticulum network	0.0186546222107435
GO:0019865	immunoglobulin binding	0.0186546222107435
GO:0044432	endoplasmic reticulum part	0.0208492312452853
GO:0044247	cellular polysaccharide catabolic process	0.0208492312452853
GO:0000272	polysaccharide catabolic process	0.0208492312452853
GO:0016780	phosphotransferase activity, for other substituted phosphate groups	0.0208492312452853
GO:0001533	cornified envelope	0.0210604286585
GO:0018149	peptide cross-linking	0.0240242630131579
GO:0000030	mannosyltransferase activity	0.0241148894453259
GO:0006506	GPI anchor biosynthetic process	0.0250619670405395
GO:0030216	keratinocyte differentiation	0.0251141318157448
GO:0006505	GPI anchor metabolic process	0.0251630157626931
GO:0009411	response to UV	0.0253310637807865
GO:0006044	N-acetylglucosamine metabolic process	0.0253310637807865
GO:0046489	phosphoinositide biosynthetic process	0.0253310637807865
GO:0006041	glucosamine metabolic process	0.0253310637807865
GO:0031424	keratinization	0.0267667332897792
GO:0044255	cellular lipid metabolic process	0.0267667332897792
GO:0006040	amino sugar metabolic process	0.0267667332897792
GO:0005178	integrin binding	0.0267667332897792
GO:0046474	glycerophospholipid biosynthetic process	0.0293051626849468
GO:0009913	epidermal cell differentiation	0.0304836773360426
GO:0006497	protein amino acid lipidation	0.0319707530670764
GO:0042158	lipoprotein biosynthetic process	0.0319707530670764
GO:0048730	epidermis morphogenesis	0.0319707530670764
GO:0005783	endoplasmic reticulum	0.0320917655350622
GO:0006629	lipid metabolic process	0.0341520913372628
GO:0048729	tissue morphogenesis	0.0384680295948203
GO:0012505	endomembrane system	0.0384680295948203
GO:0030384	phosphoinositide metabolic process	0.0415056245270081
GO:0009416	response to light stimulus	0.0415056245270081
GO:0042157	lipoprotein metabolic process	0.0415056245270081
GO:0044264	cellular polysaccharide metabolic process	0.0415056245270081
GO:0005976	polysaccharide metabolic process	0.0417151002173427
GO:0030674	protein binding, bridging	0.0433362327013298
GO:0006650	glycerophospholipid metabolic process	0.0456192018890636
GO:0009314	response to radiation	0.0456192018890636
GO:0032403	protein complex binding	0.0456192018890636

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
lymphocyte of B lineage	7.63e-29	24
pro-B cell	7.63e-29	24
antibody secreting cell	6.44e-16	1
plasma cell	6.44e-16	1
plasmablast	6.44e-16	1
lymphoid lineage restricted progenitor cell	4.40e-13	52
lymphocyte	7.94e-13	53
common lymphoid progenitor	7.94e-13	53
nucleate cell	2.42e-12	55
mature B cell	1.29e-08	2
pre-B-II cell	1.29e-08	2
transitional stage B cell	1.29e-08	2
small pre-B-II cell	1.29e-08	2
immature B cell	1.29e-08	2

Uber Anatomy

Ontology term	p-value	n
hemopoietic organ	1.38e-49	7
immune organ	1.38e-49	7
spleen	1.65e-42	3
gastrointestinal system mesentery	1.65e-42	3
stomach region	1.65e-42	3
mesentery	1.65e-42	3
gastrointestinal system serosa	1.65e-42	3
mesentery of stomach	1.65e-42	3
gut mesentery	1.65e-42	3
dorsal mesentery	1.65e-42	3
dorsal mesogastrium	1.65e-42	3
peritoneal cavity	1.65e-42	3
spleen primordium	1.65e-42	3
stomach	2.04e-16	8
food storage organ	2.04e-16	8
tonsil	2.06e-15	1
mucosa-associated lymphoid tissue	2.06e-15	1
lymphoid tissue	2.06e-15	1
tonsillar ring	2.06e-15	1
thymus	7.47e-15	4
hemolymphoid system gland	7.47e-15	4
thymic region	7.47e-15	4
pharyngeal gland	7.47e-15	4
thymus primordium	7.47e-15	4
chordate pharynx	3.58e-13	10
pharyngeal region of foregut	3.58e-13	10
mixed endoderm/mesoderm-derived structure	4.63e-12	29
pharynx	4.96e-12	11
cavity lining	3.73e-11	12
serous membrane	3.73e-11	12
intraembryonic coelom	3.73e-11	12
pharyngeal epithelium	3.19e-10	6
viscus	1.28e-07	18
upper respiratory tract	3.36e-07	19

Disease

Ontology term	p-value	n
genetic disease	5.56e-16	1
monogenic disease	5.56e-16	1
xeroderma pigmentosum	5.56e-16	1

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
BCL11A#53335	7	6.40600599113708	8.40163614903359e-05	0.00126125985017812
BCL3#602	4	4.45769068435333	0.011827171845586	0.0430854930545591
EBF1#1879	15	4.30958073221081	2.89067900838075e-07	1.46340099348656e-05
IRF4#3662	5	3.5345988204426	0.0124519761267021	0.0450723299031865
NFKB1#4790	16	2.83254886410004	2.68068349868494e-05	0.000574293136244423
POU2F2#5452	9	2.6437134361188	0.00489156889195895	0.0228884661069579
TCF12#6938	8	2.74437803927391	0.00666399209259088	0.0283552931414992
ZEB1#6935	6	3.26872877758913	0.00879126381797492	0.0333921589280435

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.