Coexpression cluster:C239

Full id: C239_CD4_lymphangiectasia_CD8_NK_mycosis_Renal_hairy

Phase1 CAGE Peaks

Hg19::chr11:133815219..133815230,-	p@chr11:133815219..133815230 -
Hg19::chr11:133815282..133815297,-	p@chr11:133815282..133815297 -
Hg19::chr11:67207655..67207691,-	p2@CORO1B
Hg19::chr11:67207696..67207709,-	p5@CORO1B
Hg19::chr13:113840599..113840624,-	p5@PCID2
Hg19::chr13:99121398..99121404,-	p@chr13:99121398..99121404 -
Hg19::chr14:100533978..100533994,+	p@chr14:100533978..100533994 +
Hg19::chr14:23008000..23008038,+	p1@TRAJ6
Hg19::chr14:91708423..91708436,-	p@chr14:91708423..91708436 -
Hg19::chr14:91709954..91709967,-	p@chr14:91709954..91709967 -
Hg19::chr14:91709994..91710001,-	p@chr14:91709994..91710001 -
Hg19::chr14:91710043..91710078,-	p@chr14:91710043..91710078 -
Hg19::chr14:91710858..91710893,-	p2@GPR68
Hg19::chr14:91710916..91710929,-	p4@GPR68
Hg19::chr16:30194118..30194165,+	p@chr16:30194118..30194165 +
Hg19::chr16:30197413..30197437,+	p2@CORO1A
Hg19::chr16:3115626..3115648,+	p1@IL32
Hg19::chr16:3117545..3117588,+	p8@IL32
Hg19::chr16:3117688..3117736,+	p7@IL32
Hg19::chr16:3118178..3118198,+	p6@IL32
Hg19::chr16:3118203..3118241,-	p@chr16:3118203..3118241 -
Hg19::chr16:3119238..3119248,+	p@chr16:3119238..3119248 +
Hg19::chr16:3119304..3119330,-	p@chr16:3119304..3119330 -
Hg19::chr16:31271243..31271270,+	p3@ITGAM
Hg19::chr17:17082907..17082918,+	p@chr17:17082907..17082918 +
Hg19::chr17:4844362..4844368,+	p@chr17:4844362..4844368 +
Hg19::chr17:78865999..78866032,-	p@chr17:78865999..78866032 -
Hg19::chr18:60867334..60867342,-	p@chr18:60867334..60867342 -
Hg19::chr18:67614645..67614674,-	p2@CD226
Hg19::chr19:14143080..14143099,+	p@chr19:14143080..14143099 +
Hg19::chr19:14143101..14143121,+	p@chr19:14143101..14143121 +
Hg19::chr19:30205532..30205579,-	p@chr19:30205532..30205579 -
Hg19::chr19:41808608..41808626,+	p33@HNRNPUL1
Hg19::chr19:41808637..41808666,+	p25@HNRNPUL1
Hg19::chr22:39493207..39493223,+	p3@APOBEC3H
Hg19::chr22:39493235..39493261,+	p2@APOBEC3H
Hg19::chr22:39493268..39493317,+	p1@APOBEC3H
Hg19::chr22:50908325..50908344,-	p@chr22:50908325..50908344 -
Hg19::chr22:50908348..50908373,-	p@chr22:50908348..50908373 -
Hg19::chr2:26017511..26017565,-	p@chr2:26017511..26017565 -
Hg19::chr3:150920950..150920962,-	p2@GPR171
Hg19::chr3:150920988..150921009,-	p1@GPR171
Hg19::chr3:151961403..151961428,+	p7@MBNL1
Hg19::chr3:48520793..48520806,-	p20@SHISA5
Hg19::chr3:48520822..48520833,-	p17@SHISA5
Hg19::chr3:48520846..48520874,-	p12@SHISA5
Hg19::chr3:48520879..48520892,-	p18@SHISA5
Hg19::chr4:90228185..90228196,-	p@chr4:90228185..90228196 -
Hg19::chr7:150691829..150691867,+	p@chr7:150691829..150691867 +
Hg19::chr8:8777580..8777590,+	p@chr8:8777580..8777590 +
Hg19::chr8:8777601..8777633,+	p@chr8:8777601..8777633 +
Hg19::chr9:132631644..132631655,+	p@chr9:132631644..132631655 +
Hg19::chr9:139001620..139001639,+	p@chr9:139001620..139001639 +
Hg19::chr9:139001642..139001662,+	p@chr9:139001642..139001662 +
Hg19::chr9:139869497..139869510,+	p12@PTGDS
Hg19::chr9:139869524..139869539,+	p7@PTGDS
Hg19::chr9:34647078..34647100,+	p4@GALT

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:0022410	circadian sleep/wake cycle process	0.0164252914164606
GO:0045187	regulation of circadian sleep/wake cycle, sleep	0.0164252914164606
GO:0042749	regulation of circadian sleep/wake cycle	0.0164252914164606
GO:0050802	circadian sleep/wake cycle, sleep	0.0164252914164606
GO:0004667	prostaglandin-D synthase activity	0.0197039680044342
GO:0042745	circadian sleep/wake cycle	0.0197039680044342
GO:0048512	circadian behavior	0.0197039680044342
GO:0008108	UDP-glucose:hexose-1-phosphate uridylyltransferase activity	0.0197039680044342
GO:0042752	regulation of circadian rhythm	0.0197039680044342
GO:0007622	rhythmic behavior	0.0197039680044342
GO:0030431	sleep	0.0298448315359082
GO:0001948	glycoprotein binding	0.032824000262067
GO:0046457	prostanoid biosynthetic process	0.0468610756854441
GO:0001516	prostaglandin biosynthetic process	0.0468610756854441
GO:0022610	biological adhesion	0.0475287231674542
GO:0007155	cell adhesion	0.0475287231674542

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	7.67e-28	140
hematopoietic cell	1.81e-26	182
hematopoietic stem cell	3.24e-26	172
angioblastic mesenchymal cell	3.24e-26	172
hematopoietic oligopotent progenitor cell	1.88e-24	165
hematopoietic multipotent progenitor cell	1.88e-24	165
hematopoietic lineage restricted progenitor cell	1.19e-20	124
nongranular leukocyte	1.28e-20	119
lymphocyte	3.26e-18	53
common lymphoid progenitor	3.26e-18	53
lymphoid lineage restricted progenitor cell	4.77e-18	52
T cell	7.08e-16	25
pro-T cell	7.08e-16	25
mature alpha-beta T cell	1.00e-12	18
alpha-beta T cell	1.00e-12	18
immature T cell	1.00e-12	18
mature T cell	1.00e-12	18
immature alpha-beta T cell	1.00e-12	18
myeloid cell	5.00e-09	112
common myeloid progenitor	5.00e-09	112
CD8-positive, alpha-beta T cell	1.82e-08	11
myeloid leukocyte	8.62e-08	76

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	1.72e-11	112
lateral plate mesoderm	8.53e-10	216
hematopoietic system	1.44e-09	102
blood island	1.44e-09	102
blood	1.11e-08	15
haemolymphatic fluid	1.11e-08	15
organism substance	1.11e-08	15
immune system	3.55e-08	115

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
BATF#10538	7	2.99130899203729	0.00858650434384103	0.0327131626296434
BCL11A#53335	10	4.97709738659773	2.78366640123425e-05	0.000588389668647042
EBF1#1879	16	2.50006086921235	0.000396266241670653	0.00387433533175822
EGR1#1958	19	1.66272636493671	0.0129223875758101	0.046457873873667
MEF2A#4205	10	3.28828612449896	0.000798642331374319	0.00616887851833463
TCF12#6938	12	2.23883471624977	0.00604571411816783	0.0270897690401291

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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