Coexpression cluster:C1120

Full id: C1120_adult_hairy_mycosis_B_plasma_CD4_cord

Phase1 CAGE Peaks

Hg19::chr10:69513561..69513563,-	p@chr10:69513561..69513563 -
Hg19::chr5:95309942..95309984,+	p@chr5:95309942..95309984 +
Hg19::chr7:142494920..142494955,+	p1@TRBJ2-6
Hg19::chr8:102980193..102980205,-	p@chr8:102980193..102980205 -
Hg19::chr8:102987548..102987571,-	p4@NCALD
Hg19::chr8:102987581..102987599,-	p5@NCALD
Hg19::chr8:103108677..103108680,-	p@chr8:103108677..103108680 -

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:0030276	clathrin binding	0.00647592134699164
GO:0030130	clathrin coat of trans-Golgi network vesicle	0.00647592134699164
GO:0012510	trans-Golgi network transport vesicle membrane	0.00647592134699164
GO:0030125	clathrin vesicle coat	0.00647592134699164
GO:0030665	clathrin coated vesicle membrane	0.00647592134699164
GO:0030140	trans-Golgi network transport vesicle	0.00647592134699164
GO:0030658	transport vesicle membrane	0.00647592134699164
GO:0030660	Golgi-associated vesicle membrane	0.00647592134699164
GO:0030120	vesicle coat	0.0079792602311147
GO:0030662	coated vesicle membrane	0.0079792602311147
GO:0030133	transport vesicle	0.0079792602311147
GO:0030118	clathrin coat	0.0079792602311147
GO:0015631	tubulin binding	0.0079792602311147
GO:0005798	Golgi-associated vesicle	0.0079792602311147
GO:0030659	cytoplasmic vesicle membrane	0.00939008595313787
GO:0044433	cytoplasmic vesicle part	0.00939008595313787
GO:0012506	vesicle membrane	0.00939008595313787
GO:0030136	clathrin-coated vesicle	0.00939008595313787
GO:0030117	membrane coat	0.00939008595313787
GO:0048475	coated membrane	0.00939008595313787
GO:0030135	coated vesicle	0.0113328623572354
GO:0016023	cytoplasmic membrane-bound vesicle	0.0246219926213745
GO:0031988	membrane-bound vesicle	0.0246219926213745
GO:0000139	Golgi membrane	0.0246219926213745
GO:0044431	Golgi apparatus part	0.0253254781248423
GO:0031410	cytoplasmic vesicle	0.0253254781248423
GO:0031982	vesicle	0.0253254781248423
GO:0003779	actin binding	0.0253254781248423
GO:0005829	cytosol	0.031648454324814
GO:0008092	cytoskeletal protein binding	0.031648454324814
GO:0016192	vesicle-mediated transport	0.031648454324814
GO:0005794	Golgi apparatus	0.0351622291887437

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	1.93e-29	24
pro-B cell	1.93e-29	24
lymphoid lineage restricted progenitor cell	1.77e-23	52
lymphocyte	5.32e-23	53
common lymphoid progenitor	5.32e-23	53
nucleate cell	4.28e-22	55
circulating cell	2.39e-14	6
antibody secreting cell	8.14e-11	1
plasma cell	8.14e-11	1
plasmablast	8.14e-11	1
nongranular leukocyte	1.88e-09	115
hematopoietic cell	4.28e-09	177
hematopoietic lineage restricted progenitor cell	5.58e-09	120
leukocyte	1.06e-07	136

Uber Anatomy

Ontology term	p-value	n
hemopoietic organ	6.77e-12	7
immune organ	6.77e-12	7
vermiform appendix	2.08e-10	1
caecum	2.08e-10	1
midgut	2.08e-10	1
tonsil	2.50e-10	1
mucosa-associated lymphoid tissue	2.50e-10	1
lymphoid tissue	2.50e-10	1
tonsillar ring	2.50e-10	1
thymus	1.12e-09	4
hemolymphoid system gland	1.12e-09	4
thymic region	1.12e-09	4
pharyngeal gland	1.12e-09	4
thymus primordium	1.12e-09	4
umbilical cord	8.05e-09	10
blastocyst	8.05e-09	10
blastula	8.05e-09	10
bilaminar disc	8.05e-09	10
inner cell mass	8.05e-09	10
cleaving embryo	8.05e-09	10
connecting stalk	8.05e-09	10
inner cell mass derived epiblast	8.05e-09	10
extraembryonic mesoderm	8.05e-09	10
chordate pharynx	1.69e-08	10
pharyngeal region of foregut	1.69e-08	10
pharynx	9.03e-08	11
pharyngeal epithelium	9.81e-07	6

Disease

Ontology term	p-value	n
lymphoma	1.45e-43	10
non-Hodgkin lymphoma	7.40e-11	1
cutaneous T cell lymphoma	7.40e-11	1
mycosis fungoides	7.40e-11	1
hematologic cancer	1.97e-10	51
immune system cancer	1.97e-10	51
anemia	3.61e-10	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
POU2F2#5452	4	5.20349946156716	0.00386671431017981	0.0190605454212899

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.