Coexpression cluster:C442

Full id: C442_diffuse_xeroderma_lymphoma_Burkitt_plasma_b_lymphangiectasia

Phase1 CAGE Peaks

Hg19::chr11:111224162..111224190,-	p@chr11:111224162..111224190 -
Hg19::chr11:111224819..111224845,+	p2@CU689419
Hg19::chr11:111224843..111224854,-	p@chr11:111224843..111224854 -
Hg19::chr11:111224975..111224995,-	p@chr11:111224975..111224995 -
Hg19::chr11:111225012..111225024,-	p@chr11:111225012..111225024 -
Hg19::chr11:111225030..111225046,-	p@chr11:111225030..111225046 -
Hg19::chr11:111225132..111225169,-	p@chr11:111225132..111225169 -
Hg19::chr11:111225158..111225201,+	p1@CU689419
Hg19::chr11:111225198..111225226,-	p@chr11:111225198..111225226 -
Hg19::chr11:111225243..111225260,-	p@chr11:111225243..111225260 -
Hg19::chr11:111228213..111228235,-	p@chr11:111228213..111228235 -
Hg19::chr11:111228281..111228290,-	p@chr11:111228281..111228290 -
Hg19::chr11:111228348..111228370,-	p@chr11:111228348..111228370 -
Hg19::chr11:111228555..111228566,-	p@chr11:111228555..111228566 -
Hg19::chr11:111249993..111250006,-	p1@POU2AF1
Hg19::chr12:6554021..6554040,+	p4@CD27
Hg19::chr19:19258534..19258541,-	p@chr19:19258534..19258541 -
Hg19::chr22:39843178..39843224,+	p@chr22:39843178..39843224 +
Hg19::chr22:39843234..39843241,+	p@chr22:39843234..39843241 +
Hg19::chr5:133880112..133880133,+	p20@PHF15
Hg19::chr6:107078354..107078388,-	p4@RTN4IP1
Hg19::chr9:37034469..37034474,-	p1@PAX5

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:0006959	humoral immune response	0.00861922938102902
GO:0007283	spermatogenesis	0.0141234610606639
GO:0048232	male gamete generation	0.0141234610606639
GO:0006955	immune response	0.0141234610606639
GO:0045579	positive regulation of B cell differentiation	0.0141234610606639
GO:0008588	release of cytoplasmic sequestered NF-kappaB	0.0141234610606639
GO:0007276	gamete generation	0.0141234610606639
GO:0002376	immune system process	0.0141234610606639
GO:0019953	sexual reproduction	0.0141234610606639
GO:0043027	caspase inhibitor activity	0.0141234610606639
GO:0042346	positive regulation of NF-kappaB import into nucleus	0.0141234610606639
GO:0045621	positive regulation of lymphocyte differentiation	0.0141234610606639
GO:0042993	positive regulation of transcription factor import into nucleus	0.0141234610606639
GO:0045577	regulation of B cell differentiation	0.0141234610606639
GO:0042307	positive regulation of protein import into nucleus	0.0141234610606639
GO:0046824	positive regulation of nucleocytoplasmic transport	0.0165489821573171
GO:0051222	positive regulation of protein transport	0.0167212129148552
GO:0042345	regulation of NF-kappaB import into nucleus	0.0167212129148552
GO:0042348	NF-kappaB import into nucleus	0.0167212129148552
GO:0046330	positive regulation of JNK cascade	0.0172079018049975
GO:0045619	regulation of lymphocyte differentiation	0.0201668720331968
GO:0050871	positive regulation of B cell activation	0.0207897414522421
GO:0046328	regulation of JNK cascade	0.0207897414522421
GO:0043028	caspase regulator activity	0.0207897414522421
GO:0042990	regulation of transcription factor import into nucleus	0.0207897414522421
GO:0042991	transcription factor import into nucleus	0.0207897414522421
GO:0042306	regulation of protein import into nucleus	0.0207897414522421
GO:0033157	regulation of intracellular protein transport	0.0207897414522421
GO:0006366	transcription from RNA polymerase II promoter	0.0211804672829906
GO:0050864	regulation of B cell activation	0.0213346757061976
GO:0032386	regulation of intracellular transport	0.0213346757061976
GO:0051223	regulation of protein transport	0.0225592436426157
GO:0046822	regulation of nucleocytoplasmic transport	0.0225592436426157
GO:0030183	B cell differentiation	0.0225592436426157
GO:0051050	positive regulation of transport	0.0287005938275852
GO:0051251	positive regulation of lymphocyte activation	0.0361440743964373
GO:0016064	immunoglobulin mediated immune response	0.0361440743964373
GO:0019724	B cell mediated immunity	0.0361440743964373
GO:0042113	B cell activation	0.0412907208792365
GO:0030098	lymphocyte differentiation	0.0418421950910473
GO:0007254	JNK cascade	0.0418421950910473
GO:0031098	stress-activated protein kinase signaling pathway	0.0426500390204998
GO:0048513	organ development	0.0426500390204998
GO:0002449	lymphocyte mediated immunity	0.0426500390204998
GO:0002250	adaptive immune response	0.0426500390204998
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0426500390204998
GO:0051249	regulation of lymphocyte activation	0.0426500390204998
GO:0002443	leukocyte mediated immunity	0.0428554367391758
GO:0050865	regulation of cell activation	0.0430521979591859
GO:0002521	leukocyte differentiation	0.0474371112883045
GO:0006606	protein import into nucleus	0.0495899158326127
GO:0051170	nuclear import	0.049643673186528

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	1.51e-88	24
pro-B cell	1.51e-88	24
B cell	7.87e-48	14
lymphocyte	7.00e-44	53
common lymphoid progenitor	7.00e-44	53
nucleate cell	4.70e-42	55
lymphoid lineage restricted progenitor cell	4.58e-41	52
nongranular leukocyte	1.57e-21	115
leukocyte	3.47e-17	136
hematopoietic lineage restricted progenitor cell	3.10e-14	120
precursor B cell	9.69e-14	3
hematopoietic stem cell	1.15e-12	168
angioblastic mesenchymal cell	1.15e-12	168
single nucleate cell	3.13e-12	3
mononuclear cell	3.13e-12	3
hematopoietic cell	1.09e-11	177
hematopoietic oligopotent progenitor cell	3.17e-10	161
hematopoietic multipotent progenitor cell	3.17e-10	161
mature B cell	4.85e-10	2
pre-B-II cell	4.85e-10	2
transitional stage B cell	4.85e-10	2
small pre-B-II cell	4.85e-10	2
immature B cell	4.85e-10	2

Uber Anatomy

Ontology term	p-value	n
hemopoietic organ	4.71e-14	7
immune organ	4.71e-14	7
spleen	4.91e-13	3
gastrointestinal system mesentery	4.91e-13	3
stomach region	4.91e-13	3
mesentery	4.91e-13	3
gastrointestinal system serosa	4.91e-13	3
mesentery of stomach	4.91e-13	3
gut mesentery	4.91e-13	3
dorsal mesentery	4.91e-13	3
dorsal mesogastrium	4.91e-13	3
peritoneal cavity	4.91e-13	3
spleen primordium	4.91e-13	3

Disease

Ontology term	p-value	n
lymphoma	2.36e-15	10

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
POLR2A#5430	17	1.65939563643124	0.00337440114494736	0.0172357353732654

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.