Coexpression cluster:C1464

Full id: C1464_Burkitt_myeloma_lymphangiectasia_splenic_b_xeroderma_B

Phase1 CAGE Peaks

Hg19::chr1:154832272..154832279,-	p19@KCNN3
Hg19::chr1:154832291..154832302,-	p14@KCNN3
Hg19::chr1:154832316..154832336,-	p5@KCNN3
Hg19::chr1:154832342..154832360,-	p6@KCNN3
Hg19::chr21:43283391..43283426,-	p4@PRDM15
Hg19::chr4:8437677..8437699,-	p@chr4:8437677..8437699 -

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:0016286	small conductance calcium-activated potassium channel activity	0.0197801226784526
GO:0015269	calcium-activated potassium channel activity	0.0420142001768272
GO:0022839	ion gated channel activity	0.0420142001768272
GO:0005227	calcium activated cation channel activity	0.0420142001768272

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	7.03e-38	24
pro-B cell	7.03e-38	24
lymphocyte	7.30e-22	53
common lymphoid progenitor	7.30e-22	53
nucleate cell	5.76e-21	55
lymphoid lineage restricted progenitor cell	3.37e-19	52
mature B cell	2.16e-14	2
pre-B-II cell	2.16e-14	2
transitional stage B cell	2.16e-14	2
small pre-B-II cell	2.16e-14	2
immature B cell	2.16e-14	2
precursor B cell	6.84e-10	3
nongranular leukocyte	1.76e-08	115
B-1 B cell	3.55e-08	1
antibody secreting cell	6.52e-08	1
plasma cell	6.52e-08	1
plasmablast	6.52e-08	1
hematopoietic lineage restricted progenitor cell	8.15e-07	120
leukocyte	9.08e-07	136

Uber Anatomy

Ontology term	p-value	n
spleen	1.02e-09	3
gastrointestinal system mesentery	1.02e-09	3
stomach region	1.02e-09	3
mesentery	1.02e-09	3
gastrointestinal system serosa	1.02e-09	3
mesentery of stomach	1.02e-09	3
gut mesentery	1.02e-09	3
dorsal mesentery	1.02e-09	3
dorsal mesogastrium	1.02e-09	3
peritoneal cavity	1.02e-09	3
spleen primordium	1.02e-09	3
adult organism	2.03e-09	114
tonsil	6.97e-08	1
mucosa-associated lymphoid tissue	6.97e-08	1
lymphoid tissue	6.97e-08	1
tonsillar ring	6.97e-08	1
lymph node	8.51e-08	1
submandibular gland	9.10e-08	1
submandibular gland primordium	9.10e-08	1
vermiform appendix	1.26e-07	1
caecum	1.26e-07	1
midgut	1.26e-07	1
dura mater	1.64e-07	1
future meninx	1.64e-07	1
ectomeninx	1.64e-07	1
future dura mater	1.64e-07	1

Disease

Ontology term	p-value	n
lymphoma	7.50e-24	10
hematologic cancer	3.36e-09	51
immune system cancer	3.36e-09	51
bone marrow cancer	3.10e-08	1
myeloma	3.10e-08	1
lymphatic system cancer	3.55e-08	1
lymphosarcoma	3.55e-08	1
genetic disease	4.35e-08	1
monogenic disease	4.35e-08	1
xeroderma pigmentosum	4.35e-08	1
anemia	7.45e-08	1
acute leukemia	9.72e-08	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
BATF#10538	4	16.2385345282024	3.98325915717398e-05	0.000742605503598881
EBF1#1879	4	5.93764456437934	0.00197515363642171	0.0114908127581466
MEF2A#4205	4	12.495487273096	0.000111333627719979	0.00154642542165805
NFKB1#4790	5	4.5733861868282	0.0010219625937113	0.0072464356931641
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.0380404908246201
POU2F2#5452	5	7.58843671478544	8.70203885493171e-05	0.00129077153241047
TAF1#6872	5	2.78587190478774	0.0107863634029041	0.039796411044473

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.