Coexpression cluster:C682

Full id: C682_Burkitt_lymphoma_CD19_appendix_tonsil_spleen_diffuse

Phase1 CAGE Peaks

Hg19::chr11:113848216..113848228,+	p2@HTR3A
Hg19::chr11:64900812..64900834,-	p5@SYVN1
Hg19::chr12:27977018..27977041,-	p@chr12:27977018..27977041 -
Hg19::chr12:32418225..32418236,+	p@chr12:32418225..32418236 +
Hg19::chr15:89191020..89191067,+	p13@ISG20
Hg19::chr1:155953595..155953599,-	p@chr1:155953595..155953599 -
Hg19::chr20:43214306..43214347,-	p@chr20:43214306..43214347 -
Hg19::chr20:57698461..57698483,+	p@chr20:57698461..57698483 +
Hg19::chr22:22398325..22398339,-	p1@PRAMEL
Hg19::chr2:220142973..220142983,-	p26@TUBA4A
Hg19::chr2:65257848..65257867,+	p@chr2:65257848..65257867 +
Hg19::chr2:65257873..65257887,+	p@chr2:65257873..65257887 +

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:0008310	single-stranded DNA specific 3'-5' exodeoxyribonuclease activity	0.0101844084028938
GO:0008859	exoribonuclease II activity	0.0101844084028938
GO:0005232	serotonin-activated cation-selective channel activity	0.0101844084028938
GO:0008297	single-stranded DNA specific exodeoxyribonuclease activity	0.0101844084028938
GO:0008296	3'-5'-exodeoxyribonuclease activity	0.0122207504459862
GO:0000738	DNA catabolic process, exonucleolytic	0.0135780120329791
GO:0016895	exodeoxyribonuclease activity, producing 5'-phosphomonoesters	0.0187936840949419
GO:0004529	exodeoxyribonuclease activity	0.0187936840949419
GO:0043285	biopolymer catabolic process	0.0187936840949419
GO:0030433	ER-associated protein catabolic process	0.0187936840949419
GO:0006515	misfolded or incompletely synthesized protein catabolic process	0.0187936840949419
GO:0044265	cellular macromolecule catabolic process	0.0187936840949419
GO:0000175	3'-5'-exoribonuclease activity	0.0187936840949419
GO:0004993	serotonin receptor activity	0.0189047164366943
GO:0016896	exoribonuclease activity, producing 5'-phosphomonoesters	0.019014415156573
GO:0004532	exoribonuclease activity	0.019014415156573
GO:0016605	PML body	0.019014415156573
GO:0009057	macromolecule catabolic process	0.019014415156573
GO:0016796	exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	0.0234024274421159
GO:0043161	proteasomal ubiquitin-dependent protein catabolic process	0.0234024274421159
GO:0008408	3'-5' exonuclease activity	0.0258852662218033
GO:0044248	cellular catabolic process	0.0258852662218033
GO:0006308	DNA catabolic process	0.0309508886207327
GO:0009056	catabolic process	0.0341070749707598
GO:0006401	RNA catabolic process	0.0374058692672204
GO:0004536	deoxyribonuclease activity	0.0390878569504989
GO:0044446	intracellular organelle part	0.0403333517367145
GO:0044422	organelle part	0.0403333517367145
GO:0008227	amine receptor activity	0.0469240956780526
GO:0004527	exonuclease activity	0.0471621932387917
GO:0005231	excitatory extracellular ligand-gated ion channel activity	0.0471621932387917

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	2.37e-93	24
pro-B cell	2.37e-93	24
B cell	4.93e-69	14
lymphocyte	2.98e-44	53
common lymphoid progenitor	2.98e-44	53
nucleate cell	1.76e-42	55
lymphoid lineage restricted progenitor cell	8.62e-41	52
nongranular leukocyte	7.05e-24	115
leukocyte	1.91e-19	136
single nucleate cell	2.82e-17	3
mononuclear cell	2.82e-17	3
hematopoietic lineage restricted progenitor cell	4.52e-15	120
hematopoietic stem cell	8.30e-15	168
angioblastic mesenchymal cell	8.30e-15	168
hematopoietic cell	8.36e-14	177
mature B cell	2.57e-12	2
pre-B-II cell	2.57e-12	2
transitional stage B cell	2.57e-12	2
small pre-B-II cell	2.57e-12	2
immature B cell	2.57e-12	2
hematopoietic oligopotent progenitor cell	1.89e-11	161
hematopoietic multipotent progenitor cell	1.89e-11	161
circulating cell	6.67e-09	6
precursor B cell	1.68e-08	3
B-1 B cell	4.06e-07	1
antibody secreting cell	7.29e-07	1
plasma cell	7.29e-07	1
plasmablast	7.29e-07	1

Uber Anatomy

Ontology term	p-value	n
blood	4.29e-09	15
haemolymphatic fluid	4.29e-09	15
organism substance	4.29e-09	15
spleen	1.44e-08	3
gastrointestinal system mesentery	1.44e-08	3
stomach region	1.44e-08	3
mesentery	1.44e-08	3
gastrointestinal system serosa	1.44e-08	3
mesentery of stomach	1.44e-08	3
gut mesentery	1.44e-08	3
dorsal mesentery	1.44e-08	3
dorsal mesogastrium	1.44e-08	3
peritoneal cavity	1.44e-08	3
spleen primordium	1.44e-08	3
vermiform appendix	2.52e-07	1
caecum	2.52e-07	1
midgut	2.52e-07	1
tonsil	3.01e-07	1
mucosa-associated lymphoid tissue	3.01e-07	1
lymphoid tissue	3.01e-07	1
tonsillar ring	3.01e-07	1
lymph node	4.85e-07	1

Disease

Ontology term	p-value	n
lymphoma	8.76e-10	10
acute leukemia	3.82e-07	1
lymphatic system cancer	4.06e-07	1
lymphosarcoma	4.06e-07	1
genetic disease	5.45e-07	1
monogenic disease	5.45e-07	1
xeroderma pigmentosum	5.45e-07	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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No analysis results for this cluster

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.