Coexpression cluster:C1337

Full id: C1337_Burkitt_CD19_lymphoma_diffuse_acute_tonsil_appendix

Phase1 CAGE Peaks

Hg19::chr11:2406614..2406631,+	p17@CD81
Hg19::chr11:2415061..2415109,+	p20@CD81
Hg19::chr11:64900193..64900215,+	p@chr11:64900193..64900215 +
Hg19::chr15:89182587..89182600,+	p11@ISG20
Hg19::chr3:32001842..32001868,-	p5@OSBPL10
Hg19::chr9:95824637..95824655,+	p@chr9:95824637..95824655 +

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

---

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

---

GO ID	GO name	FDR corrected p-value
GO:0043128	positive regulation of 1-phosphatidylinositol 4-kinase activity	0.00307311903920876
GO:0008310	single-stranded DNA specific 3'-5' exodeoxyribonuclease activity	0.00307311903920876
GO:0043126	regulation of 1-phosphatidylinositol 4-kinase activity	0.00307311903920876
GO:0046813	virion attachment, binding of host cell surface receptor	0.00307311903920876
GO:0008859	exoribonuclease II activity	0.00307311903920876
GO:0008297	single-stranded DNA specific exodeoxyribonuclease activity	0.00512171429365841
GO:0008296	3'-5'-exodeoxyribonuclease activity	0.00552014538017045
GO:0019062	virion attachment to host cell surface receptor	0.00552014538017045
GO:0051704	multi-organism process	0.00552014538017045
GO:0000738	DNA catabolic process, exonucleolytic	0.0061456953109873
GO:0006661	phosphatidylinositol biosynthetic process	0.00768053622240581
GO:0043550	regulation of lipid kinase activity	0.00768053622240581
GO:0016895	exodeoxyribonuclease activity, producing 5'-phosphomonoesters	0.00768053622240581
GO:0004529	exodeoxyribonuclease activity	0.00768053622240581
GO:0044409	entry into host	0.00768053622240581
GO:0030260	entry into host cell	0.00768053622240581
GO:0019059	initiation of viral infection	0.00768053622240581
GO:0052192	movement in environment of other organism during symbiotic interaction	0.00768053622240581
GO:0046718	entry of virus into host cell	0.00768053622240581
GO:0052126	movement in host environment	0.00768053622240581
GO:0051828	entry into other organism during symbiotic interaction	0.00768053622240581
GO:0051806	entry into cell of other organism during symbiotic interaction	0.00768053622240581
GO:0000175	3'-5'-exoribonuclease activity	0.00801423663574463
GO:0016896	exoribonuclease activity, producing 5'-phosphomonoesters	0.00904943320919911
GO:0004532	exoribonuclease activity	0.00904943320919911
GO:0016605	PML body	0.00904943320919911
GO:0008283	cell proliferation	0.00904943320919911
GO:0050731	positive regulation of peptidyl-tyrosine phosphorylation	0.00904943320919911
GO:0044255	cellular lipid metabolic process	0.00904943320919911
GO:0016796	exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	0.0106295800771421
GO:0051701	interaction with host	0.0106295800771421
GO:0042327	positive regulation of phosphorylation	0.0106295800771421
GO:0045937	positive regulation of phosphate metabolic process	0.0106295800771421
GO:0046488	phosphatidylinositol metabolic process	0.0106295800771421
GO:0006629	lipid metabolic process	0.0106295800771421
GO:0001934	positive regulation of protein amino acid phosphorylation	0.0106295800771421
GO:0033240	positive regulation of amine metabolic process	0.0106295800771421
GO:0008408	3'-5' exonuclease activity	0.0106295800771421
GO:0045764	positive regulation of amino acid metabolic process	0.0106295800771421
GO:0050730	regulation of peptidyl-tyrosine phosphorylation	0.0107473700634525
GO:0044403	symbiosis, encompassing mutualism through parasitism	0.0116964400431298
GO:0044419	interspecies interaction between organisms	0.0116964400431298
GO:0046489	phosphoinositide biosynthetic process	0.0122104034369311
GO:0006308	DNA catabolic process	0.0122104034369311
GO:0018108	peptidyl-tyrosine phosphorylation	0.0138408135504591
GO:0018212	peptidyl-tyrosine modification	0.0138408135504591
GO:0001932	regulation of protein amino acid phosphorylation	0.0138408135504591
GO:0046474	glycerophospholipid biosynthetic process	0.0138408135504591
GO:0033238	regulation of amine metabolic process	0.0138408135504591
GO:0006401	RNA catabolic process	0.0138408135504591
GO:0006521	regulation of amino acid metabolic process	0.0138408135504591
GO:0019058	viral infectious cycle	0.0144749454686281
GO:0004536	deoxyribonuclease activity	0.0144749454686281
GO:0000187	activation of MAPK activity	0.0158981075577646
GO:0022415	viral reproductive process	0.0158981075577646
GO:0042325	regulation of phosphorylation	0.0175281333520275
GO:0043406	positive regulation of MAP kinase activity	0.0177577205244823
GO:0051174	regulation of phosphorus metabolic process	0.017933986465953
GO:0019220	regulation of phosphate metabolic process	0.017933986465953
GO:0004527	exonuclease activity	0.0184002034618907
GO:0030384	phosphoinositide metabolic process	0.0201047733179097
GO:0051247	positive regulation of protein metabolic process	0.0210136885862123
GO:0008654	phospholipid biosynthetic process	0.0222677156438762
GO:0043405	regulation of MAP kinase activity	0.0222677156438762
GO:0009615	response to virus	0.0230949428438987
GO:0004540	ribonuclease activity	0.0230949428438987
GO:0006650	glycerophospholipid metabolic process	0.0230949428438987
GO:0016604	nuclear body	0.024327393602476
GO:0046467	membrane lipid biosynthetic process	0.0250810723586737
GO:0018193	peptidyl-amino acid modification	0.026466815327271
GO:0006869	lipid transport	0.0291011781757484
GO:0045860	positive regulation of protein kinase activity	0.0299671166871473
GO:0033674	positive regulation of kinase activity	0.0299873162667024
GO:0030145	manganese ion binding	0.0299873162667024
GO:0051347	positive regulation of transferase activity	0.0299873162667024
GO:0000165	MAPKKK cascade	0.0301940094590606
GO:0051707	response to other organism	0.0408603841728031
GO:0006644	phospholipid metabolic process	0.0420876339425699
GO:0008202	steroid metabolic process	0.0430909364360579
GO:0008284	positive regulation of cell proliferation	0.0444473594883361
GO:0045859	regulation of protein kinase activity	0.0446469816440654
GO:0043549	regulation of kinase activity	0.0448557680711419
GO:0004518	nuclease activity	0.0448557680711419
GO:0051338	regulation of transferase activity	0.0448557680711419
GO:0043085	positive regulation of catalytic activity	0.0459310451268304
GO:0006643	membrane lipid metabolic process	0.0482115020772507

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>

---

Cell Type

Ontology term	p-value	n
lymphocyte of B lineage	8.56e-83	24
pro-B cell	8.56e-83	24
B cell	5.47e-75	14
lymphocyte	1.03e-39	53
common lymphoid progenitor	1.03e-39	53
nucleate cell	3.97e-38	55
lymphoid lineage restricted progenitor cell	3.08e-36	52
precursor B cell	2.75e-19	3
nongranular leukocyte	5.19e-16	115
mature B cell	1.12e-13	2
pre-B-II cell	1.12e-13	2
transitional stage B cell	1.12e-13	2
small pre-B-II cell	1.12e-13	2
immature B cell	1.12e-13	2
hematopoietic lineage restricted progenitor cell	1.91e-13	120
leukocyte	5.90e-13	136
hematopoietic oligopotent progenitor cell	2.36e-10	161
hematopoietic multipotent progenitor cell	2.36e-10	161
hematopoietic stem cell	9.16e-10	168
angioblastic mesenchymal cell	9.16e-10	168
hematopoietic cell	4.48e-09	177
B-1 B cell	6.80e-08	1
antibody secreting cell	1.80e-07	1
plasma cell	1.80e-07	1
plasmablast	1.80e-07	1

Uber Anatomy

Ontology term	p-value	n
hemopoietic organ	4.27e-14	7
immune organ	4.27e-14	7
spleen	3.39e-09	3
gastrointestinal system mesentery	3.39e-09	3
stomach region	3.39e-09	3
mesentery	3.39e-09	3
gastrointestinal system serosa	3.39e-09	3
mesentery of stomach	3.39e-09	3
gut mesentery	3.39e-09	3
dorsal mesentery	3.39e-09	3
dorsal mesogastrium	3.39e-09	3
peritoneal cavity	3.39e-09	3
spleen primordium	3.39e-09	3
tonsil	1.01e-07	1
mucosa-associated lymphoid tissue	1.01e-07	1
lymphoid tissue	1.01e-07	1
tonsillar ring	1.01e-07	1
vermiform appendix	1.07e-07	1
caecum	1.07e-07	1
midgut	1.07e-07	1
submandibular gland	1.58e-07	1
submandibular gland primordium	1.58e-07	1
thymus	6.86e-07	4
hemolymphoid system gland	6.86e-07	4
thymic region	6.86e-07	4
pharyngeal gland	6.86e-07	4
thymus primordium	6.86e-07	4

Disease

Ontology term	p-value	n
lymphoma	9.06e-11	10
lymphatic system cancer	6.80e-08	1
lymphosarcoma	6.80e-08	1
acute leukemia	1.22e-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

---

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

---

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
MEF2C#4208	2	13.7704514975413	0.00823559694227006	0.0324646149714555

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

---

This analysis result is provided for C0 - C305 clusters.