Coexpression cluster:C2115

Full id: C2115_b_myeloma_CD19_acute_non_xeroderma_Burkitt

Phase1 CAGE Peaks

Hg19::chr11:1543284..1543298,+	p@chr11:1543284..1543298 +
Hg19::chr14:106328021..106328027,-	p15@IGHM
Hg19::chr14:106328158..106328168,-	p6@IGHM
Hg19::chr5:59817936..59817963,-	p19@PDE4D

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:0042571	immunoglobulin complex, circulating	0.00794748769705615
GO:0045022	early endosome to late endosome transport	0.00794748769705615
GO:0019814	immunoglobulin complex	0.00794748769705615
GO:0019815	B cell receptor complex	0.00794748769705615
GO:0004115	3',5'-cyclic-AMP phosphodiesterase activity	0.0116168295419799
GO:0030890	positive regulation of B cell proliferation	0.0116168295419799
GO:0030888	regulation of B cell proliferation	0.0116168295419799
GO:0050853	B cell receptor signaling pathway	0.0116168295419799
GO:0000267	cell fraction	0.0116168295419799
GO:0001772	immunological synapse	0.0116168295419799
GO:0050731	positive regulation of peptidyl-tyrosine phosphorylation	0.0116168295419799
GO:0045807	positive regulation of endocytosis	0.0116168295419799
GO:0050871	positive regulation of B cell activation	0.0116168295419799
GO:0042100	B cell proliferation	0.0116168295419799
GO:0005626	insoluble fraction	0.0116168295419799
GO:0042327	positive regulation of phosphorylation	0.0116168295419799
GO:0045937	positive regulation of phosphate metabolic process	0.0116168295419799
GO:0050864	regulation of B cell activation	0.0116168295419799
GO:0001934	positive regulation of protein amino acid phosphorylation	0.0116168295419799
GO:0033240	positive regulation of amine metabolic process	0.0116168295419799
GO:0045764	positive regulation of amino acid metabolic process	0.0116168295419799
GO:0050851	antigen receptor-mediated signaling pathway	0.0116168295419799
GO:0050730	regulation of peptidyl-tyrosine phosphorylation	0.0116168295419799
GO:0032946	positive regulation of mononuclear cell proliferation	0.0116168295419799
GO:0002455	humoral immune response mediated by circulating immunoglobulin	0.0116168295419799
GO:0002429	immune response-activating cell surface receptor signaling pathway	0.0116168295419799
GO:0050671	positive regulation of lymphocyte proliferation	0.0116168295419799
GO:0002768	immune response-regulating cell surface receptor signaling pathway	0.0116168295419799
GO:0002757	immune response-activating signal transduction	0.0116168295419799
GO:0002764	immune response-regulating signal transduction	0.0116168295419799
GO:0030100	regulation of endocytosis	0.0116168295419799
GO:0051050	positive regulation of transport	0.0116918571153127
GO:0016197	endosome transport	0.0116918571153127
GO:0018108	peptidyl-tyrosine phosphorylation	0.0116918571153127
GO:0050670	regulation of lymphocyte proliferation	0.0116918571153127
GO:0032944	regulation of mononuclear cell proliferation	0.0116918571153127
GO:0018212	peptidyl-tyrosine modification	0.0116918571153127
GO:0004114	3',5'-cyclic-nucleotide phosphodiesterase activity	0.0116918571153127
GO:0001932	regulation of protein amino acid phosphorylation	0.0116918571153127
GO:0033238	regulation of amine metabolic process	0.0116918571153127
GO:0006521	regulation of amino acid metabolic process	0.0116918571153127
GO:0004112	cyclic-nucleotide phosphodiesterase activity	0.0116918571153127
GO:0009897	external side of plasma membrane	0.0116918571153127
GO:0051251	positive regulation of lymphocyte activation	0.0116918571153127
GO:0016064	immunoglobulin mediated immune response	0.0116918571153127
GO:0019724	B cell mediated immunity	0.0116918571153127
GO:0032943	mononuclear cell proliferation	0.0116918571153127
GO:0046651	lymphocyte proliferation	0.0116918571153127
GO:0000187	activation of MAPK activity	0.0123169181045036
GO:0042113	B cell activation	0.0129168768328704
GO:0042325	regulation of phosphorylation	0.013030321291359
GO:0048471	perinuclear region of cytoplasm	0.013030321291359
GO:0043406	positive regulation of MAP kinase activity	0.0131835922851881
GO:0051174	regulation of phosphorus metabolic process	0.0131881982696865
GO:0019220	regulation of phosphate metabolic process	0.0131881982696865
GO:0002253	activation of immune response	0.0131881982696865
GO:0002449	lymphocyte mediated immunity	0.0131881982696865
GO:0006959	humoral immune response	0.0131881982696865
GO:0002250	adaptive immune response	0.0131881982696865
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0131881982696865
GO:0051249	regulation of lymphocyte activation	0.0131881982696865
GO:0002443	leukocyte mediated immunity	0.0133165530938861
GO:0050865	regulation of cell activation	0.013440813355957
GO:0050778	positive regulation of immune response	0.0137908879340018
GO:0051247	positive regulation of protein metabolic process	0.0137908879340018
GO:0002684	positive regulation of immune system process	0.0137908879340018
GO:0043405	regulation of MAP kinase activity	0.0146892985009627
GO:0050776	regulation of immune response	0.0152502888001131
GO:0002682	regulation of immune system process	0.0153355378312316
GO:0051240	positive regulation of multicellular organismal process	0.0158711118749748
GO:0043235	receptor complex	0.0159424075836415
GO:0002252	immune effector process	0.0159424075836415
GO:0051049	regulation of transport	0.0159424075836415
GO:0018193	peptidyl-amino acid modification	0.0172968612425269
GO:0005813	centrosome	0.0181924364789254
GO:0008081	phosphoric diester hydrolase activity	0.0192030526561742
GO:0045860	positive regulation of protein kinase activity	0.0193204581157774
GO:0033674	positive regulation of kinase activity	0.0193204581157774
GO:0005815	microtubule organizing center	0.0193204581157774
GO:0051347	positive regulation of transferase activity	0.0193204581157774
GO:0009986	cell surface	0.0193204581157774
GO:0000165	MAPKKK cascade	0.019342175429056
GO:0046649	lymphocyte activation	0.0197446520568577
GO:0003823	antigen binding	0.0222714703628157
GO:0045321	leukocyte activation	0.0223815037690259
GO:0010324	membrane invagination	0.0239261978510177
GO:0006897	endocytosis	0.0239261978510177
GO:0001775	cell activation	0.0250907357025209
GO:0008284	positive regulation of cell proliferation	0.0274576146727099
GO:0005625	soluble fraction	0.0274576146727099
GO:0045859	regulation of protein kinase activity	0.0275028163566002
GO:0043549	regulation of kinase activity	0.0277757427115939
GO:0051338	regulation of transferase activity	0.0280427158273869
GO:0043085	positive regulation of catalytic activity	0.028751495277678
GO:0051239	regulation of multicellular organismal process	0.0307729921850535
GO:0016044	membrane organization and biogenesis	0.0312187665397194
GO:0044444	cytoplasmic part	0.0338985011741535
GO:0031325	positive regulation of cellular metabolic process	0.0392568258729603
GO:0007243	protein kinase cascade	0.0400249082645411
GO:0009893	positive regulation of metabolic process	0.0408226657216295
GO:0007165	signal transduction	0.0408226657216295
GO:0019882	antigen processing and presentation	0.0428523724164199
GO:0051246	regulation of protein metabolic process	0.0431476503037833
GO:0007154	cell communication	0.0463533562117629
GO:0042127	regulation of cell proliferation	0.0470070566661671
GO:0006520	amino acid metabolic process	0.0470565201783836

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><br>

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Cell Type

Ontology term	p-value	n
leukocyte	5.56e-37	140
nongranular leukocyte	1.04e-36	119
hematopoietic lineage restricted progenitor cell	1.88e-33	124
hematopoietic stem cell	2.74e-32	172
angioblastic mesenchymal cell	2.74e-32	172
hematopoietic cell	1.96e-30	182
hematopoietic oligopotent progenitor cell	2.04e-30	165
hematopoietic multipotent progenitor cell	2.04e-30	165
lymphocyte of B lineage	3.71e-29	24
pro-B cell	3.71e-29	24
granulocyte monocyte progenitor cell	4.95e-23	71
macrophage dendritic cell progenitor	5.68e-23	65
monopoietic cell	3.63e-21	63
monocyte	3.63e-21	63
monoblast	3.63e-21	63
promonocyte	3.63e-21	63
myeloid lineage restricted progenitor cell	2.12e-19	70
myeloid leukocyte	1.53e-18	76
B cell	4.48e-18	14
myeloid cell	5.38e-17	112
common myeloid progenitor	5.38e-17	112
CD14-positive, CD16-negative classical monocyte	9.72e-15	42
classical monocyte	4.05e-13	45
lymphocyte	6.48e-13	53
common lymphoid progenitor	6.48e-13	53
lymphoid lineage restricted progenitor cell	4.40e-12	52
conventional dendritic cell	5.04e-10	8
dendritic cell	9.80e-08	10
immature conventional dendritic cell	1.83e-07	5
common dendritic progenitor	1.83e-07	5

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	1.04e-28	102
blood island	1.04e-28	102
hemolymphoid system	1.46e-27	112
bone marrow	3.69e-21	80
adult organism	1.64e-19	115
bone element	1.56e-18	86
immune system	2.29e-17	115
skeletal element	4.07e-14	101
skeletal system	4.07e-14	101
lateral plate mesoderm	9.74e-10	216

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	3	18.2683513442277	0.000268166010572129	0.00286575155818506
BCL11A#53335	3	21.2770913277053	0.000170483911460614	0.00208052923919549
BCL3#602	3	25.9103271028037	9.48553136097325e-05	0.00137343603189891
BCLAF1#9774	2	10.8263238050609	0.0120220381643258	0.0436370779496063
EBF1#1879	3	6.67985013492675	0.00518429411827891	0.024031001438859
IRF4#3662	3	16.4358845150581	0.000366943139555461	0.00365644256769705
MEF2A#4205	3	14.057423182233	0.000583003885418661	0.00488513661659495
MEF2C#4208	3	30.983515869468	5.56692972943475e-05	0.00094063189453557
PAX5#5079	3	5.00217414838337	0.0119653317478641	0.0434690163634053
PBX3#5090	2	10.9572563433721	0.0117453018068803	0.0428081512967641
POU2F2#5452	4	9.10612405774252	0.00014539566517493	0.00188002697476841
RXRA#6256	2	10.0373085695666	0.0139170380592011	0.0488680206389706
TCF12#6938	3	7.97584867663982	0.00309092039601307	0.0162707981471375
WRNIP1#56897	2	54.909982174688	0.000491193103231144	0.00439134707313452

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.