Coexpression cluster:C350

Full id: C350_b_lymph_acute_CD19_lymphoma_spleen_B

Phase1 CAGE Peaks

Hg19::chr14:106320405..106320425,-	p8@IGHM
Hg19::chr14:106321136..106321178,+	p@chr14:106321136..106321178 +
Hg19::chr14:106321203..106321218,+	p@chr14:106321203..106321218 +
Hg19::chr14:106321227..106321242,+	p@chr14:106321227..106321242 +
Hg19::chr14:106321246..106321254,-	p3@J00257
Hg19::chr14:106321254..106321276,+	p@chr14:106321254..106321276 +
Hg19::chr14:106321619..106321630,-	p8@FJ197674
Hg19::chr14:106321667..106321674,-	p9@FJ197674
Hg19::chr14:106321677..106321684,-	p10@FJ197674
Hg19::chr14:106321687..106321692,-	p12@FJ197674
Hg19::chr14:106321710..106321722,-	p3@FJ197674
Hg19::chr14:106321725..106321735,-	p7@FJ197674
Hg19::chr14:106321756..106321783,-	p1@FJ197674
Hg19::chr14:106321811..106321832,-	p5@FJ197674
Hg19::chr14:106321813..106321821,+	p5@AY671148 p5@AY671772 p5@AY671782 p5@AY671783
Hg19::chr14:106321849..106321852,-	p11@FJ197674
Hg19::chr14:106321854..106321877,-	p2@FJ197674
Hg19::chr14:106321879..106321890,+	p2@AY671148 p2@AY671772 p2@AY671782 p2@AY671783
Hg19::chr14:106321882..106321895,-	p6@FJ197674
Hg19::chr14:106322016..106322079,+	p1@AY671148 p1@AY671760 p1@AY671772 p1@AY671782 p1@AY671783
Hg19::chr14:106322056..106322063,-	p4@AJ294734
Hg19::chr14:106322107..106322112,-	p6@AJ294734
Hg19::chr14:106322129..106322143,-	p1@AJ294734
Hg19::chr14:106322148..106322185,+	p1@HM995588
Hg19::chr14:106322154..106322163,-	p3@AJ294734
Hg19::chr14:106322242..106322254,-	p2@AJ294734
Hg19::chr14:106322276..106322283,-	p5@AJ294734
Hg19::chr14:106322288..106322325,-	p2@IGHM
Hg19::chr14:106328131..106328143,-	p4@IGHM
Hg19::chr14:106725347..106725368,-	p1@AF460666 p1@AF460671 p1@AF460672 p1@AF460678 p1@AF460691 p1@AF460699 p1@AF460700 p1@AF460800 p1@DQ454508 p1@U64467
Hg19::chr17:3599428..3599456,-	p1@ENST00000550383
Hg19::chr21:43955104..43955124,-	p@chr21:43955104..43955124 -

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:0006955	immune response	0.00395619922288943
GO:0002376	immune system process	0.00395619922288943
GO:0003823	antigen binding	0.00395619922288943
GO:0045321	leukocyte activation	0.00395619922288943
GO:0042571	immunoglobulin complex, circulating	0.00395619922288943
GO:0001775	cell activation	0.00420175109836318
GO:0005153	interleukin-8 receptor binding	0.00565154680679548
GO:0045022	early endosome to late endosome transport	0.00593394946336459
GO:0019814	immunoglobulin complex	0.00593394946336459
GO:0019815	B cell receptor complex	0.00593394946336459
GO:0045091	regulation of retroviral genome replication	0.00719245428245118
GO:0045090	retroviral genome replication	0.00904548478924136
GO:0042119	neutrophil activation	0.00904548478924136
GO:0042127	regulation of cell proliferation	0.00904548478924136
GO:0050930	induction of positive chemotaxis	0.00941702662374834
GO:0005615	extracellular space	0.00941702662374834
GO:0030890	positive regulation of B cell proliferation	0.00941702662374834
GO:0050926	regulation of positive chemotaxis	0.00941702662374834
GO:0030888	regulation of B cell proliferation	0.00941702662374834
GO:0050927	positive regulation of positive chemotaxis	0.00941702662374834
GO:0050918	positive chemotaxis	0.00941702662374834
GO:0050853	B cell receptor signaling pathway	0.0094576917801139
GO:0050921	positive regulation of chemotaxis	0.0094576917801139
GO:0050920	regulation of chemotaxis	0.009491803941921
GO:0030593	neutrophil chemotaxis	0.009491803941921
GO:0045069	regulation of viral genome replication	0.00988700469035434
GO:0005624	membrane fraction	0.00991146325799091
GO:0008283	cell proliferation	0.0104670522674057
GO:0050792	regulation of viral reproduction	0.0104670522674057
GO:0001772	immunological synapse	0.0104670522674057
GO:0050731	positive regulation of peptidyl-tyrosine phosphorylation	0.0104670522674057
GO:0045807	positive regulation of endocytosis	0.0104670522674057
GO:0050871	positive regulation of B cell activation	0.0104670522674057
GO:0042100	B cell proliferation	0.0104670522674057
GO:0042327	positive regulation of phosphorylation	0.0115598019496547
GO:0030595	leukocyte chemotaxis	0.0115598019496547
GO:0000267	cell fraction	0.0115598019496547
GO:0044421	extracellular region part	0.0115598019496547
GO:0045937	positive regulation of phosphate metabolic process	0.0115598019496547
GO:0050864	regulation of B cell activation	0.0115598019496547
GO:0001934	positive regulation of protein amino acid phosphorylation	0.0115598019496547
GO:0002274	myeloid leukocyte activation	0.0115598019496547
GO:0033240	positive regulation of amine metabolic process	0.0115598019496547
GO:0045764	positive regulation of amino acid metabolic process	0.0115598019496547
GO:0050851	antigen receptor-mediated signaling pathway	0.0115598019496547
GO:0050730	regulation of peptidyl-tyrosine phosphorylation	0.0115598019496547
GO:0019079	viral genome replication	0.0115598019496547
GO:0032946	positive regulation of mononuclear cell proliferation	0.0115598019496547
GO:0002455	humoral immune response mediated by circulating immunoglobulin	0.0115598019496547
GO:0002429	immune response-activating cell surface receptor signaling pathway	0.0115598019496547
GO:0050671	positive regulation of lymphocyte proliferation	0.0115598019496547
GO:0050900	leukocyte migration	0.0115598019496547
GO:0002768	immune response-regulating cell surface receptor signaling pathway	0.0115598019496547
GO:0002757	immune response-activating signal transduction	0.011711378025305
GO:0002764	immune response-regulating signal transduction	0.0118574210887758
GO:0030100	regulation of endocytosis	0.0119982275520463
GO:0019722	calcium-mediated signaling	0.0128266931832893
GO:0051050	positive regulation of transport	0.0129458524290536
GO:0016197	endosome transport	0.013383863320157
GO:0018108	peptidyl-tyrosine phosphorylation	0.013383863320157
GO:0050670	regulation of lymphocyte proliferation	0.013383863320157
GO:0032944	regulation of mononuclear cell proliferation	0.013383863320157
GO:0018212	peptidyl-tyrosine modification	0.0137685000000387
GO:0001932	regulation of protein amino acid phosphorylation	0.0137685000000387
GO:0033238	regulation of amine metabolic process	0.0137685000000387
GO:0006521	regulation of amino acid metabolic process	0.0137685000000387
GO:0019058	viral infectious cycle	0.014339572658952
GO:0009897	external side of plasma membrane	0.014339572658952
GO:0051251	positive regulation of lymphocyte activation	0.014339572658952
GO:0016064	immunoglobulin mediated immune response	0.014339572658952
GO:0019724	B cell mediated immunity	0.014339572658952
GO:0032943	mononuclear cell proliferation	0.014339572658952
GO:0046651	lymphocyte proliferation	0.014339572658952
GO:0000187	activation of MAPK activity	0.0150087881311616
GO:0022415	viral reproductive process	0.0150087881311616
GO:0042113	B cell activation	0.0158488264866682
GO:0042325	regulation of phosphorylation	0.0162004792785023
GO:0048471	perinuclear region of cytoplasm	0.0162004792785023
GO:0043406	positive regulation of MAP kinase activity	0.0162881160672838
GO:0030155	regulation of cell adhesion	0.0162881160672838
GO:0051174	regulation of phosphorus metabolic process	0.0166116880525676
GO:0019220	regulation of phosphate metabolic process	0.0166116880525676
GO:0002253	activation of immune response	0.0168543714380707
GO:0002449	lymphocyte mediated immunity	0.0168543714380707
GO:0006959	humoral immune response	0.0168543714380707
GO:0002250	adaptive immune response	0.0168543714380707
GO:0008009	chemokine activity	0.0168543714380707
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0168543714380707
GO:0051249	regulation of lymphocyte activation	0.0168543714380707
GO:0042379	chemokine receptor binding	0.0168859071514165
GO:0002443	leukocyte mediated immunity	0.016916737003196
GO:0050865	regulation of cell activation	0.0171608959655122
GO:0050778	positive regulation of immune response	0.0178428776647907
GO:0051247	positive regulation of protein metabolic process	0.0178428776647907
GO:0002684	positive regulation of immune system process	0.0178622382061167
GO:0043405	regulation of MAP kinase activity	0.0191109896713727
GO:0050776	regulation of immune response	0.0199279131796443
GO:0002682	regulation of immune system process	0.0201212644956015
GO:0007050	cell cycle arrest	0.0201212644956015
GO:0001664	G-protein-coupled receptor binding	0.0205015089564397
GO:0051240	positive regulation of multicellular organismal process	0.0205015089564397
GO:0007242	intracellular signaling cascade	0.0206565267277989
GO:0043235	receptor complex	0.0206565267277989
GO:0002252	immune effector process	0.0206565267277989
GO:0051049	regulation of transport	0.0206565267277989
GO:0018193	peptidyl-amino acid modification	0.0225005239824122
GO:0001525	angiogenesis	0.0237583710023897
GO:0045860	positive regulation of protein kinase activity	0.0255539605278058
GO:0033674	positive regulation of kinase activity	0.0255539605278058
GO:0042330	taxis	0.0255539605278058
GO:0006935	chemotaxis	0.0255539605278058
GO:0051347	positive regulation of transferase activity	0.0255696250733866
GO:0048514	blood vessel morphogenesis	0.0255696250733866
GO:0009986	cell surface	0.0255696250733866
GO:0000165	MAPKKK cascade	0.0256882967032008
GO:0048646	anatomical structure formation	0.0259738855056701
GO:0046649	lymphocyte activation	0.0260869742473664
GO:0001568	blood vessel development	0.0273422372844919
GO:0001944	vasculature development	0.0273422372844919
GO:0007166	cell surface receptor linked signal transduction	0.0273422372844919
GO:0007626	locomotory behavior	0.029433244533981
GO:0010324	membrane invagination	0.0314993158407173
GO:0006897	endocytosis	0.0314993158407173
GO:0005515	protein binding	0.0336362671547079
GO:0045786	negative regulation of progression through cell cycle	0.0350908007506085
GO:0008285	negative regulation of cell proliferation	0.0350908007506085
GO:0016477	cell migration	0.0357622432664774
GO:0008284	positive regulation of cell proliferation	0.0357622432664774
GO:0045859	regulation of protein kinase activity	0.0360899418582341
GO:0043549	regulation of kinase activity	0.0365624667764168
GO:0051338	regulation of transferase activity	0.0370275569021061
GO:0043085	positive regulation of catalytic activity	0.0380758925119667
GO:0019932	second-messenger-mediated signaling	0.0395469873936715
GO:0051239	regulation of multicellular organismal process	0.0405592445225359
GO:0016044	membrane organization and biogenesis	0.0412676483960112
GO:0006954	inflammatory response	0.0419652184692328
GO:0007610	behavior	0.0420846488799162
GO:0022414	reproductive process	0.0433287996253402
GO:0005125	cytokine activity	0.0437158255262933
GO:0000074	regulation of progression through cell cycle	0.0493613408533506
GO:0051726	regulation of cell cycle	0.049835479474263
GO:0009887	organ morphogenesis	0.0498936231862632
GO:0031325	positive regulation of cellular metabolic process	0.0499508811830772

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	5.72e-67	24
pro-B cell	5.72e-67	24
B cell	1.97e-40	14
lymphocyte	7.51e-30	53
common lymphoid progenitor	7.51e-30	53
nucleate cell	1.55e-28	55
lymphoid lineage restricted progenitor cell	1.27e-27	52
nongranular leukocyte	7.60e-14	115
hematopoietic stem cell	6.71e-11	168
angioblastic mesenchymal cell	6.71e-11	168
leukocyte	1.00e-10	136
hematopoietic cell	5.54e-10	177
hematopoietic oligopotent progenitor cell	8.54e-10	161
hematopoietic multipotent progenitor cell	8.54e-10	161
hematopoietic lineage restricted progenitor cell	1.28e-09	120

Uber Anatomy

Ontology term	p-value	n
adult organism	1.07e-12	114
hemopoietic organ	1.91e-11	7
immune organ	1.91e-11	7
spleen	7.46e-11	3
gastrointestinal system mesentery	7.46e-11	3
stomach region	7.46e-11	3
mesentery	7.46e-11	3
gastrointestinal system serosa	7.46e-11	3
mesentery of stomach	7.46e-11	3
gut mesentery	7.46e-11	3
dorsal mesentery	7.46e-11	3
dorsal mesogastrium	7.46e-11	3
peritoneal cavity	7.46e-11	3
spleen primordium	7.46e-11	3
blood	2.22e-07	15
haemolymphatic fluid	2.22e-07	15
organism substance	2.22e-07	15

Disease

Ontology term	p-value	n
lymphoma	2.13e-08	10
hematologic cancer	6.18e-07	51
immune system cancer	6.18e-07	51

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)
MA0003.1	0.00040238
MA0004.1	11.2345
MA0006.1	0.279119
MA0007.1	0.265481
MA0009.1	0.395891
MA0014.1	0.00277835
MA0017.1	2.99133
MA0019.1	2.91722
MA0024.1	0.312615
MA0025.1	0.508683
MA0027.1	1.93196
MA0028.1	0.032054
MA0029.1	0.327543
MA0030.1	0.318663
MA0031.1	0.270046
MA0038.1	3.39844
MA0040.1	0.332103
MA0041.1	0.0940493
MA0042.1	0.0792314
MA0043.1	1.02525
MA0046.1	0.386991
MA0048.1	0.915538
MA0050.1	0.0796249
MA0051.1	0.136135
MA0052.1	0.335128
MA0055.1	0.828339
MA0056.1	0
MA0057.1	2.06674
MA0058.1	20.4269
MA0059.1	6.04104
MA0060.1	0.00694078
MA0061.1	4.04258
MA0063.1	0
MA0066.1	2.65769
MA0067.1	0.673046
MA0068.1	0.0455946
MA0069.1	0.383853
MA0070.1	0.374777
MA0071.1	0.1171
MA0072.1	0.371146
MA0073.1	1.696e-05
MA0074.1	2.62648
MA0076.1	0.0525452
MA0077.1	0.364942
MA0078.1	0.197204
MA0081.1	0.0465806
MA0083.1	0.40206
MA0084.1	0.847335
MA0087.1	0.369175
MA0088.1	1.26589
MA0089.1	0
MA0090.1	0.0579073
MA0091.1	0.0865076
MA0092.1	6.0767
MA0093.1	14.38
MA0095.1	0
MA0098.1	0
MA0100.1	4.3091
MA0101.1	1.2308
MA0103.1	9.58
MA0105.1	3.84914
MA0106.1	0.163029
MA0107.1	3.5716
MA0108.2	0.267801
MA0109.1	0
MA0111.1	0.490476
MA0113.1	0.173209
MA0114.1	1.169
MA0115.1	0.603788
MA0116.1	2.5408
MA0117.1	0.427006
MA0119.1	0.0412526
MA0122.1	1.99005
MA0124.1	0.566745
MA0125.1	0.493194
MA0130.1	0
MA0131.1	0.2093
MA0132.1	0
MA0133.1	0
MA0135.1	0.420972
MA0136.1	0.142619
MA0139.1	0.00355142
MA0140.1	0.115685
MA0141.1	1.52412
MA0142.1	2.76951
MA0143.1	1.57513
MA0144.1	0.144799
MA0145.1	2.37335
MA0146.1	0.443429
MA0147.1	6.922
MA0148.1	0.0971411
MA0149.1	0.110599
MA0062.2	0.004042
MA0035.2	0.11531
MA0039.2	0.00370508
MA0138.2	0.575161
MA0002.2	0.361695
MA0137.2	0.136268
MA0104.2	3.40818
MA0047.2	0.155654
MA0112.2	1.33369
MA0065.2	0.163186
MA0150.1	0.44969
MA0151.1	0
MA0152.1	0.119196
MA0153.1	0.478697
MA0154.1	0.737639
MA0155.1	0.000754999
MA0156.1	0.0345163
MA0157.1	0.227782
MA0158.1	0
MA0159.1	3.10997
MA0160.1	1.14983
MA0161.1	0
MA0162.1	0.00415725
MA0163.1	1.71831
MA0164.1	0.181076
MA0080.2	0.838393
MA0018.2	6.37996
MA0099.2	0.119388
MA0079.2	5.55621e-08
MA0102.2	0.88257
MA0258.1	1.02444
MA0259.1	2.16494
MA0442.1	0

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	32	2.14745317655807	2.38288969218142e-11	2.83124705986046e-09

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.