Coexpression cluster:C577

Full id: C577_lymphoma_Burkitt_diffuse_b_myeloma_plasma_appendix

Phase1 CAGE Peaks

Hg19::chr10:11715600..11715620,+	p1@uc001ikv.1
Hg19::chr12:25157568..25157581,+	p@chr12:25157568..25157581 +
Hg19::chr12:25205026..25205040,+	p9@LRMP
Hg19::chr14:106320502..106320513,-	p12@IGHM
Hg19::chr15:59691821..59691828,+	p@chr15:59691821..59691828 +
Hg19::chr15:59705215..59705224,-	p@chr15:59705215..59705224 -
Hg19::chr15:75639773..75639782,+	p15@NEIL1
Hg19::chr18:56563687..56563711,+	p@chr18:56563687..56563711 +
Hg19::chr19:19281060..19281078,-	p2@MEF2BNB-MEF2B p2@MEF2B
Hg19::chr2:175462951..175462965,-	p7@WIPF1
Hg19::chr2:220142900..220142916,-	p22@TUBA4A
Hg19::chr2:42795391..42795403,+	p17@MTA3
Hg19::chr2:64370395..64370418,+	p1@ENST00000438115
Hg19::chr5:96293965..96293986,+	p10@LNPEP
Hg19::chr7:101923076..101923085,+	p@chr7:101923076..101923085 +

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:0051649	establishment of cellular localization	0.00552662192040757
GO:0051641	cellular localization	0.00552662192040757
GO:0042571	immunoglobulin complex, circulating	0.0192416604751251
GO:0007010	cytoskeleton organization and biogenesis	0.0192416604751251
GO:0019814	immunoglobulin complex	0.0216076366368423
GO:0045022	early endosome to late endosome transport	0.0216076366368423
GO:0019815	B cell receptor complex	0.0216076366368423
GO:0046907	intracellular transport	0.0216076366368423
GO:0030705	cytoskeleton-dependent intracellular transport	0.0216076366368423
GO:0006906	vesicle fusion	0.0234837102650863
GO:0005522	profilin binding	0.026683677801369
GO:0000702	oxidized base lesion DNA N-glycosylase activity	0.0270918033101799
GO:0008534	oxidized purine base lesion DNA N-glycosylase activity	0.0270918033101799
GO:0016044	membrane organization and biogenesis	0.0273904043885752
GO:0007516	hemocyte development	0.0273904043885752
GO:0042386	hemocyte differentiation	0.0277973802242663
GO:0007017	microtubule-based process	0.0277973802242663
GO:0003906	DNA-(apurinic or apyrimidinic site) lyase activity	0.0277973802242663
GO:0030890	positive regulation of B cell proliferation	0.0277973802242663
GO:0006903	vesicle targeting	0.0279419887118174
GO:0030888	regulation of B cell proliferation	0.0279419887118174
GO:0050853	B cell receptor signaling pathway	0.0280609975354872
GO:0051650	establishment of vesicle localization	0.0280609975354872
GO:0016043	cellular component organization and biogenesis	0.0281605506756081
GO:0051648	vesicle localization	0.0281605506756081
GO:0006996	organelle organization and biogenesis	0.0302840317239506
GO:0005622	intracellular	0.0310429794423133
GO:0030048	actin filament-based movement	0.0310429794423133
GO:0001772	immunological synapse	0.0310429794423133
GO:0050731	positive regulation of peptidyl-tyrosine phosphorylation	0.0310429794423133
GO:0050871	positive regulation of B cell activation	0.0310429794423133
GO:0045807	positive regulation of endocytosis	0.0310429794423133
GO:0042100	B cell proliferation	0.0310429794423133
GO:0019104	DNA N-glycosylase activity	0.0310429794423133
GO:0051656	establishment of organelle localization	0.0331805783503322
GO:0042327	positive regulation of phosphorylation	0.0331805783503322
GO:0016799	hydrolase activity, hydrolyzing N-glycosyl compounds	0.0331805783503322
GO:0045937	positive regulation of phosphate metabolic process	0.0331805783503322
GO:0050864	regulation of B cell activation	0.0331805783503322
GO:0006810	transport	0.0331805783503322
GO:0001934	positive regulation of protein amino acid phosphorylation	0.0331805783503322
GO:0033240	positive regulation of amine metabolic process	0.0331805783503322
GO:0045764	positive regulation of amino acid metabolic process	0.0331805783503322
GO:0050851	antigen receptor-mediated signaling pathway	0.0331805783503322
GO:0051234	establishment of localization	0.0331805783503322
GO:0050730	regulation of peptidyl-tyrosine phosphorylation	0.0331805783503322
GO:0032946	positive regulation of mononuclear cell proliferation	0.0331805783503322
GO:0002429	immune response-activating cell surface receptor signaling pathway	0.0331805783503322
GO:0002455	humoral immune response mediated by circulating immunoglobulin	0.0331805783503322
GO:0050671	positive regulation of lymphocyte proliferation	0.0331805783503322
GO:0043170	macromolecule metabolic process	0.0331805783503322
GO:0016192	vesicle-mediated transport	0.0331805783503322
GO:0002768	immune response-regulating cell surface receptor signaling pathway	0.0331805783503322
GO:0002757	immune response-activating signal transduction	0.0331805783503322
GO:0004520	endodeoxyribonuclease activity	0.0331805783503322
GO:0051640	organelle localization	0.0331805783503322
GO:0002764	immune response-regulating signal transduction	0.0331805783503322
GO:0004179	membrane alanyl aminopeptidase activity	0.0331805783503322
GO:0030100	regulation of endocytosis	0.0331805783503322
GO:0016284	alanine aminopeptidase activity	0.0331805783503322
GO:0006284	base-excision repair	0.0335935694889657
GO:0051179	localization	0.0343797278606345
GO:0006944	membrane fusion	0.0343797278606345
GO:0051050	positive regulation of transport	0.0347541396382348
GO:0016197	endosome transport	0.0357691233612271
GO:0032944	regulation of mononuclear cell proliferation	0.0357691233612271
GO:0018108	peptidyl-tyrosine phosphorylation	0.0357691233612271
GO:0050670	regulation of lymphocyte proliferation	0.0357691233612271
GO:0044459	plasma membrane part	0.0357691233612271
GO:0006289	nucleotide-excision repair	0.035940294858417
GO:0018212	peptidyl-tyrosine modification	0.036254941554881
GO:0001932	regulation of protein amino acid phosphorylation	0.0363598696327606
GO:0033238	regulation of amine metabolic process	0.0363598696327606
GO:0006521	regulation of amino acid metabolic process	0.0363598696327606
GO:0003684	damaged DNA binding	0.03774397245156
GO:0009897	external side of plasma membrane	0.03774397245156
GO:0004536	deoxyribonuclease activity	0.03774397245156
GO:0016064	immunoglobulin mediated immune response	0.03774397245156
GO:0051251	positive regulation of lymphocyte activation	0.03774397245156
GO:0019724	B cell mediated immunity	0.037782428412284
GO:0032943	mononuclear cell proliferation	0.037782428412284
GO:0046651	lymphocyte proliferation	0.037782428412284
GO:0000187	activation of MAPK activity	0.0401301956548925
GO:0008154	actin polymerization and/or depolymerization	0.0419210442296136
GO:0042113	B cell activation	0.0419210442296136
GO:0044237	cellular metabolic process	0.0424084858387849
GO:0042325	regulation of phosphorylation	0.0424720760935587
GO:0048471	perinuclear region of cytoplasm	0.0424720760935587
GO:0044238	primary metabolic process	0.042725642634001
GO:0043406	positive regulation of MAP kinase activity	0.0428184511525644
GO:0051174	regulation of phosphorus metabolic process	0.043780004563187
GO:0019220	regulation of phosphate metabolic process	0.043780004563187
GO:0044424	intracellular part	0.044082719341471
GO:0002253	activation of immune response	0.044082719341471
GO:0002449	lymphocyte mediated immunity	0.0442291349268762
GO:0006959	humoral immune response	0.0447841817368642
GO:0002250	adaptive immune response	0.0447841817368642
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0447841817368642
GO:0051249	regulation of lymphocyte activation	0.0447841817368642
GO:0002443	leukocyte mediated immunity	0.0454950552453424
GO:0050865	regulation of cell activation	0.0461914459110638
GO:0007565	female pregnancy	0.0463062344559114
GO:0004177	aminopeptidase activity	0.0468465567744402
GO:0050778	positive regulation of immune response	0.0468465567744402
GO:0051247	positive regulation of protein metabolic process	0.0468465567744402
GO:0044260	cellular macromolecule metabolic process	0.0468465567744402
GO:0002684	positive regulation of immune system process	0.0468465567744402

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	9.30e-109	24
pro-B cell	9.30e-109	24
B cell	7.86e-63	14
lymphocyte	9.83e-53	53
common lymphoid progenitor	9.83e-53	53
nucleate cell	1.09e-50	55
lymphoid lineage restricted progenitor cell	2.12e-48	52
nongranular leukocyte	3.91e-22	115
hematopoietic lineage restricted progenitor cell	8.25e-19	120
leukocyte	3.55e-18	136
mature B cell	1.33e-15	2
pre-B-II cell	1.33e-15	2
transitional stage B cell	1.33e-15	2
small pre-B-II cell	1.33e-15	2
immature B cell	1.33e-15	2
hematopoietic oligopotent progenitor cell	8.48e-15	161
hematopoietic multipotent progenitor cell	8.48e-15	161
hematopoietic stem cell	4.96e-14	168
angioblastic mesenchymal cell	4.96e-14	168
hematopoietic cell	3.93e-13	177
precursor B cell	1.03e-10	3
B-1 B cell	1.13e-08	1
antibody secreting cell	1.22e-08	1
plasma cell	1.22e-08	1
plasmablast	1.22e-08	1

Uber Anatomy

Ontology term	p-value	n
hemopoietic organ	1.86e-16	7
immune organ	1.86e-16	7
spleen	1.69e-10	3
gastrointestinal system mesentery	1.69e-10	3
stomach region	1.69e-10	3
mesentery	1.69e-10	3
gastrointestinal system serosa	1.69e-10	3
mesentery of stomach	1.69e-10	3
gut mesentery	1.69e-10	3
dorsal mesentery	1.69e-10	3
dorsal mesogastrium	1.69e-10	3
peritoneal cavity	1.69e-10	3
spleen primordium	1.69e-10	3
vermiform appendix	3.87e-09	1
caecum	3.87e-09	1
midgut	3.87e-09	1
tonsil	5.70e-09	1
mucosa-associated lymphoid tissue	5.70e-09	1
lymphoid tissue	5.70e-09	1
tonsillar ring	5.70e-09	1
thymus	5.35e-08	4
hemolymphoid system gland	5.35e-08	4
thymic region	5.35e-08	4
pharyngeal gland	5.35e-08	4
thymus primordium	5.35e-08	4
chordate pharynx	4.61e-07	10
pharyngeal region of foregut	4.61e-07	10

Disease

Ontology term	p-value	n
lymphoma	1.52e-12	10
acute leukemia	9.74e-09	1
lymphatic system cancer	1.13e-08	1
lymphosarcoma	1.13e-08	1
genetic disease	1.32e-08	1
monogenic disease	1.32e-08	1
xeroderma pigmentosum	1.32e-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
EBF1#1879	7	4.15635119506554	0.000635940891991327	0.00521531455191851
TCF12#6938	5	3.54482163406214	0.00985505923893219	0.0370314647713477
ZEB1#6935	4	4.50358187134503	0.00989309630417724	0.0371169696774784

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.