Coexpression cluster:C782

Full id: C782_B_Burkitt_lymphoma_splenic_acute_CD19_xeroderma

Phase1 CAGE Peaks

Hg19::chr10:49880649..49880677,+	p@chr10:49880649..49880677 +
Hg19::chr12:54446974..54447007,+	p@chr12:54446974..54447007 +
Hg19::chr19:39108743..39108750,-	p5@MAP4K1
Hg19::chr2:65159543..65159557,-	p2@LOC400958
Hg19::chr2:65159562..65159594,-	p1@LOC400958
Hg19::chr2:65159616..65159630,-	p4@LOC400958
Hg19::chr2:65159651..65159662,-	p5@LOC400958
Hg19::chr2:65159748..65159759,-	p3@LOC400958
Hg19::chr5:85961934..85961944,+	p@chr5:85961934..85961944 +
Hg19::chr6:6587579..6587601,-	p3@LY86-AS1

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:0008349	MAP kinase kinase kinase kinase activity	0.00120687625103026
GO:0045610	regulation of hemocyte differentiation	0.00120687625103026
GO:0000185	activation of MAPKKK activity	0.00402292083676753
GO:0042386	hemocyte differentiation	0.00402292083676753
GO:0018209	peptidyl-serine modification	0.00402292083676753
GO:0018105	peptidyl-serine phosphorylation	0.00402292083676753
GO:0007257	activation of JNK activity	0.00670486806127922
GO:0043507	positive regulation of JNK activity	0.00670486806127922
GO:0043506	regulation of JNK activity	0.00670486806127922
GO:0000187	activation of MAPK activity	0.0120687625103026
GO:0007254	JNK cascade	0.0120687625103026
GO:0043406	positive regulation of MAP kinase activity	0.0120687625103026
GO:0031098	stress-activated protein kinase signaling pathway	0.0120687625103026
GO:0032147	activation of protein kinase activity	0.0120687625103026
GO:0004702	receptor signaling protein serine/threonine kinase activity	0.012390596177244
GO:0043405	regulation of MAP kinase activity	0.0140299364182268
GO:0018193	peptidyl-amino acid modification	0.0164574034231399
GO:0045860	positive regulation of protein kinase activity	0.0164574034231399
GO:0045595	regulation of cell differentiation	0.0164574034231399
GO:0033674	positive regulation of kinase activity	0.0164574034231399
GO:0051347	positive regulation of transferase activity	0.0164574034231399
GO:0000165	MAPKKK cascade	0.0164574034231399
GO:0030097	hemopoiesis	0.0168962675144236
GO:0048534	hemopoietic or lymphoid organ development	0.0168962675144236
GO:0005057	receptor signaling protein activity	0.0168962675144236
GO:0002520	immune system development	0.0168962675144236
GO:0050793	regulation of developmental process	0.0198732289336316
GO:0045859	regulation of protein kinase activity	0.0198732289336316
GO:0043549	regulation of kinase activity	0.0198732289336316
GO:0051338	regulation of transferase activity	0.0198732289336316
GO:0043085	positive regulation of catalytic activity	0.0199329238879836
GO:0007243	protein kinase cascade	0.0283615918992111
GO:0005083	small GTPase regulator activity	0.0345971191962008
GO:0050790	regulation of catalytic activity	0.0429505959925475
GO:0065009	regulation of a molecular function	0.0456655878768206
GO:0004674	protein serine/threonine kinase activity	0.0456655878768206
GO:0030695	GTPase regulator activity	0.0456655878768206

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	1.14e-109	24
pro-B cell	1.14e-109	24
B cell	3.80e-61	14
lymphocyte	3.03e-52	53
common lymphoid progenitor	3.03e-52	53
nucleate cell	3.50e-50	55
lymphoid lineage restricted progenitor cell	2.53e-48	52
nongranular leukocyte	7.25e-26	115
hematopoietic lineage restricted progenitor cell	2.61e-22	120
leukocyte	3.72e-21	136
hematopoietic oligopotent progenitor cell	3.87e-17	161
hematopoietic multipotent progenitor cell	3.87e-17	161
hematopoietic stem cell	3.17e-16	168
angioblastic mesenchymal cell	3.17e-16	168
hematopoietic cell	3.70e-15	177
mature B cell	3.18e-13	2
pre-B-II cell	3.18e-13	2
transitional stage B cell	3.18e-13	2
small pre-B-II cell	3.18e-13	2
immature B cell	3.18e-13	2
precursor B cell	4.15e-09	3
antibody secreting cell	1.42e-07	1
plasma cell	1.42e-07	1
plasmablast	1.42e-07	1
B-1 B cell	2.50e-07	1

Uber Anatomy

Ontology term	p-value	n
spleen	1.06e-18	3
gastrointestinal system mesentery	1.06e-18	3
stomach region	1.06e-18	3
mesentery	1.06e-18	3
gastrointestinal system serosa	1.06e-18	3
mesentery of stomach	1.06e-18	3
gut mesentery	1.06e-18	3
dorsal mesentery	1.06e-18	3
dorsal mesogastrium	1.06e-18	3
peritoneal cavity	1.06e-18	3
spleen primordium	1.06e-18	3
hemopoietic organ	8.10e-14	7
immune organ	8.10e-14	7
vermiform appendix	2.35e-07	1
caecum	2.35e-07	1
midgut	2.35e-07	1
stomach	2.51e-07	8
food storage organ	2.51e-07	8
tonsil	2.66e-07	1
mucosa-associated lymphoid tissue	2.66e-07	1
lymphoid tissue	2.66e-07	1
tonsillar ring	2.66e-07	1

Disease

Ontology term	p-value	n
lymphoma	7.25e-22	10
acute leukemia	1.10e-07	1
lymphatic system cancer	2.50e-07	1
lymphosarcoma	2.50e-07	1
genetic disease	2.83e-07	1
monogenic disease	2.83e-07	1
xeroderma pigmentosum	2.83e-07	1
anemia	3.62e-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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
BCL11A#53335	6	17.0216730621642	3.55593058662976e-07	1.75592356755095e-05
EBF1#1879	9	8.0158201619121	2.54528393136776e-08	1.77099872423796e-06
ELF1#1997	9	3.83228816292678	1.71269377095518e-05	0.000392005313926775
IRF4#3662	5	10.9572563433721	4.10495409675721e-05	0.000745724997236435
MEF2A#4205	3	5.62296927289322	0.0137240387818804	0.0483251816028592
NFKB1#4790	8	4.39045073935507	3.83990628335229e-05	0.000723630408385114
PAX5#5079	7	4.66869587182448	0.000134123573520654	0.00175910233516559
PBX3#5090	6	13.1487076120465	1.61405405165394e-06	6.12982513093401e-05
POLR2A#5430	9	1.93270785890226	0.00598008918360611	0.0268106689953483
POU2F2#5452	9	8.19551165196827	2.08994783441932e-08	1.48484395836e-06
SP1#6667	8	4.55870510251272	2.88273233272976e-05	0.000603587975336736
TAF1#6872	7	2.3401324000217	0.0104083984434833	0.038631178259318
TBP#6908	8	2.96541654967711	0.000730287566864471	0.00581640381268653
TCF12#6938	8	8.50757192174914	2.30735866354801e-07	1.21767676332638e-05
YY1#7528	6	2.94670244991231	0.00698724787395188	0.0295370023762511
ZEB1#6935	7	11.8219024122807	2.60652199876196e-07	1.34696957461009e-05

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.