Coexpression cluster:C650

Full id: C650_CD19_B_lymphoma_xeroderma_splenic_Burkitt_plasma

Phase1 CAGE Peaks

Hg19::chr10:97055058..97055067,-	p@chr10:97055058..97055067 -
Hg19::chr11:60236497..60236513,+	p@chr11:60236497..60236513 +
Hg19::chr14:106329470..106329481,-	p1@IGHJ6
Hg19::chr17:27065235..27065253,+	p@chr17:27065235..27065253 +
Hg19::chr21:45627309..45627320,-	p1@ENST00000423967
Hg19::chr3:122295630..122295664,+	p@chr3:122295630..122295664 +
Hg19::chr4:38807359..38807364,-	p6@TLR1
Hg19::chr5:130545735..130545751,+	p@chr5:130545735..130545751 +
Hg19::chr5:14213197..14213223,+	p@chr5:14213197..14213223 +
Hg19::chr5:88120151..88120177,-	p6@MEF2C
Hg19::chr6:167507611..167507627,-	p@chr6:167507611..167507627 -
Hg19::chr8:11351178..11351208,+	p10@BLK
Hg19::chr9:37371328..37371339,+	p@chr9:37371328..37371339 +

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:0001958	endochondral ossification	0.0123160677063456
GO:0031325	positive regulation of cellular metabolic process	0.0123160677063456
GO:0009893	positive regulation of metabolic process	0.0123160677063456
GO:0045410	positive regulation of interleukin-6 biosynthetic process	0.0123160677063456
GO:0042535	positive regulation of tumor necrosis factor biosynthetic process	0.0123160677063456
GO:0001974	blood vessel remodeling	0.0123160677063456
GO:0042534	regulation of tumor necrosis factor biosynthetic process	0.0123160677063456
GO:0042533	tumor necrosis factor biosynthetic process	0.0123160677063456
GO:0002062	chondrocyte differentiation	0.0123160677063456
GO:0042116	macrophage activation	0.0123160677063456
GO:0045408	regulation of interleukin-6 biosynthetic process	0.0124401061933039
GO:0042226	interleukin-6 biosynthetic process	0.0136829082768297
GO:0032640	tumor necrosis factor production	0.0136829082768297
GO:0032635	interleukin-6 production	0.0146593956705327
GO:0001649	osteoblast differentiation	0.0217227219629222
GO:0048522	positive regulation of cellular process	0.0217227219629222
GO:0002274	myeloid leukocyte activation	0.0217227219629222
GO:0048518	positive regulation of biological process	0.0246979622636769
GO:0051216	cartilage development	0.0259079593262972
GO:0004715	non-membrane spanning protein tyrosine kinase activity	0.0266922339851133
GO:0042108	positive regulation of cytokine biosynthetic process	0.0266922339851133
GO:0045727	positive regulation of translation	0.0329245666875084
GO:0042035	regulation of cytokine biosynthetic process	0.0341599596012095
GO:0031328	positive regulation of cellular biosynthetic process	0.0341599596012095
GO:0042089	cytokine biosynthetic process	0.0354147101214926
GO:0042107	cytokine metabolic process	0.0354147101214926
GO:0009891	positive regulation of biosynthetic process	0.0354147101214926
GO:0051247	positive regulation of protein metabolic process	0.0400479728323247
GO:0001503	ossification	0.0400479728323247
GO:0031214	biomineral formation	0.0400479728323247
GO:0007507	heart development	0.0409485010238248
GO:0046849	bone remodeling	0.0409485010238248
GO:0048771	tissue remodeling	0.043418712488239
GO:0001816	cytokine production	0.0444347976444298
GO:0045087	innate immune response	0.0444347976444298

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	2.01e-117	24
pro-B cell	2.01e-117	24
B cell	3.53e-71	14
lymphocyte	1.80e-55	53
common lymphoid progenitor	1.80e-55	53
nucleate cell	2.78e-53	55
lymphoid lineage restricted progenitor cell	9.17e-52	52
nongranular leukocyte	2.67e-27	115
leukocyte	2.31e-24	136
hematopoietic lineage restricted progenitor cell	1.26e-21	120
hematopoietic stem cell	9.38e-19	168
angioblastic mesenchymal cell	9.38e-19	168
hematopoietic oligopotent progenitor cell	4.39e-18	161
hematopoietic multipotent progenitor cell	4.39e-18	161
hematopoietic cell	1.54e-17	177
mature B cell	5.28e-13	2
pre-B-II cell	5.28e-13	2
transitional stage B cell	5.28e-13	2
small pre-B-II cell	5.28e-13	2
immature B cell	5.28e-13	2
precursor B cell	5.85e-09	3
antibody secreting cell	2.09e-07	1
plasma cell	2.09e-07	1
plasmablast	2.09e-07	1
B-1 B cell	2.84e-07	1

Uber Anatomy

Ontology term	p-value	n
spleen	1.10e-17	3
gastrointestinal system mesentery	1.10e-17	3
stomach region	1.10e-17	3
mesentery	1.10e-17	3
gastrointestinal system serosa	1.10e-17	3
mesentery of stomach	1.10e-17	3
gut mesentery	1.10e-17	3
dorsal mesentery	1.10e-17	3
dorsal mesogastrium	1.10e-17	3
peritoneal cavity	1.10e-17	3
spleen primordium	1.10e-17	3
hemopoietic organ	7.06e-08	7
immune organ	7.06e-08	7
vermiform appendix	2.67e-07	1
caecum	2.67e-07	1
midgut	2.67e-07	1
tonsil	3.21e-07	1
mucosa-associated lymphoid tissue	3.21e-07	1
lymphoid tissue	3.21e-07	1
tonsillar ring	3.21e-07	1
lymph node	3.41e-07	1
stomach	6.00e-07	8
food storage organ	6.00e-07	8

Disease

Ontology term	p-value	n
lymphoma	1.71e-20	10
genetic disease	1.97e-07	1
monogenic disease	1.97e-07	1
xeroderma pigmentosum	1.97e-07	1
lymphatic system cancer	2.84e-07	1
lymphosarcoma	2.84e-07	1
anemia	3.85e-07	1
acute leukemia	6.20e-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	13.0935946632033	2.65123192532282e-06	9.28544637990577e-05
EBF1#1879	7	4.79578984046023	0.000208000078453033	0.00242285525245999
IRF4#3662	5	8.42865872567082	0.000186792261757661	0.00225948540950989
MEF2A#4205	7	10.0925089513468	1.58302422844669e-06	6.02073806972848e-05
NFKB1#4790	11	4.64374597431786	3.97495193507342e-07	1.92461754820182e-05
PAX5#5079	7	3.59130451678806	0.00126360149248748	0.0084829514863984
POLR2A#5430	12	1.98226447066899	0.000770364995918076	0.00604070499351963
POU2F2#5452	8	5.60376865091848	1.62953252116393e-05	0.00037668602695405
SP1#6667	7	3.06835920361433	0.00326017741207416	0.0168851806962367
TBP#6908	10	2.85136206699722	0.000251623408840283	0.00271004405443646
TCF12#6938	8	6.54428609365318	5.08413564000193e-06	0.000156678088553013
WRNIP1#56897	2	16.8953791306732	0.00604689891007867	0.0270939154519588

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.