Coexpression cluster:C1118

Full id: C1118_Burkitt_lymphoma_diffuse_b_acute_CD19_plasma

Phase1 CAGE Peaks

Hg19::chr10:45869433..45869467,-	p@chr10:45869433..45869467 -
Hg19::chr13:30951306..30951346,-	p3@LINC00426
Hg19::chr13:31019875..31019895,+	p@chr13:31019875..31019895 +
Hg19::chr13:41593493..41593506,-	p8@ELF1
Hg19::chr17:37934138..37934150,-	p12@IKZF3
Hg19::chr3:186739636..186739649,+	p2@ST6GAL1
Hg19::chr7:50348268..50348366,+	p4@IKZF1

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:0007498	mesoderm development	0.00113915997785516
GO:0050858	negative regulation of antigen receptor-mediated signaling pathway	0.0110510789473724
GO:0050860	negative regulation of T cell receptor signaling pathway	0.0110510789473724
GO:0003835	beta-galactoside alpha-2,6-sialyltransferase activity	0.0110510789473724
GO:0009888	tissue development	0.0110510789473724
GO:0050856	regulation of T cell receptor signaling pathway	0.0136552916438453
GO:0006357	regulation of transcription from RNA polymerase II promoter	0.0151262752753576
GO:0050854	regulation of antigen receptor-mediated signaling pathway	0.0170660998902863
GO:0050852	T cell receptor signaling pathway	0.0203224915910323
GO:0006366	transcription from RNA polymerase II promoter	0.0203224915910323
GO:0009311	oligosaccharide metabolic process	0.0203224915910323
GO:0043283	biopolymer metabolic process	0.0203224915910323
GO:0050851	antigen receptor-mediated signaling pathway	0.0203224915910323
GO:0002429	immune response-activating cell surface receptor signaling pathway	0.0203224915910323
GO:0006355	regulation of transcription, DNA-dependent	0.0203224915910323
GO:0002768	immune response-regulating cell surface receptor signaling pathway	0.0203224915910323
GO:0002757	immune response-activating signal transduction	0.0203224915910323
GO:0006351	transcription, DNA-dependent	0.0203224915910323
GO:0032774	RNA biosynthetic process	0.0203224915910323
GO:0002764	immune response-regulating signal transduction	0.0203224915910323
GO:0003677	DNA binding	0.0203224915910323
GO:0008373	sialyltransferase activity	0.0203224915910323
GO:0043231	intracellular membrane-bound organelle	0.0203224915910323
GO:0043227	membrane-bound organelle	0.0203224915910323
GO:0045449	regulation of transcription	0.0203224915910323
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0203224915910323
GO:0001817	regulation of cytokine production	0.0203224915910323
GO:0006350	transcription	0.0203224915910323
GO:0032501	multicellular organismal process	0.0203224915910323
GO:0010468	regulation of gene expression	0.0203224915910323
GO:0031323	regulation of cellular metabolic process	0.0211958981572183
GO:0048513	organ development	0.0226650306162141
GO:0019222	regulation of metabolic process	0.0226650306162141
GO:0016070	RNA metabolic process	0.0226650306162141
GO:0006955	immune response	0.023081999290727
GO:0030173	integral to Golgi membrane	0.023081999290727
GO:0031228	intrinsic to Golgi membrane	0.0254406974024787
GO:0002253	activation of immune response	0.0254406974024787
GO:0006959	humoral immune response	0.0261802736985663
GO:0002376	immune system process	0.0266008630112318
GO:0050778	positive regulation of immune response	0.0266008630112318
GO:0043229	intracellular organelle	0.0266008630112318
GO:0002684	positive regulation of immune system process	0.0266008630112318
GO:0043226	organelle	0.0266008630112318
GO:0003700	transcription factor activity	0.0283306583325041
GO:0050776	regulation of immune response	0.0283306583325041
GO:0043170	macromolecule metabolic process	0.0283306583325041
GO:0002682	regulation of immune system process	0.0283306583325041
GO:0051240	positive regulation of multicellular organismal process	0.0291327884348958
GO:0048731	system development	0.0291327884348958
GO:0001816	cytokine production	0.0301131886371956
GO:0010467	gene expression	0.0324642110987445
GO:0031301	integral to organelle membrane	0.0348911570496159
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0348911570496159
GO:0050794	regulation of cellular process	0.0348911570496159
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0361800227319635
GO:0031300	intrinsic to organelle membrane	0.0361800227319635
GO:0048856	anatomical structure development	0.0373638643779623
GO:0044237	cellular metabolic process	0.0373638643779623
GO:0005634	nucleus	0.0373638643779623
GO:0044238	primary metabolic process	0.0373638643779623
GO:0006486	protein amino acid glycosylation	0.0373638643779623
GO:0050789	regulation of biological process	0.0373638643779623
GO:0043413	biopolymer glycosylation	0.0373638643779623
GO:0044424	intracellular part	0.0373638643779623
GO:0009101	glycoprotein biosynthetic process	0.0373638643779623
GO:0003676	nucleic acid binding	0.0393452323018888
GO:0009100	glycoprotein metabolic process	0.0413980314412772
GO:0016564	transcription repressor activity	0.0415170191575038
GO:0007275	multicellular organismal development	0.0415170191575038
GO:0045893	positive regulation of transcription, DNA-dependent	0.0424799337304436
GO:0065007	biological regulation	0.0426644596032794

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
hematopoietic stem cell	8.20e-44	172
angioblastic mesenchymal cell	8.20e-44	172
hematopoietic cell	7.81e-42	182
hematopoietic oligopotent progenitor cell	7.66e-41	165
hematopoietic multipotent progenitor cell	7.66e-41	165
leukocyte	5.37e-34	140
hematopoietic lineage restricted progenitor cell	2.98e-31	124
nongranular leukocyte	6.06e-31	119
lymphocyte	5.10e-30	53
common lymphoid progenitor	5.10e-30	53
lymphoid lineage restricted progenitor cell	2.83e-29	52
lymphocyte of B lineage	5.96e-18	24
pro-B cell	5.96e-18	24
myeloid cell	2.22e-14	112
common myeloid progenitor	2.22e-14	112
T cell	3.64e-12	25
pro-T cell	3.64e-12	25
B cell	2.86e-11	14
mature alpha-beta T cell	1.24e-08	18
alpha-beta T cell	1.24e-08	18
immature T cell	1.24e-08	18
mature T cell	1.24e-08	18
immature alpha-beta T cell	1.24e-08	18
granulocyte monocyte progenitor cell	1.86e-07	71
myeloid lineage restricted progenitor cell	4.82e-07	70
myeloid leukocyte	5.48e-07	76

Uber Anatomy

Ontology term	p-value	n
adult organism	4.01e-26	115
hematopoietic system	9.44e-14	102
blood island	9.44e-14	102
hemolymphoid system	4.61e-12	112
neural tube	7.19e-11	57
neural rod	7.19e-11	57
future spinal cord	7.19e-11	57
neural keel	7.19e-11	57
regional part of forebrain	2.46e-09	41
forebrain	2.46e-09	41
future forebrain	2.46e-09	41
anterior neural tube	2.61e-09	42
blood	2.91e-09	15
haemolymphatic fluid	2.91e-09	15
organism substance	2.91e-09	15
telencephalon	3.79e-08	34
gray matter	6.41e-08	34
brain grey matter	6.41e-08	34
regional part of telencephalon	8.97e-08	33
regional part of brain	1.05e-07	59
cerebral hemisphere	2.55e-07	32

Disease

Ontology term	p-value	n
hematologic cancer	7.13e-16	51
immune system cancer	7.13e-16	51
leukemia	4.65e-12	39
myeloid leukemia	3.60e-08	31
lymphoma	2.30e-07	10

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	3	12.1583379015459	0.00137698016345987	0.00897021153265877
MEF2C#4208	2	11.8032441407497	0.0113453818123496	0.0415958832795051
PAX5#5079	4	3.81118030353019	0.0120826168155519	0.0438219342130651
POLR2A#5430	7	2.14745317655807	0.00474763644761028	0.0223229967113258
SRF#6722	3	5.91307639807192	0.0106686813016745	0.0393886597308253

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.