Coexpression cluster:C651

Full id: C651_splenic_CD19_B_xeroderma_plasma_Burkitt_lymphoma

Phase1 CAGE Peaks

Hg19::chr10:98460583..98460643,-	p2@PIK3AP1
Hg19::chr11:60222928..60222933,+	p5@MS4A1
Hg19::chr11:60223277..60223297,+	p2@MS4A1
Hg19::chr17:29645385..29645411,+	p@chr17:29645385..29645411 +
Hg19::chr19:55128576..55128604,+	p3@LILRB1
Hg19::chr1:111670644..111670656,-	p7@DRAM2
Hg19::chr1:220943820..220943841,+	p@chr1:220943820..220943841 +
Hg19::chr1:221220442..221220467,+	p@chr1:221220442..221220467 +
Hg19::chr4:38784572..38784589,-	p2@TLR10
Hg19::chr4:38784592..38784619,-	p1@TLR10
Hg19::chr6:41700616..41700664,-	p8@TFEB
Hg19::chr9:37025706..37025716,-	p@chr9:37025706..37025716 -
Hg19::chr9:37025731..37025750,-	p@chr9:37025731..37025750 -

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	0.0148625519068601
GO:0008157	protein phosphatase 1 binding	0.0148625519068601
GO:0002376	immune system process	0.0148625519068601
GO:0019903	protein phosphatase binding	0.0437448317277681
GO:0019902	phosphatase binding	0.0452754369404383

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
leukocyte	2.13e-53	140
hematopoietic stem cell	2.03e-52	172
angioblastic mesenchymal cell	2.03e-52	172
hematopoietic cell	2.00e-49	182
hematopoietic oligopotent progenitor cell	5.32e-49	165
hematopoietic multipotent progenitor cell	5.32e-49	165
nongranular leukocyte	5.67e-47	119
hematopoietic lineage restricted progenitor cell	1.15e-43	124
lymphocyte	1.30e-24	53
common lymphoid progenitor	1.30e-24	53
lymphoid lineage restricted progenitor cell	7.44e-24	52
myeloid cell	1.61e-23	112
common myeloid progenitor	1.61e-23	112
myeloid leukocyte	4.20e-23	76
lymphocyte of B lineage	1.05e-20	24
pro-B cell	1.05e-20	24
granulocyte monocyte progenitor cell	5.04e-20	71
myeloid lineage restricted progenitor cell	9.70e-20	70
monopoietic cell	1.44e-19	63
monocyte	1.44e-19	63
monoblast	1.44e-19	63
promonocyte	1.44e-19	63
macrophage dendritic cell progenitor	3.42e-19	65
CD14-positive, CD16-negative classical monocyte	7.00e-19	42
classical monocyte	4.45e-17	45
B cell	9.66e-13	14

Uber Anatomy

Ontology term	p-value	n
adult organism	5.65e-35	115
hematopoietic system	4.45e-28	102
blood island	4.45e-28	102
hemolymphoid system	8.58e-25	112
bone marrow	6.20e-17	80
neural tube	1.74e-15	57
neural rod	1.74e-15	57
future spinal cord	1.74e-15	57
neural keel	1.74e-15	57
bone element	1.48e-14	86
anterior neural tube	1.81e-12	42
immune system	2.42e-12	115
regional part of forebrain	4.24e-12	41
forebrain	4.24e-12	41
future forebrain	4.24e-12	41
regional part of brain	2.12e-11	59
gray matter	1.59e-10	34
brain grey matter	1.59e-10	34
telencephalon	1.76e-10	34
blood	2.91e-10	15
haemolymphatic fluid	2.91e-10	15
organism substance	2.91e-10	15
regional part of telencephalon	3.76e-10	33
central nervous system	6.84e-10	82
brain	8.26e-10	69
future brain	8.26e-10	69
skeletal element	8.93e-10	101
skeletal system	8.93e-10	101
cerebral hemisphere	2.12e-09	32
regional part of cerebral cortex	8.11e-09	22
neocortex	5.10e-08	20
neural plate	3.03e-07	86
presumptive neural plate	3.03e-07	86
regional part of nervous system	5.28e-07	94
nervous system	5.28e-07	94
cerebral cortex	6.50e-07	25
pallium	6.50e-07	25

Disease

Ontology term	p-value	n
hematologic cancer	1.39e-07	51
immune system cancer	1.39e-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)
{{{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	9.28856125624925e-05
BCL3#602	4	10.6298777857656	0.00040648606589517	0.00387663210994664
EBF1#1879	8	5.4809026748117	1.92247936454994e-05	0.000434310669163381
MEF2A#4205	8	11.5342959443963	6.61255911623314e-08	4.04101264798287e-06
NFKB1#4790	9	3.79942852444189	7.7463744424886e-05	0.00119395454604349
POU2F2#5452	6	4.20282648818886	0.00151318059670815	0.00965630382131263
SPI1#6688	8	5.04881446678322	3.53708006891545e-05	0.000685232990757671
TCF12#6938	6	4.90821457023989	0.000660680428346316	0.0054084341790297
YY1#7528	7	2.64447655761361	0.00776069714688224	0.031919011118152

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.