Coexpression cluster:C3725

Full id: C3725_CD14_CD4_CD8_Burkitt_CD19_Basophils_lymphoma

Phase1 CAGE Peaks

Hg19::chr18:48405033..48405061,+	p3@ME2
Hg19::chr4:110481348..110481368,+	p2@CCDC109B
Hg19::chr4:110481374..110481458,+	p1@CCDC109B

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:0016619	malate dehydrogenase (oxaloacetate-decarboxylating) activity	0.00129518426939833
GO:0004471	malate dehydrogenase (decarboxylating) activity	0.00129518426939833
GO:0004470	malic enzyme activity	0.00518005080645473
GO:0006108	malate metabolic process	0.00518005080645473
GO:0016615	malate dehydrogenase activity	0.00518005080645473
GO:0043648	dicarboxylic acid metabolic process	0.00690612438981643
GO:0006100	tricarboxylic acid cycle intermediate metabolic process	0.0118362817252174
GO:0051287	NAD binding	0.0232889542237499
GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	0.0393973010196954
GO:0016614	oxidoreductase activity, acting on CH-OH group of donors	0.0393973010196954
GO:0031980	mitochondrial lumen	0.0393973010196954
GO:0005759	mitochondrial matrix	0.0393973010196954

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><br>

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Cell Type

Ontology term	p-value	n
nongranular leukocyte	3.43e-45	115
hematopoietic lineage restricted progenitor cell	4.54e-41	120
leukocyte	6.57e-39	136
hematopoietic stem cell	1.28e-31	168
angioblastic mesenchymal cell	1.28e-31	168
hematopoietic oligopotent progenitor cell	1.45e-28	161
hematopoietic multipotent progenitor cell	1.45e-28	161
hematopoietic cell	5.02e-27	177
defensive cell	6.75e-26	48
phagocyte	6.75e-26	48
classical monocyte	2.20e-25	42
CD14-positive, CD16-negative classical monocyte	2.20e-25	42
nucleate cell	1.56e-22	55
lymphocyte	2.00e-22	53
common lymphoid progenitor	2.00e-22	53
lymphoid lineage restricted progenitor cell	5.08e-22	52
monopoietic cell	2.85e-20	59
monocyte	2.85e-20	59
monoblast	2.85e-20	59
promonocyte	2.85e-20	59
macrophage dendritic cell progenitor	5.70e-20	61
myeloid lineage restricted progenitor cell	7.23e-19	66
granulocyte monocyte progenitor cell	7.28e-19	67
myeloid leukocyte	4.89e-16	72
stem cell	9.42e-13	441
somatic stem cell	1.43e-12	433
multi fate stem cell	1.66e-12	427
native cell	2.00e-12	722
lymphocyte of B lineage	6.83e-12	24
pro-B cell	6.83e-12	24
mesenchymal cell	5.42e-11	354
somatic cell	8.57e-11	588
T cell	4.65e-10	25
pro-T cell	4.65e-10	25
stuff accumulating cell	5.40e-10	87
myeloid cell	1.02e-09	108
common myeloid progenitor	1.02e-09	108
mature alpha-beta T cell	1.06e-09	18
alpha-beta T cell	1.06e-09	18
immature T cell	1.06e-09	18
mature T cell	1.06e-09	18
immature alpha-beta T cell	1.06e-09	18
connective tissue cell	1.58e-09	361
motile cell	2.48e-09	386
B cell	6.03e-09	14
animal cell	3.64e-07	679
eukaryotic cell	3.64e-07	679
meso-epithelial cell	4.77e-07	45
CD8-positive, alpha-beta T cell	7.86e-07	11
endothelial cell of vascular tree	8.45e-07	24
endothelial cell	9.23e-07	36

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	1.48e-25	108
hematopoietic system	2.23e-23	98
blood island	2.23e-23	98
immune system	1.34e-22	93
bone marrow	4.15e-18	76
bone element	9.66e-17	82
lateral plate mesoderm	6.34e-16	203
skeletal element	3.51e-14	90
skeletal system	3.71e-13	100
connective tissue	2.83e-09	371
musculoskeletal system	1.63e-08	167
mesoderm	1.46e-07	315
mesoderm-derived structure	1.46e-07	315
presumptive mesoderm	1.46e-07	315

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)
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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
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.046204157320272
ZNF263#10127	3	8.22184163701068	0.00179904392556587	0.0109359378698664

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.