Coexpression cluster:C2717

Full id: C2717_acute_B_xeroderma_b_splenic_plasma_Dendritic

Phase1 CAGE Peaks

Hg19::chr3:127454947..127454961,-	p16@MGLL
Hg19::chr3:127454965..127454984,-	p27@MGLL
Hg19::chr3:174988853..174988868,-	p1@NAALADL2-AS2
Hg19::chr7:150130832..150130852,+	p2@ENST00000486954

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:0047372	acylglycerol lipase activity	0.000824208171435299
GO:0004622	lysophospholipase activity	0.00185446838572942
GO:0004620	phospholipase activity	0.0145266690215472
GO:0016298	lipase activity	0.0145266690215472
GO:0004091	carboxylesterase activity	0.0154126928058401
GO:0006954	inflammatory response	0.019987048157306
GO:0009611	response to wounding	0.0249028611797951
GO:0006952	defense response	0.028984654028808
GO:0009605	response to external stimulus	0.028984654028808
GO:0006629	lipid metabolic process	0.0389850465088896
GO:0016788	hydrolase activity, acting on ester bonds	0.041965932728914
GO:0006950	response to stress	0.041965932728914

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
nongranular leukocyte	1.05e-29	119
leukocyte	6.17e-29	140
hematopoietic stem cell	1.36e-25	172
angioblastic mesenchymal cell	1.36e-25	172
hematopoietic lineage restricted progenitor cell	2.45e-24	124
hematopoietic cell	1.17e-23	182
macrophage dendritic cell progenitor	1.35e-23	65
monopoietic cell	2.24e-23	63
monocyte	2.24e-23	63
monoblast	2.24e-23	63
promonocyte	2.24e-23	63
hematopoietic oligopotent progenitor cell	6.32e-22	165
hematopoietic multipotent progenitor cell	6.32e-22	165
granulocyte monocyte progenitor cell	1.91e-20	71
myeloid lineage restricted progenitor cell	1.05e-19	70
myeloid leukocyte	4.04e-17	76
myeloid cell	2.04e-15	112
common myeloid progenitor	2.04e-15	112
CD14-positive, CD16-negative classical monocyte	2.97e-15	42
classical monocyte	1.08e-14	45
lymphocyte of B lineage	3.57e-09	24
pro-B cell	3.57e-09	24
dendritic cell	4.11e-09	10

Uber Anatomy

Ontology term	p-value	n
hematopoietic system	1.84e-20	102
blood island	1.84e-20	102
immune system	2.38e-19	115
hemolymphoid system	2.57e-19	112
bone marrow	6.49e-19	80
bone element	1.81e-17	86
skeletal element	1.40e-13	101
skeletal system	1.40e-13	101
adult organism	6.36e-12	115
hemopoietic organ	8.09e-07	7

Disease

Ontology term	p-value	n
lymphoma	3.31e-08	10
hematologic cancer	5.45e-07	51
immune system cancer	5.45e-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)
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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
BATF#10538	3	18.2683513442277	0.000268166010572129	0.00286751202806825
EBF1#1879	3	6.67985013492675	0.00518429411827891	0.0240576954331703
POU2F2#5452	3	6.82959304330689	0.00486047377520374	0.0227684691907828
SPI1#6688	3	6.15324263139204	0.00658038711305903	0.0281094952636416

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.