Coexpression cluster:C2740

Full id: C2740_Mast_acute_small_leukemia_chronic_biphenotypic_adult

Phase1 CAGE Peaks

Hg19::chr3:42888864..42888881,+	p@chr3:42888864..42888881 +
Hg19::chr4:79697338..79697350,+	p10@BMP2K
Hg19::chr4:79697376..79697386,+	p9@BMP2K
Hg19::chrX:155227410..155227421,+	p4@IL9R

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:0004919	interleukin-9 receptor activity	0.00176616036736136
GO:0019983	interleukin-9 binding	0.00176616036736136
GO:0004907	interleukin receptor activity	0.035302931154496
GO:0019965	interleukin binding	0.035302931154496
GO:0004896	hematopoietin/interferon-class (D200-domain) cytokine receptor activity	0.048697238500048
GO:0019838	growth factor binding	0.0498850490643833
GO:0019955	cytokine binding	0.0498850490643833

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
myeloid cell	1.56e-28	108
common myeloid progenitor	1.56e-28	108
hematopoietic oligopotent progenitor cell	8.10e-26	161
hematopoietic multipotent progenitor cell	8.10e-26	161
hematopoietic stem cell	4.71e-25	168
angioblastic mesenchymal cell	4.71e-25	168
hematopoietic cell	9.94e-23	177
myeloid lineage restricted progenitor cell	3.19e-14	66
hematopoietic lineage restricted progenitor cell	2.28e-13	120
granulocyte monocyte progenitor cell	6.00e-13	67
myeloid leukocyte	2.22e-11	72
leukocyte	5.44e-11	136
histamine secreting cell	1.01e-09	5
biogenic amine secreting cell	1.01e-09	5
granulocytopoietic cell	1.01e-09	5
mast cell	1.01e-09	5
mast cell progenitor	1.01e-09	5
basophil mast progenitor cell	1.01e-09	5
macrophage dendritic cell progenitor	5.63e-09	61
monopoietic cell	1.74e-08	59
monocyte	1.74e-08	59
monoblast	1.74e-08	59
promonocyte	1.74e-08	59
nongranular leukocyte	9.26e-08	115
mesenchymal cell	1.30e-07	354
connective tissue cell	4.23e-07	361
defensive cell	7.90e-07	48
phagocyte	7.90e-07	48

Uber Anatomy

Ontology term	p-value	n
immune system	3.42e-15	93
hemolymphoid system	2.66e-13	108
hematopoietic system	6.90e-13	98
blood island	6.90e-13	98
bone element	1.06e-11	82
bone marrow	1.91e-11	76
skeletal element	7.64e-10	90
adult organism	2.32e-09	114
skeletal system	1.08e-08	100
neural tube	3.72e-07	56
neural rod	3.72e-07	56
future spinal cord	3.72e-07	56
neural keel	3.72e-07	56
regional part of nervous system	6.25e-07	53
regional part of brain	6.25e-07	53
connective tissue	9.22e-07	371

Disease

Ontology term	p-value	n
leukemia	3.14e-20	39
myeloid leukemia	4.16e-19	31
hematologic cancer	1.23e-17	51
immune system cancer	1.23e-17	51
chronic leukemia	2.72e-07	8

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
ATF3#467	2	11.2315872630044	0.0111955903992222	0.041133337990022
CCNT2#905	3	4.75215118272197	0.0138620699668949	0.0487356333829035
JUND#3727	3	5.24599795640327	0.0104343275174842	0.0387081565587516
NANOG#79923	2	14.6223892405063	0.00669875771536376	0.028493933818062

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.