MCL coexpression mm9:2281

Phase1 CAGE Peaks

	Short description
Mm9::chr1:132774997..132775019,+	p4@Faim3
Mm9::chr2:13715640..13715652,-	p3@St8sia6
Mm9::chr2:13715659..13715668,-	p6@St8sia6
Mm9::chrX:10294577..10294582,-	p2@ENSMUST00000101687

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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GO ID	GO name	FDR corrected p-value
GO:0009247	glycolipid biosynthetic process	0.0250935186815063
GO:0006493	protein amino acid O-linked glycosylation	0.0250935186815063
GO:0006664	glycolipid metabolic process	0.0250935186815063
GO:0008373	sialyltransferase activity	0.0250935186815063
GO:0030173	integral to Golgi membrane	0.0250935186815063
GO:0031228	intrinsic to Golgi membrane	0.0250935186815063
GO:0031301	integral to organelle membrane	0.0360762254170714
GO:0031300	intrinsic to organelle membrane	0.0360762254170714
GO:0000139	Golgi membrane	0.0360762254170714
GO:0046467	membrane lipid biosynthetic process	0.0360762254170714
GO:0006486	protein amino acid glycosylation	0.0360762254170714
GO:0043413	biopolymer glycosylation	0.0360762254170714
GO:0016051	carbohydrate biosynthetic process	0.0360762254170714
GO:0009101	glycoprotein biosynthetic process	0.0360762254170714
GO:0009100	glycoprotein metabolic process	0.0392679008747741
GO:0044431	Golgi apparatus part	0.0495394347287502

Relative expression of the co-expression cluster over median <br>Analyst:

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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
thymocyte	1.27e-09	6
double negative thymocyte	1.27e-09	6
naive T cell	1.27e-09	6
double-positive, alpha-beta thymocyte	1.27e-09	6
CD4-positive, alpha-beta thymocyte	1.27e-09	6
naive thymus-derived CD4-positive, alpha-beta T cell	1.27e-09	6
DN4 thymocyte	1.27e-09	6
DN1 thymic pro-T cell	1.27e-09	6
DN2 thymocyte	1.27e-09	6
DN3 thymocyte	1.27e-09	6
immature single positive thymocyte	1.27e-09	6
early T lineage precursor	1.27e-09	6
mature CD4 single-positive thymocyte	1.27e-09	6
resting double-positive thymocyte	1.27e-09	6
double-positive blast	1.27e-09	6
CD69-positive double-positive thymocyte	1.27e-09	6
CD69-positive, CD4-positive single-positive thymocyte	1.27e-09	6
CD4-positive, CD8-intermediate double-positive thymocyte	1.27e-09	6
CD24-positive, CD4 single-positive thymocyte	1.27e-09	6
CD4-positive, alpha-beta T cell	1.32e-09	8
mature alpha-beta T cell	2.17e-08	9
alpha-beta T cell	2.17e-08	9
immature T cell	2.17e-08	9
mature T cell	2.17e-08	9
immature alpha-beta T cell	2.17e-08	9
lymphoid lineage restricted progenitor cell	7.39e-08	12
lymphocyte	3.99e-07	13
common lymphoid progenitor	3.99e-07	13

Uber Anatomy

Ontology term	p-value	n
segment of respiratory tract	1.90e-09	27
respiratory tract	9.92e-09	41
organ segment	1.35e-08	35
respiratory system	2.07e-08	42
mixed endoderm/mesoderm-derived structure	1.69e-07	35
hemopoietic organ	3.70e-07	29
immune organ	3.70e-07	29
organism subdivision	4.50e-07	150
thymus	5.80e-07	23
neck	5.80e-07	23
respiratory system epithelium	5.80e-07	23
hemolymphoid system gland	5.80e-07	23
pharyngeal epithelium	5.80e-07	23
thymic region	5.80e-07	23
pharyngeal gland	5.80e-07	23
entire pharyngeal arch endoderm	5.80e-07	23
thymus primordium	5.80e-07	23
early pharyngeal endoderm	5.80e-07	23

TFBS overrepresentation<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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