MCL coexpression mm9:718

Phase1 CAGE Peaks

	Short description
Mm9::chr11:98219716..98219771,+	p1@Stard3
Mm9::chr13:24893063..24893082,+	p1@BC005537
Mm9::chr15:76181104..76181175,-	p2@Sharpin
Mm9::chr17:34056590..34056621,+	p1@Tapbp
Mm9::chr17:34056624..34056635,+	p2@Tapbp
Mm9::chr17:35400032..35400045,+	p1@H2-D1
Mm9::chr5:34868446..34868518,+	p1@Sh3bp2
Mm9::chr7:20408047..20408125,-	p1@Bcl3
Mm9::chr7:51809271..51809325,-	p1@Nr1h2
Mm9::chr7:86993077..86993110,-	p2@Anpep

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:0002474	antigen processing and presentation of peptide antigen via MHC class I	0.00724505164829319
GO:0048002	antigen processing and presentation of peptide antigen	0.00924049014773828
GO:0019882	antigen processing and presentation	0.00924049014773828
GO:0050823	peptide antigen stabilization	0.00924049014773828
GO:0045082	positive regulation of interleukin-10 biosynthetic process	0.00924049014773828
GO:0002312	B cell activation during immune response	0.00924049014773828
GO:0045074	regulation of interleukin-10 biosynthetic process	0.00924049014773828
GO:0002315	marginal zone B cell differentiation	0.00924049014773828
GO:0042536	negative regulation of tumor necrosis factor biosynthetic process	0.00924049014773828
GO:0002313	mature B cell differentiation during immune response	0.00924049014773828
GO:0042091	interleukin-10 biosynthetic process	0.00924049014773828
GO:0050822	peptide stabilization	0.00924049014773828
GO:0002266	follicular dendritic cell activation	0.0138580772896944
GO:0002268	follicular dendritic cell differentiation	0.0138580772896944
GO:0042832	defense response to protozoan	0.0138580772896944
GO:0002335	mature B cell differentiation	0.0138580772896944
GO:0001562	response to protozoan	0.0195605928569083
GO:0045064	T-helper 2 cell differentiation	0.0211089724546047
GO:0019883	antigen processing and presentation of endogenous antigen	0.0211089724546047
GO:0002483	antigen processing and presentation of endogenous peptide antigen	0.0211089724546047
GO:0019885	antigen processing and presentation of endogenous peptide antigen via MHC class I	0.0211089724546047
GO:0032613	interleukin-10 production	0.0221431809126398
GO:0019730	antimicrobial humoral response	0.0221431809126398
GO:0042534	regulation of tumor necrosis factor biosynthetic process	0.0221431809126398
GO:0042092	T-helper 2 type immune response	0.0221431809126398
GO:0042533	tumor necrosis factor biosynthetic process	0.0221431809126398
GO:0002376	immune system process	0.0221431809126398
GO:0002467	germinal center formation	0.0221431809126398
GO:0017127	cholesterol transporter activity	0.0221431809126398
GO:0032729	positive regulation of interferon-gamma production	0.0221431809126398
GO:0015248	sterol transporter activity	0.0221431809126398
GO:0048536	spleen development	0.0221431809126398
GO:0002294	CD4-positive, alpha-beta T cell differentiation during immune response	0.0221431809126398
GO:0002292	T cell differentiation during immune response	0.0221431809126398
GO:0042093	T-helper cell differentiation	0.0221431809126398
GO:0002285	lymphocyte activation during immune response	0.0221431809126398
GO:0015485	cholesterol binding	0.0221431809126398
GO:0042088	T-helper 1 type immune response	0.0221431809126398
GO:0002293	alpha-beta T cell differentiation during immune response	0.0221431809126398
GO:0002286	T cell activation during immune response	0.0221431809126398
GO:0006518	peptide metabolic process	0.0221431809126398
GO:0002366	leukocyte activation during immune response	0.0221431809126398
GO:0042771	DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis	0.0221431809126398
GO:0032649	regulation of interferon-gamma production	0.0221431809126398
GO:0002263	cell activation during immune response	0.0221431809126398
GO:0042036	negative regulation of cytokine biosynthetic process	0.0240640605136774
GO:0004179	membrane alanyl aminopeptidase activity	0.0248450617340259
GO:0043367	CD4-positive, alpha beta T cell differentiation	0.0248450617340259
GO:0016284	alanine aminopeptidase activity	0.0248450617340259
GO:0030330	DNA damage response, signal transduction by p53 class mediator	0.028764067195156
GO:0032934	sterol binding	0.0297795669440622
GO:0006700	C21-steroid hormone biosynthetic process	0.0297795669440622
GO:0032640	tumor necrosis factor production	0.0312986652257444
GO:0032609	interferon-gamma production	0.0321650672965152
GO:0042612	MHC class I protein complex	0.0321650672965152
GO:0008630	DNA damage response, signal transduction resulting in induction of apoptosis	0.0329699268078963
GO:0008207	C21-steroid hormone metabolic process	0.0329699268078963
GO:0001819	positive regulation of cytokine production	0.0380974731358029
GO:0046632	alpha-beta T cell differentiation	0.0393168040238089
GO:0017148	negative regulation of translation	0.0459903513050557
GO:0031327	negative regulation of cellular biosynthetic process	0.0470368520117554
GO:0042611	MHC protein complex	0.0472862331522246
GO:0005770	late endosome	0.0472862331522246

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
motile cell	1.44e-09	54
connective tissue cell	2.12e-09	46
mesenchymal cell	2.12e-09	46

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	3.82e-15	118
endoderm	3.82e-15	118
presumptive endoderm	3.82e-15	118
digestive system	1.66e-14	116
digestive tract	1.66e-14	116
primitive gut	1.66e-14	116
subdivision of digestive tract	1.83e-13	114
hemolymphoid system	1.11e-11	48
immune system	1.11e-11	48
hematopoietic system	4.82e-10	45
blood island	4.82e-10	45
connective tissue	2.12e-09	46
organ component layer	2.75e-09	24
unilaminar epithelium	8.16e-09	66
intestine	2.22e-08	31
mucosa	2.61e-08	15
gut epithelium	3.28e-08	55
endo-epithelium	1.78e-07	69
gastrointestinal system	1.81e-07	47
bone marrow	3.60e-07	16
intestinal mucosa	4.14e-07	13
anatomical wall	4.14e-07	13
wall of intestine	4.14e-07	13
gastrointestinal system mucosa	4.14e-07	13
musculoskeletal system	9.52e-07	32

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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