MCL coexpression mm9:1643

Phase1 CAGE Peaks

	Short description
Mm9::chr13:37437253..37437276,+	p2@Ly86
Mm9::chr13:37437284..37437301,+	p1@Ly86
Mm9::chr17:34272526..34272616,+	p1@H2-DMa
Mm9::chr19:44463324..44463335,+	p@chr19:44463324..44463335 +
Mm9::chr7:100027264..100027271,-	p@chr7:100027264..100027271 -

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:0010008	endosome membrane	0.0111713463617682
GO:0044440	endosomal part	0.0111713463617682
GO:0006955	immune response	0.0111713463617682
GO:0005765	lysosomal membrane	0.0111713463617682
GO:0045059	positive thymic T cell selection	0.0111713463617682
GO:0043368	positive T cell selection	0.0111713463617682
GO:0005771	multivesicular body	0.0111713463617682
GO:0042613	MHC class II protein complex	0.0111713463617682
GO:0045582	positive regulation of T cell differentiation	0.0111713463617682
GO:0051085	chaperone cofactor-dependent protein folding	0.0111713463617682
GO:0045061	thymic T cell selection	0.0111713463617682
GO:0006458	'de novo' protein folding	0.0111713463617682
GO:0051084	'de novo' posttranslational protein folding	0.0111713463617682
GO:0002376	immune system process	0.0111713463617682
GO:0045621	positive regulation of lymphocyte differentiation	0.0111713463617682
GO:0002495	antigen processing and presentation of peptide antigen via MHC class II	0.0111713463617682
GO:0005774	vacuolar membrane	0.0111713463617682
GO:0019886	antigen processing and presentation of exogenous peptide antigen via MHC class II	0.0111713463617682
GO:0045580	regulation of T cell differentiation	0.0111713463617682
GO:0045058	T cell selection	0.0111713463617682
GO:0002478	antigen processing and presentation of exogenous peptide antigen	0.0112649144841956
GO:0002504	antigen processing and presentation of peptide or polysaccharide antigen via MHC class II	0.0113499436687616
GO:0044437	vacuolar part	0.0114275476899699
GO:0045619	regulation of lymphocyte differentiation	0.0120893513204155
GO:0019884	antigen processing and presentation of exogenous antigen	0.0120893513204155
GO:0033077	T cell differentiation in the thymus	0.0126344989165626
GO:0005770	late endosome	0.0126699028249458
GO:0042611	MHC protein complex	0.0126699028249458
GO:0048002	antigen processing and presentation of peptide antigen	0.0154015745624465
GO:0050870	positive regulation of T cell activation	0.018824533378516
GO:0019882	antigen processing and presentation	0.0241392290912958
GO:0051251	positive regulation of lymphocyte activation	0.0242648977314301
GO:0030217	T cell differentiation	0.0242648977314301
GO:0050863	regulation of T cell activation	0.0243220607194743
GO:0016064	immunoglobulin mediated immune response	0.0258820835066117
GO:0019724	B cell mediated immunity	0.0258820835066117
GO:0051249	regulation of lymphocyte activation	0.0282219397142
GO:0050865	regulation of cell activation	0.0282219397142
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0282219397142
GO:0002250	adaptive immune response	0.0282219397142
GO:0030098	lymphocyte differentiation	0.0282219397142
GO:0002449	lymphocyte mediated immunity	0.0282219397142
GO:0050778	positive regulation of immune response	0.0282219397142
GO:0002684	positive regulation of immune system process	0.0282219397142
GO:0005886	plasma membrane	0.0282219397142
GO:0002443	leukocyte mediated immunity	0.0282219397142
GO:0050776	regulation of immune response	0.0308588446470944
GO:0002682	regulation of immune system process	0.0308588446470944
GO:0051240	positive regulation of multicellular organismal process	0.0309310587511431
GO:0042110	T cell activation	0.0309310587511431
GO:0006461	protein complex assembly	0.0320018973692504
GO:0002521	leukocyte differentiation	0.0320018973692504
GO:0006457	protein folding	0.0321371246181744
GO:0002252	immune effector process	0.0327506438198464
GO:0005768	endosome	0.0390333443011157
GO:0005764	lysosome	0.0390333443011157
GO:0000323	lytic vacuole	0.0390333443011157
GO:0046649	lymphocyte activation	0.0423440093609866
GO:0005773	vacuole	0.0423440093609866
GO:0045321	leukocyte activation	0.0438610383771851
GO:0030097	hemopoiesis	0.0438610383771851
GO:0006954	inflammatory response	0.0438610383771851
GO:0001775	cell activation	0.0458462073904284
GO:0048534	hemopoietic or lymphoid organ development	0.0473617803066281

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
common myeloid progenitor	1.32e-07	19

Uber Anatomy

Ontology term	p-value	n
bone marrow	2.96e-11	16
bone element	3.55e-11	22
skeletal element	3.55e-11	22
skeletal system	3.55e-11	22
hemolymphoid system	1.09e-09	48
immune system	1.09e-09	48
adult organism	3.05e-08	51
hematopoietic system	3.53e-08	45
blood island	3.53e-08	45
musculoskeletal system	3.40e-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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