MCL coexpression mm9:589

Phase1 CAGE Peaks

	Short description
Mm9::chr10:12684247..12684278,-	p3@Stx11
Mm9::chr11:70265457..70265476,+	p2@Med11
Mm9::chr13:42147384..42147441,+	p1@Hivep1
Mm9::chr19:46379199..46379301,+	p1@Nfkb2
Mm9::chr19:46380172..46380231,+	p2@Nfkb2
Mm9::chr19:46380235..46380277,+	p3@Nfkb2
Mm9::chr1:179726582..179726645,-	p1@Adss
Mm9::chr3:135354452..135354475,-	p5@Nfkb1
Mm9::chr6:140573180..140573187,-	p@chr6:140573180..140573187 -
Mm9::chr7:20214704..20214800,-	p1@Relb
Mm9::chr7:29551464..29551487,-	p2@Nfkbib
Mm9::chr9:7872886..7872909,-	p3@Birc3

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:0048535	lymph node development	0.00570946332167024
GO:0048534	hemopoietic or lymphoid organ development	0.0128876724140671
GO:0002520	immune system development	0.0128876724140671
GO:0045083	negative regulation of interleukin-12 biosynthetic process	0.0130337800136663
GO:0006355	regulation of transcription, DNA-dependent	0.0130337800136663
GO:0002250	adaptive immune response	0.0130337800136663
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0130337800136663
GO:0006351	transcription, DNA-dependent	0.0130337800136663
GO:0032774	RNA biosynthetic process	0.0130337800136663
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0130337800136663
GO:0044424	intracellular part	0.0130337800136663
GO:0004019	adenylosuccinate synthase activity	0.0130337800136663
GO:0002266	follicular dendritic cell activation	0.0130337800136663
GO:0002268	follicular dendritic cell differentiation	0.0130337800136663
GO:0045449	regulation of transcription	0.0130337800136663
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0132348084367286
GO:0006350	transcription	0.0132348084367286
GO:0005622	intracellular	0.0132348084367286
GO:0050794	regulation of cellular process	0.0132348084367286
GO:0010468	regulation of gene expression	0.0132348084367286
GO:0045063	T-helper 1 cell differentiation	0.0137294915714405
GO:0031323	regulation of cellular metabolic process	0.0144716931784834
GO:0019222	regulation of metabolic process	0.0160142300704282
GO:0005484	SNAP receptor activity	0.0160142300704282
GO:0016070	RNA metabolic process	0.0169374732737577
GO:0016564	transcription repressor activity	0.0175102895173719
GO:0050789	regulation of biological process	0.0175102895173719
GO:0043011	myeloid dendritic cell differentiation	0.0187319398928385
GO:0042090	interleukin-12 biosynthetic process	0.0187319398928385
GO:0002467	germinal center formation	0.0187319398928385
GO:0045075	regulation of interleukin-12 biosynthetic process	0.0187319398928385
GO:0001773	myeloid dendritic cell activation	0.0187319398928385
GO:0045892	negative regulation of transcription, DNA-dependent	0.0187319398928385
GO:0048536	spleen development	0.0187319398928385
GO:0002294	CD4-positive, alpha-beta T cell differentiation during immune response	0.0187319398928385
GO:0002292	T cell differentiation during immune response	0.0187319398928385
GO:0042093	T-helper cell differentiation	0.0187319398928385
GO:0002285	lymphocyte activation during immune response	0.0187319398928385
GO:0042088	T-helper 1 type immune response	0.0187319398928385
GO:0002293	alpha-beta T cell differentiation during immune response	0.0187319398928385
GO:0002286	T cell activation during immune response	0.0187319398928385
GO:0065007	biological regulation	0.0189737725871486
GO:0002376	immune system process	0.019196031657158
GO:0002366	leukocyte activation during immune response	0.019196031657158
GO:0002263	cell activation during immune response	0.019196031657158
GO:0005634	nucleus	0.0193334072601023
GO:0010467	gene expression	0.0197681334926949
GO:0042036	negative regulation of cytokine biosynthetic process	0.0197681334926949
GO:0001775	cell activation	0.0197681334926949
GO:0043367	CD4-positive, alpha beta T cell differentiation	0.0211063835598012
GO:0016481	negative regulation of transcription	0.0213149087903502
GO:0003700	transcription factor activity	0.0213149087903502
GO:0032615	interleukin-12 production	0.0213149087903502
GO:0016566	specific transcriptional repressor activity	0.0213149087903502
GO:0048523	negative regulation of cellular process	0.0217987727723372
GO:0045934	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0228427797082627
GO:0048519	negative regulation of biological process	0.0257071905748928
GO:0031324	negative regulation of cellular metabolic process	0.0286053142831292
GO:0003677	DNA binding	0.0286053142831292
GO:0043231	intracellular membrane-bound organelle	0.0300439899962125
GO:0043227	membrane-bound organelle	0.0300439899962125
GO:0000119	mediator complex	0.0319093911503508
GO:0046632	alpha-beta T cell differentiation	0.0319093911503508
GO:0009892	negative regulation of metabolic process	0.0323932094042333
GO:0006944	membrane fusion	0.0323932094042333
GO:0017148	negative regulation of translation	0.0357783254503515
GO:0005515	protein binding	0.0357783254503515
GO:0031327	negative regulation of cellular biosynthetic process	0.0365618912224776
GO:0002274	myeloid leukocyte activation	0.0374096624706259
GO:0046631	alpha-beta T cell activation	0.0423011722615465
GO:0009890	negative regulation of biosynthetic process	0.0430412916192999

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
hematopoietic cell	3.05e-09	32
hematopoietic oligopotent progenitor cell	3.05e-09	32
hematopoietic stem cell	3.05e-09	32
angioblastic mesenchymal cell	3.05e-09	32
hematopoietic multipotent progenitor cell	3.05e-09	32
connective tissue cell	1.62e-08	46
mesenchymal cell	1.62e-08	46
motile cell	1.90e-08	54
leukocyte	1.37e-07	17
nongranular leukocyte	1.37e-07	17

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	1.89e-17	48
immune system	1.89e-17	48
hematopoietic system	1.36e-15	45
blood island	1.36e-15	45
lateral plate mesoderm	1.61e-14	87
mixed endoderm/mesoderm-derived structure	4.55e-11	35
endoderm-derived structure	1.38e-10	118
endoderm	1.38e-10	118
presumptive endoderm	1.38e-10	118
mesoderm	1.60e-10	120
mesoderm-derived structure	1.60e-10	120
presumptive mesoderm	1.60e-10	120
hemopoietic organ	2.31e-10	29
immune organ	2.31e-10	29
digestive system	2.85e-10	116
digestive tract	2.85e-10	116
primitive gut	2.85e-10	116
segment of respiratory tract	6.29e-10	27
respiratory system	1.36e-09	42
subdivision of digestive tract	2.10e-09	114
respiratory tract	2.55e-09	41
gland of gut	4.29e-09	24
pharynx	6.31e-09	24
upper respiratory tract	6.31e-09	24
chordate pharynx	6.31e-09	24
pharyngeal arch system	6.31e-09	24
pharyngeal region of foregut	6.31e-09	24
thymus	7.81e-09	23
neck	7.81e-09	23
respiratory system epithelium	7.81e-09	23
hemolymphoid system gland	7.81e-09	23
pharyngeal epithelium	7.81e-09	23
thymic region	7.81e-09	23
pharyngeal gland	7.81e-09	23
entire pharyngeal arch endoderm	7.81e-09	23
thymus primordium	7.81e-09	23
early pharyngeal endoderm	7.81e-09	23
connective tissue	1.62e-08	46
organ component layer	1.34e-07	24
organ segment	4.56e-07	35
musculoskeletal system	5.62e-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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