MCL coexpression mm9:2223

Phase1 CAGE Peaks

	Short description
Mm9::chr17:71202091..71202110,+	p@chr17:71202091..71202110 +
Mm9::chr5:122286819..122286854,-	p1@Sh2b3
Mm9::chr7:26472013..26472031,+	p1@Tgfb1
Mm9::chr7:26472296..26472360,+	p2@Tgfb1

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:0030097	hemopoiesis	0.00745062589058729
GO:0048534	hemopoietic or lymphoid organ development	0.00745062589058729
GO:0002520	immune system development	0.00745062589058729
GO:0048298	positive regulation of isotype switching to IgA isotypes	0.00745062589058729
GO:0048296	regulation of isotype switching to IgA isotypes	0.00745062589058729
GO:0048290	isotype switching to IgA isotypes	0.00745062589058729
GO:0045066	regulatory T cell differentiation	0.00838172450320505
GO:0002513	tolerance induction to self antigen	0.00838172450320505
GO:0002507	tolerance induction	0.00993362356088819
GO:0035162	embryonic hemopoiesis	0.0111747141761175
GO:0005160	transforming growth factor beta receptor binding	0.0111747141761175
GO:0008354	germ cell migration	0.0111747141761175
GO:0045830	positive regulation of isotype switching	0.0117615679119517
GO:0042306	regulation of protein import into nucleus	0.0117615679119517
GO:0033157	regulation of intracellular protein transport	0.0117615679119517
GO:0030279	negative regulation of ossification	0.0117615679119517
GO:0032386	regulation of intracellular transport	0.0117615679119517
GO:0043029	T cell homeostasis	0.0117615679119517
GO:0051101	regulation of DNA binding	0.0117615679119517
GO:0051223	regulation of protein transport	0.0121036186066592
GO:0045191	regulation of isotype switching	0.0121036186066592
GO:0046822	regulation of nucleocytoplasmic transport	0.0121036186066592
GO:0016202	regulation of striated muscle development	0.0121036186066592
GO:0046851	negative regulation of bone remodeling	0.0121036186066592
GO:0042130	negative regulation of T cell proliferation	0.012124272964592
GO:0002376	immune system process	0.012124272964592
GO:0048535	lymph node development	0.0132830238819138
GO:0050868	negative regulation of T cell activation	0.0132830238819138
GO:0002260	lymphocyte homeostasis	0.0132830238819138
GO:0050672	negative regulation of lymphocyte proliferation	0.0132830238819138
GO:0032945	negative regulation of mononuclear cell proliferation	0.0132830238819138
GO:0051098	regulation of binding	0.0132830238819138
GO:0002208	somatic diversification of immunoglobulins during immune response	0.0132830238819138
GO:0002204	somatic recombination of immunoglobulin genes during immune response	0.0132830238819138
GO:0045190	isotype switching	0.0132830238819138
GO:0002381	immunoglobulin production during immune response	0.0132830238819138
GO:0030879	mammary gland development	0.0132830238819138
GO:0030278	regulation of ossification	0.0137813829400792
GO:0051250	negative regulation of lymphocyte activation	0.0137813829400792
GO:0001776	leukocyte homeostasis	0.0137813829400792
GO:0050871	positive regulation of B cell activation	0.0137813829400792
GO:0016447	somatic recombination of immunoglobulin gene segments	0.0137813829400792
GO:0048872	homeostasis of number of cells	0.0137813829400792
GO:0051241	negative regulation of multicellular organismal process	0.0137813829400792
GO:0046850	regulation of bone remodeling	0.0137813829400792
GO:0016444	somatic cell DNA recombination	0.0137813829400792
GO:0002562	somatic diversification of immune receptors via germline recombination within a single locus	0.0137813829400792
GO:0016445	somatic diversification of immunoglobulins	0.0139592077719214
GO:0002200	somatic diversification of immune receptors	0.0145851479348968
GO:0050864	regulation of B cell activation	0.0162005197383997
GO:0048568	embryonic organ development	0.0162005197383997
GO:0002377	immunoglobulin production	0.0167469160996042
GO:0002440	production of molecular mediator of immune response	0.0168517804801941
GO:0042129	regulation of T cell proliferation	0.0173657434817174
GO:0007179	transforming growth factor beta receptor signaling pathway	0.0186717639494633
GO:0048513	organ development	0.0191244399477819
GO:0050670	regulation of lymphocyte proliferation	0.0203964549816058
GO:0032944	regulation of mononuclear cell proliferation	0.0203964549816058
GO:0042098	T cell proliferation	0.0208062428871481
GO:0006606	protein import into nucleus	0.0208308910676066
GO:0051170	nuclear import	0.0208547110346113
GO:0051251	positive regulation of lymphocyte activation	0.0216073136941783
GO:0030217	T cell differentiation	0.0216073136941783
GO:0050863	regulation of T cell activation	0.0219658610872752
GO:0017038	protein import	0.0219706222464948
GO:0016064	immunoglobulin mediated immune response	0.0229274507513982
GO:0019724	B cell mediated immunity	0.0229274507513982
GO:0048731	system development	0.0229274507513982
GO:0032943	mononuclear cell proliferation	0.0229274507513982
GO:0006310	DNA recombination	0.0229274507513982
GO:0048732	gland development	0.0229274507513982
GO:0046651	lymphocyte proliferation	0.0229274507513982
GO:0048869	cellular developmental process	0.0232573811711488
GO:0030154	cell differentiation	0.0232573811711488
GO:0007178	transmembrane receptor protein serine/threonine kinase signaling pathway	0.0234943137786506
GO:0051249	regulation of lymphocyte activation	0.0237979600484555
GO:0051049	regulation of transport	0.0237979600484555
GO:0042113	B cell activation	0.0237979600484555
GO:0050865	regulation of cell activation	0.0237979600484555
GO:0002250	adaptive immune response	0.0237979600484555
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0237979600484555
GO:0030098	lymphocyte differentiation	0.0237979600484555
GO:0006913	nucleocytoplasmic transport	0.0237979600484555
GO:0002449	lymphocyte mediated immunity	0.0237979600484555
GO:0001503	ossification	0.0237979600484555
GO:0051169	nuclear transport	0.0237979600484555
GO:0016049	cell growth	0.0237979600484555
GO:0031214	biomineral formation	0.0237979600484555
GO:0007519	skeletal muscle development	0.0237979600484555
GO:0002443	leukocyte mediated immunity	0.0243809033882287
GO:0048856	anatomical structure development	0.0243809033882287
GO:0046849	bone remodeling	0.0249551449177405
GO:0008361	regulation of cell size	0.0256427030608344
GO:0042110	T cell activation	0.0276751578299701
GO:0008285	negative regulation of cell proliferation	0.0276751578299701
GO:0048771	tissue remodeling	0.0280202532627508
GO:0014706	striated muscle development	0.0280202532627508
GO:0007275	multicellular organismal development	0.028361058193276
GO:0002521	leukocyte differentiation	0.0285754315903206
GO:0002252	immune effector process	0.030065091026619
GO:0008083	growth factor activity	0.0328417615019168
GO:0007517	muscle development	0.0362131531844413
GO:0008284	positive regulation of cell proliferation	0.0380114415527461
GO:0016563	transcription activator activity	0.0380716457215351
GO:0001501	skeletal development	0.0381306564905467
GO:0006605	protein targeting	0.0392790963079813
GO:0046649	lymphocyte activation	0.0392790963079813
GO:0045321	leukocyte activation	0.0423958726799473
GO:0006954	inflammatory response	0.0424124169261955
GO:0032502	developmental process	0.0437515935107479
GO:0001775	cell activation	0.0442353946983323
GO:0045893	positive regulation of transcription, DNA-dependent	0.0467966770102563
GO:0007276	gamete generation	0.0491150881882739

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	1.93e-16	32
hematopoietic oligopotent progenitor cell	1.93e-16	32
hematopoietic stem cell	1.93e-16	32
angioblastic mesenchymal cell	1.93e-16	32
hematopoietic multipotent progenitor cell	1.93e-16	32
connective tissue cell	3.46e-15	46
mesenchymal cell	3.46e-15	46
hematopoietic lineage restricted progenitor cell	4.48e-14	25
common myeloid progenitor	3.93e-11	19
motile cell	1.75e-10	54
myeloid cell	1.92e-09	16
leukocyte	9.84e-09	17
nongranular leukocyte	9.84e-09	17
nucleate cell	4.17e-08	16
myeloid lineage restricted progenitor cell	6.63e-08	13
lymphoid lineage restricted progenitor cell	1.80e-07	12
T cell	8.15e-07	11
pro-T cell	8.15e-07	11

Uber Anatomy

Ontology term	p-value	n
lateral plate mesoderm	3.45e-16	87
hematopoietic system	1.22e-15	45
blood island	1.22e-15	45
hemolymphoid system	1.88e-15	48
immune system	1.88e-15	48
connective tissue	3.46e-15	46
mesoderm	1.92e-14	120
mesoderm-derived structure	1.92e-14	120
presumptive mesoderm	1.92e-14	120
bone marrow	7.77e-10	16
musculoskeletal system	2.64e-09	32
bone element	4.31e-09	22
skeletal element	4.31e-09	22
skeletal system	4.31e-09	22
foregut	1.38e-07	80
hemopoietic organ	1.95e-07	29
immune organ	1.95e-07	29
mixed endoderm/mesoderm-derived structure	2.76e-07	35

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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