MCL coexpression mm9:785

Phase1 CAGE Peaks

	Short description
Mm9::chr11:33947078..33947093,+	p2@Lcp2
Mm9::chr14:54843390..54843408,+	p@chr14:54843390..54843408 +
Mm9::chr16:48772258..48772270,-	p5@Trat1
Mm9::chr1:140072473..140072489,-	p@chr1:140072473..140072489 -
Mm9::chr1:140072490..140072513,-	p@chr1:140072490..140072513 -
Mm9::chr1:157005834..157005906,+	p1@Stx6
Mm9::chr1:36827266..36827270,+	p@chr1:36827266..36827270 +
Mm9::chr6:41492719..41492776,+	p1@ENSMUST00000103293 p1@uc009bpq.1
Mm9::chr6:41494508..41494519,+	p@chr6:41494508..41494519 +

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:0050851	antigen receptor-mediated signaling pathway	4.98032272369071e-06
GO:0002429	immune response-activating cell surface receptor signaling pathway	4.98032272369071e-06
GO:0002768	immune response-regulating cell surface receptor signaling pathway	4.98032272369071e-06
GO:0002757	immune response-activating signal transduction	4.98032272369071e-06
GO:0002764	immune response-regulating signal transduction	4.98032272369071e-06
GO:0050857	positive regulation of antigen receptor-mediated signaling pathway	9.00386442255923e-06
GO:0002253	activation of immune response	3.07476650178131e-05
GO:0050778	positive regulation of immune response	4.96385487923431e-05
GO:0002684	positive regulation of immune system process	4.96385487923431e-05
GO:0042101	T cell receptor complex	5.7239151266756e-05
GO:0050776	regulation of immune response	5.7239151266756e-05
GO:0002682	regulation of immune system process	5.7239151266756e-05
GO:0051240	positive regulation of multicellular organismal process	5.86826780191044e-05
GO:0050854	regulation of antigen receptor-mediated signaling pathway	7.06826458685156e-05
GO:0050850	positive regulation of calcium-mediated signaling	8.76915106603675e-05
GO:0050848	regulation of calcium-mediated signaling	8.76915106603675e-05
GO:0050852	T cell receptor signaling pathway	0.00016180330444394
GO:0001772	immunological synapse	0.000181633193691871
GO:0002376	immune system process	0.000181633193691871
GO:0019722	calcium-mediated signaling	0.000188708441611194
GO:0045321	leukocyte activation	0.000199043110945394
GO:0001775	cell activation	0.000234537227246329
GO:0042102	positive regulation of T cell proliferation	0.000274091506438314
GO:0051239	regulation of multicellular organismal process	0.000427113906584292
GO:0032946	positive regulation of mononuclear cell proliferation	0.000434765238743307
GO:0050671	positive regulation of lymphocyte proliferation	0.000434765238743307
GO:0042129	regulation of T cell proliferation	0.000571796048606228
GO:0050870	positive regulation of T cell activation	0.000578207652799299
GO:0009966	regulation of signal transduction	0.000595041323197565
GO:0032944	regulation of mononuclear cell proliferation	0.000796095387164107
GO:0050670	regulation of lymphocyte proliferation	0.000796095387164107
GO:0042098	T cell proliferation	0.000830919090127141
GO:0051251	positive regulation of lymphocyte activation	0.000963093465642323
GO:0030217	T cell differentiation	0.000963093465642323
GO:0050863	regulation of T cell activation	0.000998240347442248
GO:0009967	positive regulation of signal transduction	0.00103339512010087
GO:0043235	receptor complex	0.00123461326090412
GO:0032943	mononuclear cell proliferation	0.00123747495275673
GO:0046651	lymphocyte proliferation	0.00123747495275673
GO:0006955	immune response	0.0012790080426787
GO:0051249	regulation of lymphocyte activation	0.00148158064106413
GO:0050865	regulation of cell activation	0.00155289535336506
GO:0030098	lymphocyte differentiation	0.00173599562815789
GO:0001920	negative regulation of receptor recycling	0.00178648417532317
GO:0001915	negative regulation of T cell mediated cytotoxicity	0.00178648417532317
GO:0050862	positive regulation of T cell receptor signaling pathway	0.00178648417532317
GO:0042110	T cell activation	0.00261166190151548
GO:0019932	second-messenger-mediated signaling	0.00277799786397229
GO:0002521	leukocyte differentiation	0.0029006502973153
GO:0043366	beta selection	0.00322232420445744
GO:0001960	negative regulation of cytokine and chemokine mediated signaling pathway	0.00322232420445744
GO:0048522	positive regulation of cellular process	0.00330859469213209
GO:0001916	positive regulation of T cell mediated cytotoxicity	0.00391239349282106
GO:0051283	negative regulation of sequestering of calcium ion	0.00391239349282106
GO:0051208	sequestering of calcium ion	0.00391239349282106
GO:0001919	regulation of receptor recycling	0.00391239349282106
GO:0002711	positive regulation of T cell mediated immunity	0.00391239349282106
GO:0046638	positive regulation of alpha-beta T cell differentiation	0.00391239349282106
GO:0001959	regulation of cytokine and chemokine mediated signaling pathway	0.00391239349282106
GO:0001914	regulation of T cell mediated cytotoxicity	0.00391239349282106
GO:0051238	sequestering of metal ion	0.00391239349282106
GO:0051282	regulation of sequestering of calcium ion	0.00391239349282106
GO:0051209	release of sequestered calcium ion into cytosol	0.00391239349282106
GO:0048518	positive regulation of biological process	0.00409896873080155
GO:0008284	positive regulation of cell proliferation	0.00418613191979287
GO:0046649	lymphocyte activation	0.00469435774122956
GO:0046637	regulation of alpha-beta T cell differentiation	0.00469435774122956
GO:0002709	regulation of T cell mediated immunity	0.00469435774122956
GO:0001911	negative regulation of leukocyte mediated cytotoxicity	0.00469435774122956
GO:0001913	T cell mediated cytotoxicity	0.00469435774122956
GO:0030097	hemopoiesis	0.00533850869155248
GO:0001881	receptor recycling	0.00570432351252845
GO:0007242	intracellular signaling cascade	0.00593092495019197
GO:0048534	hemopoietic or lymphoid organ development	0.00635863346583675
GO:0050663	cytokine secretion	0.00639999410461072
GO:0007032	endosome organization and biogenesis	0.00639999410461072
GO:0001784	phosphotyrosine binding	0.00639999410461072
GO:0002520	immune system development	0.00692614222053051
GO:0051179	localization	0.00692614222053051
GO:0050853	B cell receptor signaling pathway	0.00692614222053051
GO:0043368	positive T cell selection	0.00692614222053051
GO:0045059	positive thymic T cell selection	0.00692614222053051
GO:0046641	positive regulation of alpha-beta T cell proliferation	0.00692614222053051
GO:0045060	negative thymic T cell selection	0.00746502352963415
GO:0002456	T cell mediated immunity	0.00746502352963415
GO:0043383	negative T cell selection	0.00746502352963415
GO:0045309	protein phosphorylated amino acid binding	0.00746502352963415
GO:0046635	positive regulation of alpha-beta T cell activation	0.00746502352963415
GO:0046640	regulation of alpha-beta T cell proliferation	0.00812039942774404
GO:0051607	defense response to virus	0.00812039942774404
GO:0050856	regulation of T cell receptor signaling pathway	0.00812039942774404
GO:0042127	regulation of cell proliferation	0.00947061860720167
GO:0046634	regulation of alpha-beta T cell activation	0.00970936502612786
GO:0045576	mast cell activation	0.0101541368611683
GO:0045582	positive regulation of T cell differentiation	0.0101541368611683
GO:0046633	alpha-beta T cell proliferation	0.0101541368611683
GO:0001912	positive regulation of leukocyte mediated cytotoxicity	0.0101541368611683
GO:0051219	phosphoprotein binding	0.0108868737395942
GO:0045061	thymic T cell selection	0.0116046262952258
GO:0045621	positive regulation of lymphocyte differentiation	0.0117217562736301
GO:0002705	positive regulation of leukocyte mediated immunity	0.0117217562736301
GO:0051235	maintenance of localization	0.0117217562736301
GO:0031341	regulation of cell killing	0.0117217562736301
GO:0002708	positive regulation of lymphocyte mediated immunity	0.0117217562736301
GO:0001910	regulation of leukocyte mediated cytotoxicity	0.0117217562736301
GO:0002699	positive regulation of immune effector process	0.0123838947730921
GO:0044459	plasma membrane part	0.0124516367663656
GO:0045058	T cell selection	0.0124516367663656
GO:0007204	elevation of cytosolic calcium ion concentration	0.0124516367663656
GO:0045580	regulation of T cell differentiation	0.0124516367663656
GO:0002703	regulation of leukocyte mediated immunity	0.0124516367663656
GO:0002706	regulation of lymphocyte mediated immunity	0.0124516367663656
GO:0002824	positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0128387463247149
GO:0051051	negative regulation of transport	0.0128387463247149
GO:0002821	positive regulation of adaptive immune response	0.0128387463247149
GO:0002697	regulation of immune effector process	0.0133188921147921
GO:0051480	cytosolic calcium ion homeostasis	0.0133188921147921
GO:0046632	alpha-beta T cell differentiation	0.0145929289081716
GO:0007165	signal transduction	0.0146620771487547
GO:0001909	leukocyte mediated cytotoxicity	0.014664766672504
GO:0001906	cell killing	0.014664766672504
GO:0002819	regulation of adaptive immune response	0.014664766672504
GO:0002822	regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains.	0.014664766672504
GO:0008283	cell proliferation	0.0147016628458098
GO:0045619	regulation of lymphocyte differentiation	0.0150843923413467
GO:0043112	receptor metabolic process	0.01613433618561
GO:0033077	T cell differentiation in the thymus	0.01613433618561
GO:0007154	cell communication	0.0168893175076412
GO:0002274	myeloid leukocyte activation	0.0168893175076412
GO:0005925	focal adhesion	0.0168893175076412
GO:0042100	B cell proliferation	0.0168893175076412
GO:0009306	protein secretion	0.0186176208445451
GO:0005924	cell-substrate adherens junction	0.0189489941709148
GO:0046631	alpha-beta T cell activation	0.0189489941709148
GO:0005802	trans-Golgi network	0.0194132338169768
GO:0046777	protein amino acid autophosphorylation	0.0198705146588119
GO:0032501	multicellular organismal process	0.0199297434493292
GO:0005886	plasma membrane	0.0203230007642845
GO:0030055	cell-matrix junction	0.0203230007642845
GO:0030183	B cell differentiation	0.0203230007642845
GO:0016540	protein autoprocessing	0.0203230007642845
GO:0006469	negative regulation of protein kinase activity	0.0206090405561041
GO:0033673	negative regulation of kinase activity	0.0206090405561041
GO:0048193	Golgi vesicle transport	0.0213023182680741
GO:0004715	non-membrane spanning protein tyrosine kinase activity	0.0213023182680741
GO:0051348	negative regulation of transferase activity	0.0213023182680741
GO:0045184	establishment of protein localization	0.0244848945667967
GO:0019221	cytokine and chemokine mediated signaling pathway	0.0248664499757035
GO:0043086	negative regulation of catalytic activity	0.0257916660588895
GO:0019901	protein kinase binding	0.0261619550246218
GO:0009615	response to virus	0.026527221150298
GO:0019900	kinase binding	0.0268875635902952
GO:0008104	protein localization	0.0272167319733423
GO:0051649	establishment of cellular localization	0.0272167319733423
GO:0051641	cellular localization	0.0279261139065417
GO:0033036	macromolecule localization	0.028415053329007
GO:0018212	peptidyl-tyrosine modification	0.0289514571859491
GO:0018108	peptidyl-tyrosine phosphorylation	0.0289514571859491
GO:0006874	cellular calcium ion homeostasis	0.0303006260442891
GO:0005912	adherens junction	0.0307587697235578
GO:0055074	calcium ion homeostasis	0.0307587697235578
GO:0051234	establishment of localization	0.0307587697235578
GO:0006793	phosphorus metabolic process	0.0307587697235578
GO:0006796	phosphate metabolic process	0.0307587697235578
GO:0006875	cellular metal ion homeostasis	0.0324413878071201
GO:0016485	protein processing	0.0324413878071201
GO:0048523	negative regulation of cellular process	0.0329202248070333
GO:0055065	metal ion homeostasis	0.0330193124676124
GO:0016323	basolateral plasma membrane	0.0337819370700022
GO:0007166	cell surface receptor linked signal transduction	0.0348292371106258
GO:0048519	negative regulation of biological process	0.0368739864133545
GO:0051049	regulation of transport	0.0397702004545595
GO:0042113	B cell activation	0.0399286764495899
GO:0044267	cellular protein metabolic process	0.0399286764495899
GO:0004725	protein tyrosine phosphatase activity	0.0400103326163405
GO:0002250	adaptive immune response	0.0407521510522234
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0407521510522234
GO:0044260	cellular macromolecule metabolic process	0.0407521510522234
GO:0009968	negative regulation of signal transduction	0.040917668044181
GO:0002449	lymphocyte mediated immunity	0.041585462606662
GO:0018193	peptidyl-amino acid modification	0.0418006464084082
GO:0030005	cellular di-, tri-valent inorganic cation homeostasis	0.0424556661987694
GO:0019538	protein metabolic process	0.0425542198268073
GO:0055066	di-, tri-valent inorganic cation homeostasis	0.0432728331933592
GO:0002443	leukocyte mediated immunity	0.0432728331933592
GO:0001816	cytokine production	0.0432728331933592
GO:0030003	cellular cation homeostasis	0.0451904702019235
GO:0006470	protein amino acid dephosphorylation	0.0458044805498022
GO:0055080	cation homeostasis	0.0459869206282985

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
mature alpha-beta T cell	2.14e-18	9
alpha-beta T cell	2.14e-18	9
immature T cell	2.14e-18	9
mature T cell	2.14e-18	9
immature alpha-beta T cell	2.14e-18	9
T cell	1.24e-17	11
pro-T cell	1.24e-17	11
CD4-positive, alpha-beta T cell	1.14e-16	8
lymphoid lineage restricted progenitor cell	5.77e-16	12
lymphocyte	1.48e-14	13
common lymphoid progenitor	1.48e-14	13
thymocyte	2.96e-13	6
double negative thymocyte	2.96e-13	6
naive T cell	2.96e-13	6
double-positive, alpha-beta thymocyte	2.96e-13	6
CD4-positive, alpha-beta thymocyte	2.96e-13	6
naive thymus-derived CD4-positive, alpha-beta T cell	2.96e-13	6
DN4 thymocyte	2.96e-13	6
DN1 thymic pro-T cell	2.96e-13	6
DN2 thymocyte	2.96e-13	6
DN3 thymocyte	2.96e-13	6
immature single positive thymocyte	2.96e-13	6
early T lineage precursor	2.96e-13	6
mature CD4 single-positive thymocyte	2.96e-13	6
resting double-positive thymocyte	2.96e-13	6
double-positive blast	2.96e-13	6
CD69-positive double-positive thymocyte	2.96e-13	6
CD69-positive, CD4-positive single-positive thymocyte	2.96e-13	6
CD4-positive, CD8-intermediate double-positive thymocyte	2.96e-13	6
CD24-positive, CD4 single-positive thymocyte	2.96e-13	6
nucleate cell	2.17e-11	16
hematopoietic lineage restricted progenitor cell	3.85e-11	25
leukocyte	1.39e-10	17
nongranular leukocyte	1.39e-10	17
hematopoietic cell	5.06e-08	32
hematopoietic oligopotent progenitor cell	5.06e-08	32
hematopoietic stem cell	5.06e-08	32
angioblastic mesenchymal cell	5.06e-08	32
hematopoietic multipotent progenitor cell	5.06e-08	32

Uber Anatomy

Ontology term	p-value	n
hemopoietic organ	6.61e-34	29
immune organ	6.61e-34	29
thymus	2.02e-30	23
neck	2.02e-30	23
respiratory system epithelium	2.02e-30	23
hemolymphoid system gland	2.02e-30	23
pharyngeal epithelium	2.02e-30	23
thymic region	2.02e-30	23
pharyngeal gland	2.02e-30	23
entire pharyngeal arch endoderm	2.02e-30	23
thymus primordium	2.02e-30	23
early pharyngeal endoderm	2.02e-30	23
pharynx	6.30e-29	24
gland of gut	6.30e-29	24
upper respiratory tract	6.30e-29	24
chordate pharynx	6.30e-29	24
pharyngeal arch system	6.30e-29	24
pharyngeal region of foregut	6.30e-29	24
mixed endoderm/mesoderm-derived structure	5.49e-27	35
respiratory tract	4.36e-26	41
hemolymphoid system	1.09e-25	48
immune system	1.09e-25	48
hematopoietic system	1.20e-25	45
blood island	1.20e-25	45
respiratory system	2.65e-25	42
segment of respiratory tract	4.14e-25	27
organ segment	3.55e-20	35
craniocervical region	1.71e-17	36
foregut	1.20e-14	80
anterior region of body	8.58e-14	43
endo-epithelium	8.86e-13	69
lateral plate mesoderm	7.14e-11	87
subdivision of digestive tract	8.82e-10	114
gut epithelium	1.12e-09	55
digestive system	1.76e-09	116
digestive tract	1.76e-09	116
primitive gut	1.76e-09	116
endocrine gland	1.80e-09	60
endoderm-derived structure	3.44e-09	118
endoderm	3.44e-09	118
presumptive endoderm	3.44e-09	118
gland	2.38e-08	65
organ part	6.29e-08	99
unilaminar epithelium	2.93e-07	66
endocrine system	4.72e-07	72

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)
MA0003.1	0.00972621
MA0004.1	1.02263
MA0006.1	0.238555
MA0007.1	0.38073
MA0009.1	0.82278
MA0014.1	0.119217
MA0017.1	0.26239
MA0019.1	0.642876
MA0024.1	0.779446
MA0025.1	1.05446
MA0027.1	2.46647
MA0028.1	0.24786
MA0029.1	0.757957
MA0030.1	0.764448
MA0031.1	0.729293
MA0038.1	0.534262
MA0040.1	0.835181
MA0041.1	0.323687
MA0042.1	0.311486
MA0043.1	0.918718
MA0046.1	0.858391
MA0048.1	0.0824771
MA0050.1	0.431976
MA0051.1	0.542972
MA0052.1	0.84317
MA0055.1	0.221677
MA0056.1	0
MA0057.1	0.258928
MA0058.1	1.49242
MA0059.1	0.849123
MA0060.1	0.505012
MA0061.1	0.194456
MA0063.1	0
MA0066.1	0.523573
MA0067.1	1.16502
MA0068.1	0.077274
MA0069.1	0.843506
MA0070.1	0.833895
MA0071.1	1.10147
MA0072.1	0.825495
MA0073.1	0.0431817
MA0074.1	0.488775
MA0076.1	0.279739
MA0077.1	0.804033
MA0078.1	0.575205
MA0081.1	0.897217
MA0083.1	0.917931
MA0084.1	1.49188
MA0087.1	0.87515
MA0088.1	0.0492918
MA0089.1	0
MA0090.1	0.362551
MA0091.1	0.407455
MA0092.1	0.362847
MA0093.1	1.30984
MA0095.1	0
MA0098.1	0
MA0100.1	0.477594
MA0101.1	0.324888
MA0103.1	0.272167
MA0105.1	0.35523
MA0106.1	0.582805
MA0107.1	0.266586
MA0108.2	0.665343
MA0109.1	0
MA0111.1	0.375908
MA0113.1	0.555251
MA0114.1	0.561811
MA0115.1	0.921497
MA0116.1	0.238371
MA0117.1	0.88947
MA0119.1	0.325434
MA0122.1	0.909168
MA0124.1	1.11203
MA0125.1	1.03833
MA0130.1	0
MA0131.1	0.638414
MA0132.1	0
MA0133.1	0
MA0135.1	0.954884
MA0136.1	0.508047
MA0139.1	0.143341
MA0140.1	0.477483
MA0141.1	1.43798
MA0142.1	0.714976
MA0143.1	0.571221
MA0144.1	0.195095
MA0145.1	0.200183
MA0146.1	0.0548413
MA0147.1	0.205697
MA0148.1	1.05634
MA0149.1	0.330018
MA0062.2	0.365726
MA0035.2	1.21101
MA0039.2	0.043355
MA0138.2	0.630612
MA0002.2	0.145685
MA0137.2	0.287486
MA0104.2	0.157347
MA0047.2	1.32079
MA0112.2	0.442124
MA0065.2	0.773848
MA0150.1	0.991233
MA0151.1	0
MA0152.1	0.53362
MA0153.1	0.971406
MA0154.1	0.0809407
MA0155.1	0.490492
MA0156.1	0.278949
MA0157.1	0.683365
MA0158.1	0
MA0159.1	0.214506
MA0160.1	0.413266
MA0161.1	0
MA0162.1	0.0672805
MA0163.1	0.0124565
MA0164.1	0.508398
MA0080.2	0.737531
MA0018.2	0.51781
MA0099.2	0.624421
MA0079.2	0.000240419
MA0102.2	1.5442
MA0258.1	2.30311
MA0259.1	0.196451
MA0442.1	0