MCL coexpression mm9:1285

Phase1 CAGE Peaks

	Short description
Mm9::chr11:33947115..33947242,+	p1@Lcp2
Mm9::chr1:140071815..140071831,-	p2@Ptprc
Mm9::chr6:129187043..129187060,-	p@chr6:129187043..129187060 -
Mm9::chr6:129187190..129187197,-	p@chr6:129187190..129187197 -
Mm9::chrX:98463521..98463548,-	p1@Il2rg
Mm9::chrX:98463557..98463568,-	p2@Il2rg

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:0045321	leukocyte activation	0.000201384263337577
GO:0001775	cell activation	0.000201384263337577
GO:0050870	positive regulation of T cell activation	0.00124494442873144
GO:0051251	positive regulation of lymphocyte activation	0.00134529211205477
GO:0030217	T cell differentiation	0.00134529211205477
GO:0050863	regulation of T cell activation	0.00134529211205477
GO:0002376	immune system process	0.00167704470278518
GO:0051249	regulation of lymphocyte activation	0.00167704470278518
GO:0050865	regulation of cell activation	0.00167704470278518
GO:0030098	lymphocyte differentiation	0.00172823782179823
GO:0042110	T cell activation	0.0025884242134679
GO:0002521	leukocyte differentiation	0.00270282578494193
GO:0001915	negative regulation of T cell mediated cytotoxicity	0.00270282578494193
GO:0009897	external side of plasma membrane	0.00270282578494193
GO:0009986	cell surface	0.00323981682805191
GO:0046649	lymphocyte activation	0.00323981682805191
GO:0001960	negative regulation of cytokine and chemokine mediated signaling pathway	0.00323981682805191
GO:0045591	positive regulation of regulatory T cell differentiation	0.00323981682805191
GO:0032831	positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation	0.00323981682805191
GO:0002361	CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation	0.00323981682805191
GO:0045589	regulation of regulatory T cell differentiation	0.00323981682805191
GO:0030097	hemopoiesis	0.00323981682805191
GO:0048534	hemopoietic or lymphoid organ development	0.00323981682805191
GO:0019976	interleukin-2 binding	0.00323981682805191
GO:0001916	positive regulation of T cell mediated cytotoxicity	0.00323981682805191
GO:0051283	negative regulation of sequestering of calcium ion	0.00323981682805191
GO:0045066	regulatory T cell differentiation	0.00323981682805191
GO:0001959	regulation of cytokine and chemokine mediated signaling pathway	0.00323981682805191
GO:0001914	regulation of T cell mediated cytotoxicity	0.00323981682805191
GO:0051208	sequestering of calcium ion	0.00323981682805191
GO:0051238	sequestering of metal ion	0.00323981682805191
GO:0002711	positive regulation of T cell mediated immunity	0.00323981682805191
GO:0051282	regulation of sequestering of calcium ion	0.00323981682805191
GO:0050857	positive regulation of antigen receptor-mediated signaling pathway	0.00323981682805191
GO:0051209	release of sequestered calcium ion into cytosol	0.00323981682805191
GO:0002520	immune system development	0.00352060068852258
GO:0002709	regulation of T cell mediated immunity	0.00387649149020192
GO:0001911	negative regulation of leukocyte mediated cytotoxicity	0.00387649149020192
GO:0001913	T cell mediated cytotoxicity	0.00387649149020192
GO:0051239	regulation of multicellular organismal process	0.00394701093829918
GO:0050663	cytokine secretion	0.00553048541377863
GO:0050853	B cell receptor signaling pathway	0.00629826326499603
GO:0002456	T cell mediated immunity	0.00703023421918479
GO:0051607	defense response to virus	0.00772883966084589
GO:0043367	CD4-positive, alpha beta T cell differentiation	0.00903465807306708
GO:0050854	regulation of antigen receptor-mediated signaling pathway	0.00903465807306708
GO:0045576	mast cell activation	0.00925205560095098
GO:0045582	positive regulation of T cell differentiation	0.00925205560095098
GO:0001912	positive regulation of leukocyte mediated cytotoxicity	0.00925205560095098
GO:0045621	positive regulation of lymphocyte differentiation	0.0103017317491084
GO:0002705	positive regulation of leukocyte mediated immunity	0.0103017317491084
GO:0051235	maintenance of localization	0.0103017317491084
GO:0001910	regulation of leukocyte mediated cytotoxicity	0.0103017317491084
GO:0031341	regulation of cell killing	0.0103017317491084
GO:0002708	positive regulation of lymphocyte mediated immunity	0.0103017317491084
GO:0002699	positive regulation of immune effector process	0.0107011816398053
GO:0045580	regulation of T cell differentiation	0.0107011816398053
GO:0002703	regulation of leukocyte mediated immunity	0.0107011816398053
GO:0007204	elevation of cytosolic calcium ion concentration	0.0107011816398053
GO:0002706	regulation of lymphocyte mediated immunity	0.0107011816398053
GO:0002824	positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0109645567172291
GO:0002821	positive regulation of adaptive immune response	0.0109645567172291
GO:0002697	regulation of immune effector process	0.0112114061902319
GO:0051480	cytosolic calcium ion homeostasis	0.0112114061902319
GO:0046632	alpha-beta T cell differentiation	0.0120389508307953
GO:0001906	cell killing	0.0120389508307953
GO:0002819	regulation of adaptive immune response	0.0120389508307953
GO:0002822	regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains.	0.0120389508307953
GO:0001909	leukocyte mediated cytotoxicity	0.0120389508307953
GO:0045619	regulation of lymphocyte differentiation	0.0124056933686874
GO:0042102	positive regulation of T cell proliferation	0.0135893450616824
GO:0002274	myeloid leukocyte activation	0.0135893450616824
GO:0050851	antigen receptor-mediated signaling pathway	0.0135893450616824
GO:0042100	B cell proliferation	0.0135893450616824
GO:0005925	focal adhesion	0.0135893450616824
GO:0009306	protein secretion	0.0148981474371567
GO:0005924	cell-substrate adherens junction	0.0149991928481333
GO:0046631	alpha-beta T cell activation	0.0149991928481333
GO:0002429	immune response-activating cell surface receptor signaling pathway	0.01528621194509
GO:0002768	immune response-regulating cell surface receptor signaling pathway	0.0154348204545951
GO:0030055	cell-matrix junction	0.0154348204545951
GO:0030183	B cell differentiation	0.0154348204545951
GO:0019965	interleukin binding	0.0154348204545951
GO:0002757	immune response-activating signal transduction	0.0154348204545951
GO:0032946	positive regulation of mononuclear cell proliferation	0.0154348204545951
GO:0006469	negative regulation of protein kinase activity	0.0154348204545951
GO:0033673	negative regulation of kinase activity	0.0154348204545951
GO:0050671	positive regulation of lymphocyte proliferation	0.0154348204545951
GO:0051348	negative regulation of transferase activity	0.0159285124615529
GO:0002764	immune response-regulating signal transduction	0.0159285124615529
GO:0042129	regulation of T cell proliferation	0.0174079160485435
GO:0019221	cytokine and chemokine mediated signaling pathway	0.0184455722071303
GO:0043086	negative regulation of catalytic activity	0.0190561308588889
GO:0019901	protein kinase binding	0.019244074682621
GO:0019838	growth factor binding	0.019244074682621
GO:0009615	response to virus	0.019244074682621
GO:0019900	kinase binding	0.0194333038375189
GO:0050670	regulation of lymphocyte proliferation	0.0201798342889598
GO:0032944	regulation of mononuclear cell proliferation	0.0201798342889598
GO:0004896	hematopoietin/interferon-class (D200-domain) cytokine receptor activity	0.0203538637423428
GO:0042098	T cell proliferation	0.0205244061748399
GO:0006874	cellular calcium ion homeostasis	0.0217964541555786
GO:0005912	adherens junction	0.0220995211409495
GO:0055074	calcium ion homeostasis	0.0220995211409495
GO:0032501	multicellular organismal process	0.0222698414508014
GO:0006875	cellular metal ion homeostasis	0.0234533739515075
GO:0019955	cytokine binding	0.0235849228369584
GO:0055065	metal ion homeostasis	0.0237139974166393
GO:0016323	basolateral plasma membrane	0.0241848559177353
GO:0032943	mononuclear cell proliferation	0.0251006750095906
GO:0046651	lymphocyte proliferation	0.0251006750095906
GO:0002253	activation of immune response	0.0258808109738987
GO:0042113	B cell activation	0.0283044698039734
GO:0004725	protein tyrosine phosphatase activity	0.0283847001189565
GO:0002250	adaptive immune response	0.0288636487410764
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.0288636487410764
GO:0009968	negative regulation of signal transduction	0.0289369016177656
GO:0048513	organ development	0.0290796100339192
GO:0002449	lymphocyte mediated immunity	0.0290796100339192
GO:0030005	cellular di-, tri-valent inorganic cation homeostasis	0.0297727236658622
GO:0050778	positive regulation of immune response	0.0297787211431084
GO:0055066	di-, tri-valent inorganic cation homeostasis	0.0297787211431084
GO:0002684	positive regulation of immune system process	0.0297787211431084
GO:0002443	leukocyte mediated immunity	0.0297787211431084
GO:0001816	cytokine production	0.0297787211431084
GO:0030003	cellular cation homeostasis	0.0310259053456914
GO:0006470	protein amino acid dephosphorylation	0.0313701166319096
GO:0055080	cation homeostasis	0.0314169453428553
GO:0050776	regulation of immune response	0.0321720903223131
GO:0044459	plasma membrane part	0.0321720903223131
GO:0002682	regulation of immune system process	0.0324081502288187
GO:0051240	positive regulation of multicellular organismal process	0.0332938216522709
GO:0016311	dephosphorylation	0.0333240854308479
GO:0045859	regulation of protein kinase activity	0.0355805098648134
GO:0006917	induction of apoptosis	0.0356054391453159
GO:0012502	induction of programmed cell death	0.0356054391453159
GO:0043549	regulation of kinase activity	0.0361615764838792
GO:0019899	enzyme binding	0.0361695157330812
GO:0002252	immune effector process	0.0361849658594344
GO:0051338	regulation of transferase activity	0.0361849658594344
GO:0048731	system development	0.0368141696897198
GO:0004721	phosphoprotein phosphatase activity	0.0375024831801309
GO:0048869	cellular developmental process	0.0375024831801309
GO:0030154	cell differentiation	0.0375024831801309
GO:0055082	cellular chemical homeostasis	0.0375024831801309
GO:0006873	cellular ion homeostasis	0.0375024831801309
GO:0043065	positive regulation of apoptosis	0.0414571660600049
GO:0051707	response to other organism	0.0414571660600049
GO:0043068	positive regulation of programmed cell death	0.0414571660600049
GO:0050801	ion homeostasis	0.0414571660600049
GO:0008284	positive regulation of cell proliferation	0.0436395050356169
GO:0005886	plasma membrane	0.0453843086993348
GO:0048856	anatomical structure development	0.0456400827179775

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	3.98e-10	32
hematopoietic oligopotent progenitor cell	3.98e-10	32
hematopoietic stem cell	3.98e-10	32
angioblastic mesenchymal cell	3.98e-10	32
hematopoietic multipotent progenitor cell	3.98e-10	32
lymphoid lineage restricted progenitor cell	9.00e-09	12
leukocyte	1.77e-08	17
nongranular leukocyte	1.77e-08	17
hematopoietic lineage restricted progenitor cell	1.79e-08	25
T cell	2.75e-08	11
pro-T cell	2.75e-08	11
lymphocyte	6.00e-08	13
common lymphoid progenitor	6.00e-08	13
mature alpha-beta T cell	2.12e-07	9
alpha-beta T cell	2.12e-07	9
immature T cell	2.12e-07	9
mature T cell	2.12e-07	9
immature alpha-beta T cell	2.12e-07	9
CD4-positive, alpha-beta T cell	8.26e-07	8

Uber Anatomy

Ontology term	p-value	n
hemolymphoid system	3.03e-19	48
immune system	3.03e-19	48
hematopoietic system	7.50e-18	45
blood island	7.50e-18	45
lateral plate mesoderm	3.82e-14	87
hemopoietic organ	4.02e-12	29
immune organ	4.02e-12	29
mixed endoderm/mesoderm-derived structure	1.79e-11	35
foregut	4.31e-10	80
mesoderm	5.81e-10	120
mesoderm-derived structure	5.81e-10	120
presumptive mesoderm	5.81e-10	120
gland of gut	1.42e-09	24
thymus	2.35e-09	23
neck	2.35e-09	23
respiratory system epithelium	2.35e-09	23
hemolymphoid system gland	2.35e-09	23
pharyngeal epithelium	2.35e-09	23
thymic region	2.35e-09	23
pharyngeal gland	2.35e-09	23
entire pharyngeal arch endoderm	2.35e-09	23
thymus primordium	2.35e-09	23
early pharyngeal endoderm	2.35e-09	23
pharynx	4.96e-09	24
upper respiratory tract	4.96e-09	24
chordate pharynx	4.96e-09	24
pharyngeal arch system	4.96e-09	24
pharyngeal region of foregut	4.96e-09	24
respiratory system	6.47e-09	42
respiratory tract	1.12e-08	41
endoderm-derived structure	6.48e-08	118
endoderm	6.48e-08	118
presumptive endoderm	6.48e-08	118
digestive system	1.03e-07	116
digestive tract	1.03e-07	116
primitive gut	1.03e-07	116
subdivision of digestive tract	3.21e-07	114
organism subdivision	9.99e-07	150

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	0.00973143
MA0004.1	0.536396
MA0006.1	0.359699
MA0007.1	0.52077
MA0009.1	0.987341
MA0014.1	0.0315641
MA0017.1	0.387481
MA0019.1	0.800946
MA0024.1	0.942716
MA0025.1	1.22395
MA0027.1	2.64231
MA0028.1	0.969171
MA0029.1	0.920529
MA0030.1	0.927235
MA0031.1	0.890871
MA0038.1	0.686534
MA0040.1	1.00009
MA0041.1	0.457338
MA0042.1	0.443591
MA0043.1	1.08567
MA0046.1	1.02391
MA0048.1	0.161427
MA0050.1	0.57678
MA0051.1	0.695779
MA0052.1	1.00829
MA0055.1	1.22706
MA0056.1	0
MA0057.1	0.457693
MA0058.1	0.436487
MA0059.1	0.449345
MA0060.1	0.757042
MA0061.1	0.307097
MA0063.1	0
MA0066.1	0.675169
MA0067.1	1.33603
MA0068.1	1.46111
MA0069.1	1.00864
MA0070.1	0.998765
MA0071.1	0.575909
MA0072.1	0.990133
MA0073.1	2.84212
MA0074.1	0.638014
MA0076.1	1.04996
MA0077.1	0.968053
MA0078.1	0.729877
MA0081.1	1.19271
MA0083.1	1.08487
MA0084.1	1.66561
MA0087.1	1.04109
MA0088.1	0.725434
MA0089.1	0
MA0090.1	0.500693
MA0091.1	0.55008
MA0092.1	0.501022
MA0093.1	0.379257
MA0095.1	0
MA0098.1	0
MA0100.1	0.626021
MA0101.1	0.458688
MA0103.1	0.398766
MA0105.1	0.199622
MA0106.1	0.737893
MA0107.1	0.392331
MA0108.2	0.824407
MA0109.1	0
MA0111.1	0.515457
MA0113.1	0.708789
MA0114.1	0.304661
MA0115.1	1.08851
MA0116.1	0.359483
MA0117.1	1.05576
MA0119.1	0.459301
MA0122.1	1.07591
MA0124.1	1.28237
MA0125.1	1.20757
MA0130.1	0
MA0131.1	0.796279
MA0132.1	0
MA0133.1	0
MA0135.1	1.1226
MA0136.1	1.58388
MA0139.1	0.243463
MA0140.1	0.625902
MA0141.1	1.07584
MA0142.1	2.03291
MA0143.1	1.72325
MA0144.1	0.829535
MA0145.1	0.119202
MA0146.1	0.0392287
MA0147.1	0.320675
MA0148.1	0.553294
MA0149.1	0.464445
MA0062.2	1.11803
MA0035.2	0.630778
MA0039.2	0.0823004
MA0138.2	0.788113
MA0002.2	0.246463
MA0137.2	0.416331
MA0104.2	0.261255
MA0047.2	0.685741
MA0112.2	0.119197
MA0065.2	0.119561
MA0150.1	0.520653
MA0151.1	0
MA0152.1	0.685852
MA0153.1	1.13945
MA0154.1	0.480757
MA0155.1	0.132921
MA0156.1	1.04798
MA0157.1	0.843181
MA0158.1	0
MA0159.1	0.331229
MA0160.1	0.556423
MA0161.1	0
MA0162.1	0.0465447
MA0163.1	0.0423021
MA0164.1	0.658997
MA0080.2	1.01893
MA0018.2	0.669032
MA0099.2	0.781628
MA0079.2	0.0267793
MA0102.2	1.7182
MA0258.1	0.290587
MA0259.1	0.309517
MA0442.1	0