MCL coexpression mm9:1955

Phase1 CAGE Peaks

	Short description
Mm9::chr11:118280270..118280329,-	p1@Cant1
Mm9::chr17:56416141..56416172,-	p2@Ticam1
Mm9::chr17:56416173..56416196,-	p1@Ticam1
Mm9::chr1:94807382..94807411,+	p1@Rnpepl1

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:0002281	macrophage activation during immune response	0.00478981928606648
GO:0002275	myeloid cell activation during immune response	0.00478981928606648
GO:0004382	guanosine-diphosphatase activity	0.00478981928606648
GO:0045134	uridine-diphosphatase activity	0.00478981928606648
GO:0032481	positive regulation of interferon type I production	0.00478981928606648
GO:0002756	MyD88-independent toll-like receptor signaling pathway	0.00478981928606648
GO:0032479	regulation of interferon type I production	0.00478981928606648
GO:0045359	positive regulation of interferon-beta biosynthetic process	0.00558781633547003
GO:0032608	interferon-beta production	0.00558781633547003
GO:0045357	regulation of interferon-beta biosynthetic process	0.00558781633547003
GO:0043496	regulation of protein homodimerization activity	0.00558781633547003
GO:0045350	interferon-beta biosynthetic process	0.00558781633547003
GO:0045080	positive regulation of chemokine biosynthetic process	0.00797909631221298
GO:0009191	ribonucleoside diphosphate catabolic process	0.00797909631221298
GO:0002224	toll-like receptor signaling pathway	0.00797909631221298
GO:0009185	ribonucleoside diphosphate metabolic process	0.00797909631221298
GO:0002221	pattern recognition receptor signaling pathway	0.00797909631221298
GO:0043393	regulation of protein binding	0.00797909631221298
GO:0032755	positive regulation of interleukin-6 production	0.00797909631221298
GO:0009134	nucleoside diphosphate catabolic process	0.00797909631221298
GO:0045073	regulation of chemokine biosynthetic process	0.00797909631221298
GO:0009261	ribonucleotide catabolic process	0.00797909631221298
GO:0032606	interferon type I production	0.00797909631221298
GO:0050755	chemokine metabolic process	0.00797909631221298
GO:0045351	interferon type I biosynthetic process	0.00797909631221298
GO:0042033	chemokine biosynthetic process	0.00797909631221298
GO:0045429	positive regulation of nitric oxide biosynthetic process	0.00797909631221298
GO:0032602	chemokine production	0.00797909631221298
GO:0032675	regulation of interleukin-6 production	0.00797909631221298
GO:0032760	positive regulation of tumor necrosis factor production	0.00797909631221298
GO:0002218	activation of innate immune response	0.00797909631221298
GO:0002758	innate immune response-activating signal transduction	0.00797909631221298
GO:0042116	macrophage activation	0.00797909631221298
GO:0002366	leukocyte activation during immune response	0.00797909631221298
GO:0045428	regulation of nitric oxide biosynthetic process	0.00797909631221298
GO:0051607	defense response to virus	0.00797909631221298
GO:0002263	cell activation during immune response	0.00797909631221298
GO:0017110	nucleoside-diphosphatase activity	0.00797909631221298
GO:0032680	regulation of tumor necrosis factor production	0.00797909631221298
GO:0045088	regulation of innate immune response	0.00797909631221298
GO:0043330	response to exogenous dsRNA	0.00797909631221298
GO:0045089	positive regulation of innate immune response	0.00797909631221298
GO:0043123	positive regulation of I-kappaB kinase/NF-kappaB cascade	0.00857241975304969
GO:0032496	response to lipopolysaccharide	0.00893560848184599
GO:0031663	lipopolysaccharide-mediated signaling pathway	0.00893560848184599
GO:0043331	response to dsRNA	0.00907473004625096
GO:0030890	positive regulation of B cell proliferation	0.00907473004625096
GO:0009132	nucleoside diphosphate metabolic process	0.00907473004625096
GO:0051092	activation of NF-kappaB transcription factor	0.0093813606238673
GO:0043122	regulation of I-kappaB kinase/NF-kappaB cascade	0.0093813606238673
GO:0032640	tumor necrosis factor production	0.00985383036871236
GO:0032635	interleukin-6 production	0.0103080576010432
GO:0046209	nitric oxide metabolic process	0.0103543449226258
GO:0002237	response to molecule of bacterial origin	0.0103543449226258
GO:0006809	nitric oxide biosynthetic process	0.0103543449226258
GO:0008624	induction of apoptosis by extracellular signals	0.011353845313042
GO:0051098	regulation of binding	0.011353845313042
GO:0001819	positive regulation of cytokine production	0.011353845313042
GO:0051091	positive regulation of transcription factor activity	0.011353845313042
GO:0030888	regulation of B cell proliferation	0.0117222027855616
GO:0009166	nucleotide catabolic process	0.0120784228007324
GO:0051090	regulation of transcription factor activity	0.0135018813592137
GO:0050871	positive regulation of B cell activation	0.0138183109552751
GO:0002274	myeloid leukocyte activation	0.0139074902637953
GO:0042100	B cell proliferation	0.0139074902637953
GO:0001817	regulation of cytokine production	0.0152161316117047
GO:0042108	positive regulation of cytokine biosynthetic process	0.015986540668856
GO:0007249	I-kappaB kinase/NF-kappaB cascade	0.0169605190275
GO:0002757	immune response-activating signal transduction	0.0169605190275
GO:0032946	positive regulation of mononuclear cell proliferation	0.0169605190275
GO:0050671	positive regulation of lymphocyte proliferation	0.0169605190275
GO:0004177	aminopeptidase activity	0.0169605190275
GO:0050864	regulation of B cell activation	0.0169605190275
GO:0002764	immune response-regulating signal transduction	0.0171825786600536
GO:0045727	positive regulation of translation	0.0178438091349992
GO:0031328	positive regulation of cellular biosynthetic process	0.018926585343238
GO:0009615	response to virus	0.0212804042114314
GO:0042035	regulation of cytokine biosynthetic process	0.021435129115765
GO:0050670	regulation of lymphocyte proliferation	0.0218761102146985
GO:0032944	regulation of mononuclear cell proliferation	0.0218761102146985
GO:0009891	positive regulation of biosynthetic process	0.0218761102146985
GO:0042089	cytokine biosynthetic process	0.0242682940231048
GO:0051251	positive regulation of lymphocyte activation	0.0242682940231048
GO:0042107	cytokine metabolic process	0.0242682940231048
GO:0009967	positive regulation of signal transduction	0.0255498198958522
GO:0009259	ribonucleotide metabolic process	0.0271877884826472
GO:0051247	positive regulation of protein metabolic process	0.0272577224380037
GO:0032943	mononuclear cell proliferation	0.0277664721503258
GO:0046651	lymphocyte proliferation	0.0277664721503258
GO:0044271	nitrogen compound biosynthetic process	0.0281969685644931
GO:0002253	activation of immune response	0.0282524973307041
GO:0051249	regulation of lymphocyte activation	0.0301130537999143
GO:0042113	B cell activation	0.0305037231379708
GO:0050865	regulation of cell activation	0.0305325895451643
GO:0045087	innate immune response	0.0312599260324409
GO:0008238	exopeptidase activity	0.0326632198979232
GO:0050778	positive regulation of immune response	0.0330106595549708
GO:0002684	positive regulation of immune system process	0.0333490289481452
GO:0001816	cytokine production	0.0333490289481452
GO:0050776	regulation of immune response	0.0369171102606543
GO:0009617	response to bacterium	0.0369171102606543
GO:0002682	regulation of immune system process	0.0369171102606543
GO:0051240	positive regulation of multicellular organismal process	0.0378444925897996
GO:0006917	induction of apoptosis	0.0409042361758859
GO:0012502	induction of programmed cell death	0.0409042361758859
GO:0006417	regulation of translation	0.0411420194124377
GO:0002252	immune effector process	0.0419927925617817
GO:0031326	regulation of cellular biosynthetic process	0.0428272703558116
GO:0009889	regulation of biosynthetic process	0.047277316629461
GO:0043065	positive regulation of apoptosis	0.0489525028519074
GO:0051707	response to other organism	0.0489525028519074
GO:0043068	positive regulation of programmed cell death	0.0489525028519074

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><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
intestine	1.66e-11	31
gastrointestinal system	9.94e-11	47
endoderm-derived structure	4.15e-09	118
endoderm	4.15e-09	118
presumptive endoderm	4.15e-09	118
digestive system	1.51e-08	116
digestive tract	1.51e-08	116
primitive gut	1.51e-08	116
subdivision of digestive tract	7.64e-08	114
adult organism	1.05e-07	51

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	2.89651
MA0004.1	1.64673
MA0006.1	0.497533
MA0007.1	0.672186
MA0009.1	1.15569
MA0014.1	0.581929
MA0017.1	0.528196
MA0019.1	0.964875
MA0024.1	1.11019
MA0025.1	1.39562
MA0027.1	2.81824
MA0028.1	2.19266
MA0029.1	2.46391
MA0030.1	1.09438
MA0031.1	1.05719
MA0038.1	0.846479
MA0040.1	1.16866
MA0041.1	0.604221
MA0042.1	0.589368
MA0043.1	1.25564
MA0046.1	1.1929
MA0048.1	0.266382
MA0050.1	0.731539
MA0051.1	0.856094
MA0052.1	1.17701
MA0055.1	0.125758
MA0056.1	0
MA0057.1	0.701847
MA0058.1	1.4226
MA0059.1	3.61572
MA0060.1	0.403071
MA0061.1	0.438628
MA0063.1	0
MA0066.1	0.834648
MA0067.1	1.50873
MA0068.1	2.83575
MA0069.1	1.17737
MA0070.1	1.16732
MA0071.1	0.73062
MA0072.1	1.15853
MA0073.1	6.10005
MA0074.1	0.795862
MA0076.1	0.550092
MA0077.1	1.13603
MA0078.1	0.891476
MA0081.1	0.621611
MA0083.1	1.25482
MA0084.1	1.84013
MA0087.1	1.21037
MA0088.1	0.582815
MA0089.1	0
MA0090.1	0.650768
MA0091.1	0.703314
MA0092.1	0.651119
MA0093.1	2.22418
MA0095.1	0
MA0098.1	0
MA0100.1	0.783305
MA0101.1	0.605676
MA0103.1	0.540576
MA0105.1	0.313353
MA0106.1	0.899777
MA0107.1	0.533522
MA0108.2	0.989014
MA0109.1	0
MA0111.1	0.666525
MA0113.1	0.869608
MA0114.1	0.43587
MA0115.1	1.25852
MA0116.1	0.497293
MA0117.1	1.22527
MA0119.1	0.606338
MA0122.1	1.24573
MA0124.1	1.45461
MA0125.1	1.37907
MA0130.1	0
MA0131.1	0.960068
MA0132.1	0
MA0133.1	0
MA0135.1	1.29308
MA0136.1	0.817395
MA0139.1	0.365453
MA0140.1	1.84211
MA0141.1	0.563066
MA0142.1	1.04199
MA0143.1	0.887119
MA0144.1	0.439506
MA0145.1	1.14526
MA0146.1	1.07887
MA0147.1	2.98268
MA0148.1	0.706718
MA0149.1	0.611881
MA0062.2	2.34802
MA0035.2	0.788288
MA0039.2	0.0220513
MA0138.2	0.951653
MA0002.2	0.965577
MA0137.2	1.37638
MA0104.2	2.66758
MA0047.2	0.845655
MA0112.2	0.608441
MA0065.2	0.609584
MA0150.1	0.67206
MA0151.1	0
MA0152.1	0.84577
MA0153.1	1.31015
MA0154.1	0.728853
MA0155.1	1.21457
MA0156.1	0.549102
MA0157.1	1.0083
MA0158.1	0
MA0159.1	0.465802
MA0160.1	0.71003
MA0161.1	0
MA0162.1	1.16288
MA0163.1	2.23835
MA0164.1	0.817786
MA0080.2	0.534538
MA0018.2	0.828253
MA0099.2	0.944966
MA0079.2	6.24625
MA0102.2	1.8929
MA0258.1	0.419871
MA0259.1	1.12353
MA0442.1	0