MCL coexpression mm9:3126

Phase1 CAGE Peaks

	Short description
Mm9::chr17:88071863..88071920,+	p1@Msh2
Mm9::chr17:88374384..88374425,+	p1@Msh6
Mm9::chr17:88374426..88374447,+	p2@Msh6

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:0032301	MutSalpha complex	1.10459508071702e-06
GO:0032137	guanine/thymine mispair binding	1.10459508071702e-06
GO:0032134	mispaired DNA binding	1.10459508071702e-06
GO:0045910	negative regulation of DNA recombination	1.32551409686043e-06
GO:0032300	mismatch repair complex	1.32551409686043e-06
GO:0000018	regulation of DNA recombination	1.84099180119504e-06
GO:0008340	determination of adult life span	3.31378524215107e-06
GO:0002566	somatic diversification of immune receptors via somatic mutation	3.43651802889741e-06
GO:0016446	somatic hypermutation of immunoglobulin genes	3.43651802889741e-06
GO:0030983	mismatched DNA binding	3.97654229058129e-06
GO:0010259	multicellular organismal aging	4.51879805747873e-06
GO:0006298	mismatch repair	5.06272745328636e-06
GO:0045005	maintenance of fidelity during DNA-dependent DNA replication	5.60794425594797e-06
GO:0051053	negative regulation of DNA metabolic process	7.17986802466065e-06
GO:0002208	somatic diversification of immunoglobulins during immune response	1.15982483475287e-05
GO:0051052	regulation of DNA metabolic process	1.15982483475287e-05
GO:0002204	somatic recombination of immunoglobulin genes during immune response	1.15982483475287e-05
GO:0003684	damaged DNA binding	1.15982483475287e-05
GO:0045190	isotype switching	1.15982483475287e-05
GO:0003690	double-stranded DNA binding	1.15982483475287e-05
GO:0002381	immunoglobulin production during immune response	1.21505458878873e-05
GO:0009411	response to UV	1.50626601915958e-05
GO:0016447	somatic recombination of immunoglobulin gene segments	1.68570814492033e-05
GO:0007568	aging	1.72486770296581e-05
GO:0016444	somatic cell DNA recombination	1.72486770296581e-05
GO:0002562	somatic diversification of immune receptors via germline recombination within a single locus	1.72486770296581e-05
GO:0016445	somatic diversification of immunoglobulins	1.77962540782187e-05
GO:0002200	somatic diversification of immune receptors	1.95671128584158e-05
GO:0042770	DNA damage response, signal transduction	2.266324389747e-05
GO:0002377	immunoglobulin production	2.72834984937105e-05
GO:0002440	production of molecular mediator of immune response	2.77930375148154e-05
GO:0006261	DNA-dependent DNA replication	3.57267471419412e-05
GO:0043566	structure-specific DNA binding	3.77570682136001e-05
GO:0016064	immunoglobulin mediated immune response	7.84262507309087e-05
GO:0019724	B cell mediated immunity	7.84262507309087e-05
GO:0009416	response to light stimulus	8.06354408923426e-05
GO:0006310	DNA recombination	8.06354408923428e-05
GO:0042113	B cell activation	0.000103773801004205
GO:0002250	adaptive immune response	0.000108139858402197
GO:0002460	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains	0.000108139858402197
GO:0002449	lymphocyte mediated immunity	0.000112510898935891
GO:0009314	response to radiation	0.000112510898935891
GO:0002443	leukocyte mediated immunity	0.000124613738059495
GO:0006260	DNA replication	0.000222023611224122
GO:0002252	immune effector process	0.000222023611224122
GO:0009628	response to abiotic stimulus	0.000336853473745617
GO:0006281	DNA repair	0.000408723681888293
GO:0046649	lymphocyte activation	0.000408838254250388
GO:0032302	MutSbeta complex	0.000411450396188717
GO:0045321	leukocyte activation	0.000466470502586799
GO:0001775	cell activation	0.000526523655141781
GO:0006974	response to DNA damage stimulus	0.000564299390754764
GO:0002520	immune system development	0.000636676331246617
GO:0009719	response to endogenous stimulus	0.000636676331246617
GO:0045934	negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.000650405667073105
GO:0004422	hypoxanthine phosphoribosyltransferase activity	0.000720018468418099
GO:0031324	negative regulation of cellular metabolic process	0.000823330291216552
GO:0009892	negative regulation of metabolic process	0.00100799824090832
GO:0031573	intra-S DNA damage checkpoint	0.00100799824090832
GO:0019237	centromeric DNA binding	0.00100799824090832
GO:0042981	regulation of apoptosis	0.00125630487721288
GO:0043067	regulation of programmed cell death	0.00125996328253913
GO:0006301	postreplication repair	0.00125996328253913
GO:0010224	response to UV-B	0.00125996328253913
GO:0006955	immune response	0.00192923478666894
GO:0006915	apoptosis	0.00302761143479985
GO:0006259	DNA metabolic process	0.00303708417443146
GO:0012501	programmed cell death	0.00303708417443146
GO:0010165	response to X-ray	0.00316136667868932
GO:0008219	cell death	0.00316136667868932
GO:0016265	death	0.00316136667868932
GO:0002376	immune system process	0.00394897343835839
GO:0006950	response to stress	0.00410388848509244
GO:0008630	DNA damage response, signal transduction resulting in induction of apoptosis	0.00456783940125631
GO:0000077	DNA damage checkpoint	0.00456783940125631
GO:0048523	negative regulation of cellular process	0.00485662842114258
GO:0031570	DNA integrity checkpoint	0.00523391578181307
GO:0010212	response to ionizing radiation	0.00539547157395146
GO:0048519	negative regulation of biological process	0.00539547157395146
GO:0043524	negative regulation of neuron apoptosis	0.00579281417436577
GO:0044428	nuclear part	0.00638815623589258
GO:0000075	cell cycle checkpoint	0.00638815623589258
GO:0008629	induction of apoptosis by intracellular signals	0.0072813443799675
GO:0000790	nuclear chromatin	0.00743427994164438
GO:0016763	transferase activity, transferring pentosyl groups	0.0078203772286416
GO:0048468	cell development	0.00786280319950723
GO:0043523	regulation of neuron apoptosis	0.00787191588747264
GO:0030183	B cell differentiation	0.00801113858398435
GO:0051402	neuron apoptosis	0.00859937199282748
GO:0005524	ATP binding	0.00930677812585996
GO:0032559	adenyl ribonucleotide binding	0.00943009814178596
GO:0007050	cell cycle arrest	0.00984950624419794
GO:0030554	adenyl nucleotide binding	0.0101680471426959
GO:0006119	oxidative phosphorylation	0.0109234700143371
GO:0006164	purine nucleotide biosynthetic process	0.0136196908178191
GO:0032553	ribonucleotide binding	0.0136196908178191
GO:0032555	purine ribonucleotide binding	0.0136196908178191
GO:0043234	protein complex	0.0136196908178191
GO:0044454	nuclear chromosome part	0.0136196908178191
GO:0017076	purine nucleotide binding	0.0144140821272926
GO:0048731	system development	0.0145733056803732
GO:0006163	purine nucleotide metabolic process	0.0145974080908556
GO:0048869	cellular developmental process	0.014926117176959
GO:0030154	cell differentiation	0.014926117176959
GO:0000228	nuclear chromosome	0.0149452030019608
GO:0000166	nucleotide binding	0.0172915378599145
GO:0030098	lymphocyte differentiation	0.0172915378599145
GO:0003677	DNA binding	0.017417163183156
GO:0003682	chromatin binding	0.0181611850926484
GO:0048856	anatomical structure development	0.0181611850926484
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0181611850926484
GO:0032991	macromolecular complex	0.0189921612564465
GO:0045786	negative regulation of progression through cell cycle	0.0206311186083919
GO:0001701	in utero embryonic development	0.0208278894505394
GO:0031323	regulation of cellular metabolic process	0.0208278894505394
GO:0009165	nucleotide biosynthetic process	0.0211335987252187
GO:0007275	multicellular organismal development	0.0214186646059709
GO:0002521	leukocyte differentiation	0.0214186646059709
GO:0019222	regulation of metabolic process	0.0214186646059709
GO:0006917	induction of apoptosis	0.0214186646059709
GO:0012502	induction of programmed cell death	0.0214186646059709
GO:0044446	intracellular organelle part	0.0236398165012331
GO:0044422	organelle part	0.0236398165012331
GO:0043066	negative regulation of apoptosis	0.0241275812678535
GO:0043069	negative regulation of programmed cell death	0.0242544955368895
GO:0043065	positive regulation of apoptosis	0.0259656376627664
GO:0043068	positive regulation of programmed cell death	0.0260758368641234
GO:0000074	regulation of progression through cell cycle	0.027900544291027
GO:0009117	nucleotide metabolic process	0.0281485248832004
GO:0000785	chromatin	0.0296989949745331
GO:0055086	nucleobase, nucleoside and nucleotide metabolic process	0.0296989949745331
GO:0003676	nucleic acid binding	0.0308758257953824
GO:0030097	hemopoiesis	0.0313512986094566
GO:0032502	developmental process	0.0323943610132257
GO:0043009	chordate embryonic development	0.0328055083993732
GO:0009792	embryonic development ending in birth or egg hatching	0.0330036116311129
GO:0048534	hemopoietic or lymphoid organ development	0.0336794882180467
GO:0016757	transferase activity, transferring glycosyl groups	0.0336794882180467
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0340527432305236
GO:0016887	ATPase activity	0.0373182871840627
GO:0050794	regulation of cellular process	0.0386077915932061
GO:0044427	chromosomal part	0.0422449277084787
GO:0006928	cell motility	0.0449610239423505
GO:0051674	localization of cell	0.0449610239423505
GO:0050789	regulation of biological process	0.0465663462567136
GO:0051726	regulation of cell cycle	0.0478692544526144
GO:0005694	chromosome	0.0482161388422169

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
anterior region of body	4.27e-09	43
hemopoietic organ	4.28e-09	29
immune organ	4.28e-09	29
primordium	9.29e-08	134
craniocervical region	2.36e-07	36
thymus	5.46e-07	23
neck	5.46e-07	23
respiratory system epithelium	5.46e-07	23
hemolymphoid system gland	5.46e-07	23
pharyngeal epithelium	5.46e-07	23
thymic region	5.46e-07	23
pharyngeal gland	5.46e-07	23
entire pharyngeal arch endoderm	5.46e-07	23
thymus primordium	5.46e-07	23
early pharyngeal endoderm	5.46e-07	23
gland of gut	9.89e-07	24

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	0.526413
MA0004.1	0.801718
MA0006.1	0.60285
MA0007.1	3.07498
MA0009.1	1.27673
MA0014.1	2.60474
MA0017.1	0.635031
MA0019.1	1.08369
MA0024.1	2.75393
MA0025.1	1.51835
MA0027.1	2.9431
MA0028.1	0.61552
MA0029.1	1.20789
MA0030.1	1.21482
MA0031.1	1.17722
MA0038.1	0.963265
MA0040.1	1.28983
MA0041.1	0.714279
MA0042.1	0.69885
MA0043.1	1.3775
MA0046.1	1.31428
MA0048.1	0.353763
MA0050.1	0.845669
MA0051.1	0.973068
MA0052.1	1.29825
MA0055.1	0.190475
MA0056.1	0
MA0057.1	0.337566
MA0058.1	0.690848
MA0059.1	0.705317
MA0060.1	3.20384
MA0061.1	0.5406
MA0063.1	0
MA0066.1	0.951196
MA0067.1	1.63197
MA0068.1	0.343188
MA0069.1	1.29861
MA0070.1	1.28847
MA0071.1	0.844726
MA0072.1	1.2796
MA0073.1	0.121346
MA0074.1	0.911576
MA0076.1	0.657929
MA0077.1	1.2569
MA0078.1	1.0091
MA0081.1	0.732313
MA0083.1	1.37668
MA0084.1	1.96428
MA0087.1	1.33189
MA0088.1	0.27999
MA0089.1	0
MA0090.1	0.762482
MA0091.1	0.816659
MA0092.1	0.762845
MA0093.1	0.62555
MA0095.1	0
MA0098.1	0
MA0100.1	0.89873
MA0101.1	0.71579
MA0103.1	0.647985
MA0105.1	1.04599
MA0106.1	1.01755
MA0107.1	0.640607
MA0108.2	1.10817
MA0109.1	0
MA0111.1	0.778753
MA0113.1	0.986839
MA0114.1	0.537669
MA0115.1	1.38041
MA0116.1	0.602598
MA0117.1	1.34691
MA0119.1	0.716476
MA0122.1	1.36752
MA0124.1	1.57762
MA0125.1	1.5017
MA0130.1	0
MA0131.1	1.07881
MA0132.1	0
MA0133.1	0
MA0135.1	1.4152
MA0136.1	0.933582
MA0139.1	0.462282
MA0140.1	0.898603
MA0141.1	0.671467
MA0142.1	1.16183
MA0143.1	1.00467
MA0144.1	0.541532
MA0145.1	0.292366
MA0146.1	1.44443
MA0147.1	0.556853
MA0148.1	0.820161
MA0149.1	0.722227
MA0062.2	1.06145
MA0035.2	0.903829
MA0039.2	3.91141
MA0138.2	1.07027
MA0002.2	0.466067
MA0137.2	0.668025
MA0104.2	0.48458
MA0047.2	0.962424
MA0112.2	0.29236
MA0065.2	0.292912
MA0150.1	0.784464
MA0151.1	0
MA0152.1	0.962542
MA0153.1	1.43238
MA0154.1	0.35067
MA0155.1	0.312898
MA0156.1	0.656895
MA0157.1	1.12772
MA0158.1	0
MA0159.1	0.569393
MA0160.1	0.823568
MA0161.1	0
MA0162.1	0.166722
MA0163.1	0.157796
MA0164.1	0.933981
MA0080.2	0.64167
MA0018.2	0.944669
MA0099.2	1.06348
MA0079.2	1.81944
MA0102.2	2.01714
MA0258.1	0.520639
MA0259.1	1.34197
MA0442.1	0