MCL coexpression mm9:797

Phase1 CAGE Peaks

	Short description
Mm9::chr11:79153143..79153195,+	p1@Nf1
Mm9::chr15:99125642..99125710,+	p1@Prpf40b
Mm9::chr16:90284545..90284593,-	p2@Scaf4
Mm9::chr2:32986085..32986140,-	p1@Garnl3
Mm9::chr3:94386470..94386495,-	p1@Snx27
Mm9::chr5:23181745..23181756,-	p5@Srpk2
Mm9::chr5:23181759..23181815,-	p2@Srpk2
Mm9::chr5:54200871..54200922,+	p1@Tbc1d19
Mm9::chr8:108020923..108020968,-	p1@Zdhhc1

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:0046929	negative regulation of neurotransmitter secretion	0.0122811985351359
GO:0021897	forebrain astrocyte development	0.0122811985351359
GO:0021896	forebrain astrocyte differentiation	0.0122811985351359
GO:0051056	regulation of small GTPase mediated signal transduction	0.0122811985351359
GO:0022011	myelination in the peripheral nervous system	0.0122811985351359
GO:0048712	negative regulation of astrocyte differentiation	0.0122811985351359
GO:0032292	ensheathment of axons in the peripheral nervous system	0.0122811985351359
GO:0005096	GTPase activator activity	0.0122811985351359
GO:0014065	phosphoinositide 3-kinase cascade	0.0122811985351359
GO:0046580	negative regulation of Ras protein signal transduction	0.0122811985351359
GO:0001937	negative regulation of endothelial cell proliferation	0.0122811985351359
GO:0048715	negative regulation of oligodendrocyte differentiation	0.0122811985351359
GO:0035021	negative regulation of Rac protein signal transduction	0.0122811985351359
GO:0048485	sympathetic nervous system development	0.0122811985351359
GO:0001953	negative regulation of cell-matrix adhesion	0.0122811985351359
GO:0014002	astrocyte development	0.0122811985351359
GO:0014044	Schwann cell development	0.0122811985351359
GO:0048853	forebrain morphogenesis	0.0122811985351359
GO:0032320	positive regulation of Ras GTPase activity	0.0122811985351359
GO:0008380	RNA splicing	0.0122811985351359
GO:0043525	positive regulation of neuron apoptosis	0.0122811985351359
GO:0048710	regulation of astrocyte differentiation	0.0122811985351359
GO:0001938	positive regulation of endothelial cell proliferation	0.0122811985351359
GO:0051224	negative regulation of protein transport	0.0122811985351359
GO:0048713	regulation of oligodendrocyte differentiation	0.0122811985351359
GO:0046823	negative regulation of nucleocytoplasmic transport	0.0122811985351359
GO:0048854	brain morphogenesis	0.0122811985351359
GO:0042308	negative regulation of protein import into nucleus	0.0122811985351359
GO:0042992	negative regulation of transcription factor import into nucleus	0.0122811985351359
GO:0051932	synaptic transmission, GABAergic	0.0122811985351359
GO:0032228	regulation of synaptic transmission, GABAergic	0.0122811985351359
GO:0048745	smooth muscle development	0.0122811985351359
GO:0022408	negative regulation of cell-cell adhesion	0.0122811985351359
GO:0008047	enzyme activator activity	0.0129742049098401
GO:0048844	artery morphogenesis	0.0132127414522
GO:0043409	negative regulation of MAPKKK cascade	0.0132127414522
GO:0007243	protein kinase cascade	0.0132127414522
GO:0007242	intracellular signaling cascade	0.0132127414522
GO:0006397	mRNA processing	0.0132127414522
GO:0014014	negative regulation of gliogenesis	0.0132127414522
GO:0045686	negative regulation of glial cell differentiation	0.0132127414522
GO:0001936	regulation of endothelial cell proliferation	0.0132127414522
GO:0007406	negative regulation of neuroblast proliferation	0.0132127414522
GO:0035020	regulation of Rac protein signal transduction	0.0132127414522
GO:0045124	regulation of bone resorption	0.0132127414522
GO:0051058	negative regulation of small GTPase mediated signal transduction	0.0132127414522
GO:0016071	mRNA metabolic process	0.0139020802348034
GO:0048708	astrocyte differentiation	0.0139020802348034
GO:0048483	autonomic nervous system development	0.0139020802348034
GO:0001952	regulation of cell-matrix adhesion	0.0139020802348034
GO:0014037	Schwann cell differentiation	0.0139020802348034
GO:0021987	cerebral cortex development	0.0139430757270679
GO:0042990	regulation of transcription factor import into nucleus	0.0139430757270679
GO:0045671	negative regulation of osteoclast differentiation	0.0139430757270679
GO:0042991	transcription factor import into nucleus	0.0139430757270679
GO:0018345	protein palmitoylation	0.0139430757270679
GO:0001935	endothelial cell proliferation	0.0139430757270679
GO:0042306	regulation of protein import into nucleus	0.0139430757270679
GO:0045685	regulation of glial cell differentiation	0.0139430757270679
GO:0002762	negative regulation of myeloid leukocyte differentiation	0.0139430757270679
GO:0014013	regulation of gliogenesis	0.0139430757270679
GO:0022407	regulation of cell-cell adhesion	0.0139430757270679
GO:0033157	regulation of intracellular protein transport	0.0139430757270679
GO:0030325	adrenal gland development	0.0139430757270679
GO:0032386	regulation of intracellular transport	0.0139430757270679
GO:0030695	GTPase regulator activity	0.0139430757270679
GO:0021782	glial cell development	0.0148901900249385
GO:0048709	oligodendrocyte differentiation	0.0148901900249385
GO:0051223	regulation of protein transport	0.0159094881213838
GO:0048169	regulation of long-term neuronal synaptic plasticity	0.0159094881213838
GO:0009966	regulation of signal transduction	0.0164158545922221
GO:0007264	small GTPase mediated signal transduction	0.0164158545922221
GO:0046822	regulation of nucleocytoplasmic transport	0.0164158545922221
GO:0051048	negative regulation of secretion	0.0164158545922221
GO:0006396	RNA processing	0.0164482517415702
GO:0051349	positive regulation of lyase activity	0.0164482517415702
GO:0045762	positive regulation of adenylate cyclase activity	0.0164482517415702
GO:0007162	negative regulation of cell adhesion	0.0164482517415702
GO:0031281	positive regulation of cyclase activity	0.0164482517415702
GO:0021510	spinal cord development	0.0164482517415702
GO:0021543	pallium development	0.0170713839836996
GO:0030336	negative regulation of cell migration	0.0170713839836996
GO:0048168	regulation of neuronal synaptic plasticity	0.0170713839836996
GO:0045453	bone resorption	0.0172496299708533
GO:0045670	regulation of osteoclast differentiation	0.0172496299708533
GO:0016601	Rac protein signal transduction	0.0172496299708533
GO:0016409	palmitoyltransferase activity	0.0172496299708533
GO:0030199	collagen fibril organization	0.0172496299708533
GO:0016525	negative regulation of angiogenesis	0.0179887538148397
GO:0045761	regulation of adenylate cyclase activity	0.0179887538148397
GO:0043407	negative regulation of MAP kinase activity	0.018393557445004
GO:0031279	regulation of cyclase activity	0.018393557445004
GO:0048593	camera-type eye morphogenesis	0.018393557445004
GO:0051051	negative regulation of transport	0.018393557445004
GO:0043408	regulation of MAPKKK cascade	0.018393557445004
GO:0051339	regulation of lyase activity	0.018393557445004
GO:0051271	negative regulation of cell motility	0.018393557445004
GO:0002761	regulation of myeloid leukocyte differentiation	0.018393557445004
GO:0046928	regulation of neurotransmitter secretion	0.018393557445004
GO:0040013	negative regulation of locomotion	0.0190288725956882
GO:0045638	negative regulation of myeloid cell differentiation	0.0190288725956882
GO:0030316	osteoclast differentiation	0.0192652183901487
GO:0050768	negative regulation of neurogenesis	0.0192652183901487
GO:0050804	regulation of synaptic transmission	0.0192652183901487
GO:0051969	regulation of transmission of nerve impulse	0.0192652183901487
GO:0001666	response to hypoxia	0.019484014560574
GO:0001889	liver development	0.019484014560574
GO:0048167	regulation of synaptic plasticity	0.019484014560574
GO:0000245	spliceosome assembly	0.019484014560574
GO:0043543	protein amino acid acylation	0.0198629027162399
GO:0007632	visual behavior	0.0198629027162399
GO:0008542	visual learning	0.0198629027162399
GO:0007422	peripheral nervous system development	0.0202218303126749
GO:0021537	telencephalon development	0.0202218303126749
GO:0050803	regulation of synapse structure and activity	0.0202218303126749
GO:0007270	nerve-nerve synaptic transmission	0.0209168425513918
GO:0001894	tissue homeostasis	0.0215997851100231
GO:0007405	neuroblast proliferation	0.0218997821277769
GO:0031644	regulation of neurological process	0.0218997821277769
GO:0048871	multicellular organismal homeostasis	0.0218997821277769
GO:0042552	myelination	0.0223668092785619
GO:0001649	osteoblast differentiation	0.0223668092785619
GO:0007272	ensheathment of neurons	0.0234419050993873
GO:0046850	regulation of bone remodeling	0.0234419050993873
GO:0008366	axon ensheathment	0.0234419050993873
GO:0045765	regulation of angiogenesis	0.0240551482023171
GO:0032318	regulation of Ras GTPase activity	0.0262436823525306
GO:0043523	regulation of neuron apoptosis	0.0268247639975477
GO:0045637	regulation of myeloid cell differentiation	0.0273966653713882
GO:0006469	negative regulation of protein kinase activity	0.0277461663059406
GO:0033673	negative regulation of kinase activity	0.0277461663059406
GO:0001508	regulation of action potential	0.028297754960841
GO:0051402	neuron apoptosis	0.0284136106874411
GO:0051348	negative regulation of transferase activity	0.0284136106874411
GO:0010001	glial cell differentiation	0.0284136106874411
GO:0002573	myeloid leukocyte differentiation	0.0295521882743893
GO:0042063	gliogenesis	0.0295521882743893
GO:0000377	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	0.0295521882743893
GO:0000398	nuclear mRNA splicing, via spliceosome	0.0295521882743893
GO:0000375	RNA splicing, via transesterification reactions	0.0295521882743893
GO:0048592	eye morphogenesis	0.0307672006968334
GO:0006497	protein amino acid lipidation	0.0312575822387891
GO:0050767	regulation of neurogenesis	0.0313031448429776
GO:0030155	regulation of cell adhesion	0.0313031448429776
GO:0001656	metanephros development	0.0313031448429776
GO:0008017	microtubule binding	0.031776118320949
GO:0043086	negative regulation of catalytic activity	0.0320246520231212
GO:0042158	lipoprotein biosynthetic process	0.0320246520231212
GO:0035270	endocrine system development	0.0324829642923157
GO:0007612	learning	0.0329350187926033
GO:0007269	neurotransmitter secretion	0.0340448277463405
GO:0030334	regulation of cell migration	0.0342548629309296
GO:0051046	regulation of secretion	0.0342548629309296
GO:0015631	tubulin binding	0.0357518516228022
GO:0007188	G-protein signaling, coupled to cAMP nucleotide second messenger	0.0357518516228022
GO:0006606	protein import into nucleus	0.0358861806290778
GO:0035023	regulation of Rho protein signal transduction	0.0358861806290778
GO:0030198	extracellular matrix organization and biogenesis	0.0358861806290778
GO:0051170	nuclear import	0.0358861806290778
GO:0042157	lipoprotein metabolic process	0.0358861806290778
GO:0007187	G-protein signaling, coupled to cyclic nucleotide second messenger	0.0362849803491617
GO:0051270	regulation of cell motility	0.0366787207857105
GO:0043405	regulation of MAP kinase activity	0.0368414737651879
GO:0019933	cAMP-mediated signaling	0.0368414737651879
GO:0019935	cyclic-nucleotide-mediated signaling	0.03789398518955
GO:0007160	cell-matrix adhesion	0.03789398518955
GO:0040012	regulation of locomotion	0.03789398518955
GO:0045055	regulated secretory pathway	0.03789398518955
GO:0043087	regulation of GTPase activity	0.03789398518955
GO:0017038	protein import	0.03789398518955
GO:0021915	neural tube development	0.0382568214182381
GO:0031589	cell-substrate adhesion	0.0391960958687573
GO:0007611	learning and/or memory	0.0395468297299959
GO:0022618	protein-RNA complex assembly	0.0404671364940083
GO:0001822	kidney development	0.0417081668276912
GO:0009416	response to light stimulus	0.0417081668276912
GO:0048732	gland development	0.0420360376301079
GO:0043010	camera-type eye development	0.042360101196051
GO:0001655	urogenital system development	0.0441042001662615
GO:0042060	wound healing	0.0441042001662615
GO:0007266	Rho protein signal transduction	0.0444108602440817
GO:0051049	regulation of transport	0.0463548636800031
GO:0045596	negative regulation of cell differentiation	0.0466452747343961
GO:0003001	generation of a signal involved in cell-cell signaling	0.0474729333330186
GO:0001505	regulation of neurotransmitter levels	0.0477538060040931
GO:0009968	negative regulation of signal transduction	0.0485658988273496
GO:0030099	myeloid cell differentiation	0.0488549614305601
GO:0006913	nucleocytoplasmic transport	0.0488549614305601
GO:0009314	response to radiation	0.0488549614305601
GO:0001503	ossification	0.0488549614305601
GO:0051169	nuclear transport	0.0488549614305601
GO:0031214	biomineral formation	0.0491177119273748
GO:0007519	skeletal muscle development	0.049377626283681

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
neuron	6.02e-15	33
neuronal stem cell	6.02e-15	33
neuroblast	6.02e-15	33
electrically signaling cell	6.02e-15	33
electrically responsive cell	1.86e-12	39
electrically active cell	1.86e-12	39
ectodermal cell	4.91e-12	44
neurectodermal cell	4.91e-12	44
neural cell	1.13e-11	43
CNS neuron (sensu Vertebrata)	3.16e-10	23
neuroblast (sensu Vertebrata)	3.16e-10	23
non-terminally differentiated cell	4.40e-10	49

Uber Anatomy

Ontology term	p-value	n
nervous system	1.21e-25	75
central nervous system	1.29e-25	73
ectoderm-derived structure	4.56e-25	95
ectoderm	4.56e-25	95
presumptive ectoderm	4.56e-25	95
neurectoderm	2.96e-21	64
neural plate	2.96e-21	64
presumptive neural plate	2.96e-21	64
ecto-epithelium	7.49e-20	73
regional part of nervous system	2.41e-19	54
neural tube	6.89e-18	52
neural rod	6.89e-18	52
future spinal cord	6.89e-18	52
neural keel	6.89e-18	52
structure with developmental contribution from neural crest	7.71e-18	92
brain	3.61e-15	47
future brain	3.61e-15	47
pre-chordal neural plate	7.51e-15	49
regional part of brain	1.59e-14	46
gray matter	1.23e-13	34
anterior neural tube	4.50e-13	40
regional part of forebrain	1.69e-12	39
forebrain	1.69e-12	39
future forebrain	1.69e-12	39
brain grey matter	7.72e-11	29
regional part of telencephalon	7.72e-11	29
telencephalon	7.72e-11	29
multi-cellular organism	1.49e-10	333
anatomical conduit	8.20e-08	122
tube	8.34e-08	114
embryo	1.10e-07	320
cerebral cortex	4.90e-07	21
cerebral hemisphere	4.90e-07	21
pallium	4.90e-07	21

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	6.75707
MA0004.1	0.394951
MA0006.1	0.238555
MA0007.1	0.38073
MA0009.1	0.82278
MA0014.1	8.01481
MA0017.1	0.726051
MA0019.1	0.642876
MA0024.1	0.779446
MA0025.1	1.05446
MA0027.1	2.46647
MA0028.1	0.692501
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	0.993388
MA0050.1	0.431976
MA0051.1	0.542972
MA0052.1	0.84317
MA0055.1	0.0882028
MA0056.1	0
MA0057.1	1.39929
MA0058.1	0.305206
MA0059.1	0.316585
MA0060.1	0.9744
MA0061.1	0.194456
MA0063.1	0
MA0066.1	0.523573
MA0067.1	1.16502
MA0068.1	0.563625
MA0069.1	0.843506
MA0070.1	0.833895
MA0071.1	0.431174
MA0072.1	0.825495
MA0073.1	2.26312
MA0074.1	0.488775
MA0076.1	0.279739
MA0077.1	0.804033
MA0078.1	0.575205
MA0081.1	0.338098
MA0083.1	0.917931
MA0084.1	1.49188
MA0087.1	0.87515
MA0088.1	2.09482
MA0089.1	0
MA0090.1	0.362551
MA0091.1	0.407455
MA0092.1	0.362847
MA0093.1	0.2553
MA0095.1	0
MA0098.1	0
MA0100.1	2.08657
MA0101.1	0.324888
MA0103.1	0.272167
MA0105.1	1.1849
MA0106.1	1.42499
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	0.670446
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	1.54167
MA0132.1	0
MA0133.1	0
MA0135.1	0.954884
MA0136.1	0.508047
MA0139.1	1.39725
MA0140.1	1.20128
MA0141.1	0.29014
MA0142.1	0.714976
MA0143.1	0.571221
MA0144.1	0.568165
MA0145.1	0.442138
MA0146.1	8.59685
MA0147.1	0.593505
MA0148.1	0.410398
MA0149.1	0.330018
MA0062.2	0.365726
MA0035.2	1.21101
MA0039.2	8.44217
MA0138.2	0.630612
MA0002.2	0.447007
MA0137.2	0.783415
MA0104.2	0.157347
MA0047.2	0.533516
MA0112.2	1.6539
MA0065.2	0.44341
MA0150.1	0.991233
MA0151.1	0
MA0152.1	0.53362
MA0153.1	0.971406
MA0154.1	0.982083
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	6.14973
MA0163.1	5.27522
MA0164.1	0.508398
MA0080.2	0.267388
MA0018.2	0.51781
MA0099.2	0.624421
MA0079.2	9.47384
MA0102.2	1.5442
MA0258.1	1.61881
MA0259.1	0.571417
MA0442.1	0