MCL coexpression mm9:403

Phase1 CAGE Peaks

	Short description
Mm9::chr12:45540065..45540076,+	p9@Nrcam
Mm9::chr13:54431398..54431402,+	p@chr13:54431398..54431402 +
Mm9::chr13:54467800..54467801,+	p@chr13:54467800..54467801 +
Mm9::chr14:122874424..122874441,-	p1@2610035F20Rik
Mm9::chr14:65208698..65208735,+	p3@ENSMUST00000164162
Mm9::chr16:16560211..16560238,-	p6@Fgd4
Mm9::chr16:16560239..16560290,-	p3@Fgd4
Mm9::chr16:16560294..16560316,-	p4@Fgd4
Mm9::chr17:26088998..26089027,-	p1@ENSMUST00000162431 p1@uc008bcv.1
Mm9::chr2:105514700..105514715,+	p13@Pax6
Mm9::chr2:79231715..79231718,-	p6@Cerkl
Mm9::chr2:79292080..79292119,-	p@chr2:79292080..79292119 -
Mm9::chr2:79294073..79294117,-	p@chr2:79294073..79294117 -
Mm9::chr2:79294856..79294867,-	p@chr2:79294856..79294867 -
Mm9::chr2:79295107..79295119,-	p@chr2:79295107..79295119 -
Mm9::chr2:79296458..79296461,-	p@chr2:79296458..79296461 -
Mm9::chr2:79296783..79296801,-	p1@Neurod1
Mm9::chr2:79296907..79296918,-	p2@Neurod1
Mm9::chr6:104443214..104443224,+	p10@Cntn6

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:0007417	central nervous system development	0.00179441931292426
GO:0032990	cell part morphogenesis	0.00179441931292426
GO:0048858	cell projection morphogenesis	0.00179441931292426
GO:0030030	cell projection organization and biogenesis	0.00179441931292426
GO:0000902	cell morphogenesis	0.00543333884663067
GO:0032989	cellular structure morphogenesis	0.00543333884663067
GO:0043010	camera-type eye development	0.00543333884663067
GO:0007411	axon guidance	0.00543333884663067
GO:0009952	anterior/posterior pattern formation	0.00579654942489049
GO:0021902	commitment of a neuronal cell to a specific type of neuron in the forebrain	0.00579654942489049
GO:0021877	forebrain neuron fate commitment	0.00579654942489049
GO:0045165	cell fate commitment	0.00579654942489049
GO:0001654	eye development	0.00579654942489049
GO:0007399	nervous system development	0.00621337240759742
GO:0048856	anatomical structure development	0.00854992126284358
GO:0003002	regionalization	0.00939158937203724
GO:0007409	axonogenesis	0.00969655818258358
GO:0048667	neuron morphogenesis during differentiation	0.00971344345791167
GO:0048812	neurite morphogenesis	0.00971344345791167
GO:0019227	action potential propagation	0.00973599120688521
GO:0007420	brain development	0.00995764535848094
GO:0000904	cellular morphogenesis during differentiation	0.00995764535848094
GO:0007423	sensory organ development	0.00995764535848094
GO:0009950	dorsal/ventral axis specification	0.00995764535848094
GO:0021798	forebrain dorsal/ventral pattern formation	0.00995764535848094
GO:0031175	neurite development	0.00995764535848094
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.00995764535848094
GO:0005515	protein binding	0.0100964278780441
GO:0048666	neuron development	0.0113321223092617
GO:0007389	pattern specification process	0.0114503423936315
GO:0045893	positive regulation of transcription, DNA-dependent	0.0114503423936315
GO:0022612	gland morphogenesis	0.0114503423936315
GO:0021871	forebrain regionalization	0.0114503423936315
GO:0007435	salivary gland morphogenesis	0.0114503423936315
GO:0021879	forebrain neuron differentiation	0.0129756327257196
GO:0009653	anatomical structure morphogenesis	0.0134212707117066
GO:0016477	cell migration	0.0135297673807931
GO:0021872	generation of neurons in the forebrain	0.0135297673807931
GO:0030182	neuron differentiation	0.0135297673807931
GO:0045941	positive regulation of transcription	0.0135699617528827
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0137588549566502
GO:0032502	developmental process	0.0137588549566502
GO:0030035	microspike biogenesis	0.0147401905676848
GO:0007257	activation of JNK activity	0.0147401905676848
GO:0048699	generation of neurons	0.0149698395928933
GO:0043507	positive regulation of JNK activity	0.0149698395928933
GO:0006928	cell motility	0.0149698395928933
GO:0051674	localization of cell	0.0149698395928933
GO:0007431	salivary gland development	0.0156176295143254
GO:0022008	neurogenesis	0.0156176295143254
GO:0031325	positive regulation of cellular metabolic process	0.0161895943822009
GO:0030175	filopodium	0.0161895943822009
GO:0042995	cell projection	0.0161895943822009
GO:0021543	pallium development	0.0161895943822009
GO:0035272	exocrine system development	0.0161895943822009
GO:0042462	eye photoreceptor cell development	0.0161895943822009
GO:0009893	positive regulation of metabolic process	0.0161895943822009
GO:0043506	regulation of JNK activity	0.0163791565715026
GO:0030032	lamellipodium biogenesis	0.0163791565715026
GO:0006357	regulation of transcription from RNA polymerase II promoter	0.0163791565715026
GO:0045665	negative regulation of neuron differentiation	0.0167262475532054
GO:0001754	eye photoreceptor cell differentiation	0.0167262475532054
GO:0009798	axis specification	0.0172143878295004
GO:0042461	photoreceptor cell development	0.0172143878295004
GO:0021983	pituitary gland development	0.0179446169784669
GO:0006366	transcription from RNA polymerase II promoter	0.0181984630979
GO:0021536	diencephalon development	0.0193390463751049
GO:0048663	neuron fate commitment	0.0197152584466631
GO:0046530	photoreceptor cell differentiation	0.0197152584466631
GO:0048731	system development	0.0209800527282815
GO:0021537	telencephalon development	0.0209800527282815
GO:0001709	cell fate determination	0.0215107127193711
GO:0048869	cellular developmental process	0.0215107127193711
GO:0030154	cell differentiation	0.0215107127193711
GO:0045664	regulation of neuron differentiation	0.0233050062515438
GO:0022610	biological adhesion	0.0298487604054241
GO:0007155	cell adhesion	0.0298487604054241
GO:0000187	activation of MAPK activity	0.0298487604054241
GO:0043406	positive regulation of MAP kinase activity	0.0334792427771437
GO:0030902	hindbrain development	0.0334792427771437
GO:0007254	JNK cascade	0.0334792427771437
GO:0009953	dorsal/ventral pattern formation	0.0334792427771437
GO:0048592	eye morphogenesis	0.0334792427771437
GO:0050767	regulation of neurogenesis	0.0346117301328483
GO:0031098	stress-activated protein kinase signaling pathway	0.0349608027389977
GO:0030031	cell projection biogenesis	0.0355554181013376
GO:0035270	endocrine system development	0.0355554181013376
GO:0007275	multicellular organismal development	0.0355554181013376
GO:0030027	lamellipodium	0.0355554181013376
GO:0007219	Notch signaling pathway	0.0358739848435849
GO:0030334	regulation of cell migration	0.0367876692441853
GO:0048522	positive regulation of cellular process	0.0367876692441853
GO:0005089	Rho guanyl-nucleotide exchange factor activity	0.0367876692441853
GO:0001764	neuron migration	0.0377614798551938
GO:0035023	regulation of Rho protein signal transduction	0.0380391672205281
GO:0005088	Ras guanyl-nucleotide exchange factor activity	0.039237748839414
GO:0051270	regulation of cell motility	0.039237748839414
GO:0043405	regulation of MAP kinase activity	0.0394912962577309
GO:0016043	cellular component organization and biogenesis	0.0398863744207733
GO:0030424	axon	0.0399827555688522
GO:0040012	regulation of locomotion	0.0402209771220318
GO:0048518	positive regulation of biological process	0.0437803629891882
GO:0048732	gland development	0.0462705259130253
GO:0031252	leading edge	0.0470538335527206
GO:0007266	Rho protein signal transduction	0.0490371344115926

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
CNS neuron (sensu Vertebrata)	1.38e-10	23
neuroblast (sensu Vertebrata)	1.38e-10	23

Uber Anatomy

Ontology term	p-value	n
neurectoderm	3.57e-31	64
neural plate	3.57e-31	64
presumptive neural plate	3.57e-31	64
pre-chordal neural plate	2.26e-28	49
ecto-epithelium	6.95e-26	73
ectoderm-derived structure	1.56e-25	95
ectoderm	1.56e-25	95
presumptive ectoderm	1.56e-25	95
regional part of nervous system	1.75e-21	54
neural tube	5.99e-21	52
neural rod	5.99e-21	52
future spinal cord	5.99e-21	52
neural keel	5.99e-21	52
brain	8.46e-21	47
future brain	8.46e-21	47
central nervous system	3.07e-20	73
regional part of brain	1.12e-19	46
nervous system	2.04e-19	75
structure with developmental contribution from neural crest	3.75e-18	92
anterior neural tube	2.41e-16	40
eye	2.17e-15	9
camera-type eye	2.17e-15	9
simple eye	2.17e-15	9
immature eye	2.17e-15	9
ocular region	2.17e-15	9
visual system	2.17e-15	9
face	2.17e-15	9
optic cup	2.17e-15	9
optic vesicle	2.17e-15	9
eye primordium	2.17e-15	9
regional part of forebrain	2.60e-15	39
forebrain	2.60e-15	39
future forebrain	2.60e-15	39
subdivision of head	3.83e-12	11
sense organ	6.26e-11	12
sensory system	6.26e-11	12
entire sense organ system	6.26e-11	12
head	6.63e-10	13
ectodermal placode	6.63e-10	13
gray matter	3.83e-09	34
brain grey matter	7.23e-09	29
regional part of telencephalon	7.23e-09	29
telencephalon	7.23e-09	29
diencephalon	2.74e-08	10
future diencephalon	2.74e-08	10

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)
{{{tfbs_overrepresentation_jaspar}}}