MCL coexpression mm9:1761

Phase1 CAGE Peaks

	Short description
Mm9::chr2:105522351..105522362,+	p19@Pax6
Mm9::chr4:97248379..97248387,+	p29@Nfia
Mm9::chr4:97248473..97248496,+	p16@Nfia
Mm9::chr4:97248607..97248649,+	p15@Nfia
Mm9::chr4:97248652..97248671,+	p19@Nfia

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:0021902	commitment of a neuronal cell to a specific type of neuron in the forebrain	0.0076699720593875
GO:0021877	forebrain neuron fate commitment	0.0076699720593875
GO:0009950	dorsal/ventral axis specification	0.0131467225601383
GO:0021798	forebrain dorsal/ventral pattern formation	0.0131467225601383
GO:0022612	gland morphogenesis	0.0131467225601383
GO:0021871	forebrain regionalization	0.0131467225601383
GO:0007435	salivary gland morphogenesis	0.0131467225601383
GO:0021879	forebrain neuron differentiation	0.0134202449153837
GO:0021872	generation of neurons in the forebrain	0.013632891141377
GO:0007431	salivary gland development	0.0145258107822522
GO:0021543	pallium development	0.0145258107822522
GO:0035272	exocrine system development	0.0145258107822522
GO:0042462	eye photoreceptor cell development	0.0145258107822522
GO:0045665	negative regulation of neuron differentiation	0.0145258107822522
GO:0001754	eye photoreceptor cell differentiation	0.0145258107822522
GO:0009798	axis specification	0.0145258107822522
GO:0042461	photoreceptor cell development	0.0145258107822522
GO:0003700	transcription factor activity	0.0145258107822522
GO:0021983	pituitary gland development	0.0145258107822522
GO:0021536	diencephalon development	0.0146346514277602
GO:0048663	neuron fate commitment	0.0146346514277602
GO:0046530	photoreceptor cell differentiation	0.0146346514277602
GO:0021537	telencephalon development	0.0153302789118187
GO:0001709	cell fate determination	0.0153302789118187
GO:0045664	regulation of neuron differentiation	0.0165553396912625
GO:0009953	dorsal/ventral pattern formation	0.0244021728980764
GO:0048592	eye morphogenesis	0.0244021728980764
GO:0050767	regulation of neurogenesis	0.0246237656104948
GO:0035270	endocrine system development	0.0253575616195415
GO:0030334	regulation of cell migration	0.0265520884597201
GO:0001764	neuron migration	0.0271757694889063
GO:0051270	regulation of cell motility	0.0282380840094746
GO:0040012	regulation of locomotion	0.0292356083395701
GO:0048732	gland development	0.032466382107537
GO:0043010	camera-type eye development	0.032466382107537
GO:0007411	axon guidance	0.032466382107537
GO:0045596	negative regulation of cell differentiation	0.032466382107537
GO:0006355	regulation of transcription, DNA-dependent	0.032466382107537
GO:0006351	transcription, DNA-dependent	0.032466382107537
GO:0032774	RNA biosynthetic process	0.032466382107537
GO:0003677	DNA binding	0.032466382107537
GO:0009952	anterior/posterior pattern formation	0.032466382107537
GO:0045449	regulation of transcription	0.032466382107537
GO:0030900	forebrain development	0.032466382107537
GO:0045165	cell fate commitment	0.032466382107537
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.032466382107537
GO:0006350	transcription	0.032466382107537
GO:0001654	eye development	0.032466382107537
GO:0051093	negative regulation of developmental process	0.032466382107537
GO:0010468	regulation of gene expression	0.0336349202078334
GO:0008285	negative regulation of cell proliferation	0.0350469293638884
GO:0031323	regulation of cellular metabolic process	0.0350469293638884
GO:0019222	regulation of metabolic process	0.036975482139595
GO:0006260	DNA replication	0.0375366993120028
GO:0016070	RNA metabolic process	0.0375366993120028
GO:0003002	regionalization	0.0401063015480455
GO:0045595	regulation of cell differentiation	0.0405594831052453
GO:0007409	axonogenesis	0.0405594831052453
GO:0048667	neuron morphogenesis during differentiation	0.041488573222029
GO:0048812	neurite morphogenesis	0.041488573222029
GO:0007420	brain development	0.0450598351751236
GO:0000904	cellular morphogenesis during differentiation	0.0450598351751236
GO:0007423	sensory organ development	0.0450598351751236
GO:0010467	gene expression	0.0455415637886521
GO:0031175	neurite development	0.0455415637886521
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.0455415637886521
GO:0003676	nucleic acid binding	0.0462836843525849
GO:0048666	neuron development	0.0488857145340564

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
ectodermal cell	1.37e-11	44
neurectodermal cell	1.37e-11	44
neural cell	7.65e-11	43
CNS neuron (sensu Vertebrata)	1.92e-10	23
neuroblast (sensu Vertebrata)	1.92e-10	23
non-terminally differentiated cell	2.18e-08	49
neuron	4.32e-08	33
neuronal stem cell	4.32e-08	33
neuroblast	4.32e-08	33
electrically signaling cell	4.32e-08	33
neuron of cerebral cortex	8.16e-07	6

Uber Anatomy

Ontology term	p-value	n
ectoderm-derived structure	3.50e-20	95
ectoderm	3.50e-20	95
presumptive ectoderm	3.50e-20	95
neurectoderm	1.59e-19	64
neural plate	1.59e-19	64
presumptive neural plate	1.59e-19	64
ecto-epithelium	1.19e-17	73
pre-chordal neural plate	1.28e-16	49
central nervous system	2.39e-16	73
nervous system	1.74e-15	75
neural tube	1.78e-13	52
neural rod	1.78e-13	52
future spinal cord	1.78e-13	52
neural keel	1.78e-13	52
regional part of nervous system	3.28e-13	54
sense organ	1.42e-12	12
sensory system	1.42e-12	12
entire sense organ system	1.42e-12	12
brain	3.72e-12	47
future brain	3.72e-12	47
regional part of brain	1.73e-11	46
structure with developmental contribution from neural crest	2.48e-11	92
head	3.01e-11	13
eye	1.74e-10	9
camera-type eye	1.74e-10	9
simple eye	1.74e-10	9
immature eye	1.74e-10	9
ocular region	1.74e-10	9
visual system	1.74e-10	9
face	1.74e-10	9
optic cup	1.74e-10	9
optic vesicle	1.74e-10	9
eye primordium	1.74e-10	9
ectodermal placode	7.08e-10	13
gray matter	1.82e-09	34
anterior neural tube	2.56e-09	40
subdivision of head	2.62e-09	11
regional part of forebrain	4.52e-09	39
forebrain	4.52e-09	39
future forebrain	4.52e-09	39
brain grey matter	6.84e-08	29
regional part of telencephalon	6.84e-08	29
telencephalon	6.84e-08	29

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)
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