MCL coexpression mm9:2001

Phase1 CAGE Peaks

	Short description
Mm9::chr11:84339016..84339044,-	p1@Lhx1
Mm9::chr5:140019816..140019825,+	p3@Uncx
Mm9::chr5:140019843..140019858,+	p2@Uncx
Mm9::chr5:140019865..140019886,+	p1@Uncx

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:0001706	endoderm formation	0.00751056046497468
GO:0005667	transcription factor complex	0.00751056046497468
GO:0021937	Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation	0.00751056046497468
GO:0044451	nucleoplasm part	0.00751056046497468
GO:0005654	nucleoplasm	0.00751056046497468
GO:0021692	cerebellar Purkinje cell layer morphogenesis	0.00751056046497468
GO:0021940	positive regulation of granule cell precursor proliferation	0.00751056046497468
GO:0021694	cerebellar Purkinje cell layer formation	0.00751056046497468
GO:0021936	regulation of granule cell precursor proliferation	0.00751056046497468
GO:0021702	cerebellar Purkinje cell differentiation	0.00751056046497468
GO:0021534	cell proliferation in hindbrain	0.00751056046497468
GO:0021930	granule cell precursor proliferation	0.00751056046497468
GO:0021924	cell proliferation in the external granule layer	0.00751056046497468
GO:0021697	cerebellar cortex formation	0.00751056046497468
GO:0021533	cell differentiation in hindbrain	0.00751056046497468
GO:0031981	nuclear lumen	0.00751056046497468
GO:0021680	cerebellar Purkinje cell layer development	0.00751056046497468
GO:0021696	cerebellar cortex morphogenesis	0.00751056046497468
GO:0031974	membrane-enclosed lumen	0.00751056046497468
GO:0043233	organelle lumen	0.00751056046497468
GO:0021587	cerebellum morphogenesis	0.00751056046497468
GO:0021575	hindbrain morphogenesis	0.00757002253337944
GO:0007492	endoderm development	0.00757002253337944
GO:0003700	transcription factor activity	0.00757002253337944
GO:0021695	cerebellar cortex development	0.00757002253337944
GO:0022037	metencephalon development	0.00895507505215965
GO:0021549	cerebellum development	0.00895507505215965
GO:0044428	nuclear part	0.00973301948905536
GO:0001704	formation of primary germ layer	0.00978640769926849
GO:0009791	post-embryonic development	0.0105101741671494
GO:0001702	gastrulation with mouth forming second	0.0105101741671494
GO:0030902	hindbrain development	0.0137904433531285
GO:0007369	gastrulation	0.0197296049695444
GO:0043234	protein complex	0.0205590795987763
GO:0006355	regulation of transcription, DNA-dependent	0.0258268232098056
GO:0006351	transcription, DNA-dependent	0.0258268232098056
GO:0032774	RNA biosynthetic process	0.0258268232098056
GO:0003677	DNA binding	0.0258268232098056
GO:0045449	regulation of transcription	0.0259339862375044
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0262942375471823
GO:0006350	transcription	0.0263286738552209
GO:0032991	macromolecular complex	0.0264238765307082
GO:0010468	regulation of gene expression	0.0268185410295017
GO:0031323	regulation of cellular metabolic process	0.0284016674325537
GO:0019222	regulation of metabolic process	0.0298621036708348
GO:0016070	RNA metabolic process	0.0307754304918284
GO:0044446	intracellular organelle part	0.0316054068440399
GO:0044422	organelle part	0.0316054068440399
GO:0008284	positive regulation of cell proliferation	0.0376007537088389
GO:0007420	brain development	0.0381683309718694
GO:0048646	anatomical structure formation	0.0381683309718694
GO:0010467	gene expression	0.0389882682277188
GO:0003676	nucleic acid binding	0.0401208433633189
GO:0007417	central nervous system development	0.0447136566776892
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0449011665679947

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)	5.12e-15	23
neuroblast (sensu Vertebrata)	5.12e-15	23
neuron	2.85e-08	33
neuronal stem cell	2.85e-08	33
neuroblast	2.85e-08	33
electrically signaling cell	2.85e-08	33

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	4.45e-10	54
cavitated compound organ	1.19e-09	21
neural tube	6.65e-09	52
neural rod	6.65e-09	52
future spinal cord	6.65e-09	52
neural keel	6.65e-09	52
neurectoderm	3.37e-08	64
neural plate	3.37e-08	64
presumptive neural plate	3.37e-08	64
central nervous system	7.95e-08	73
posterior neural tube	2.16e-07	12
chordal neural plate	2.16e-07	12
nervous system	2.46e-07	75

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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