MCL coexpression mm9:866

Phase1 CAGE Peaks

	Short description
Mm9::chr10:59740429..59740440,+	p2@Psap
Mm9::chr10:80500045..80500084,-	p1@Slc39a3
Mm9::chr11:118216683..118216691,-	p2@Timp2
Mm9::chr11:49944844..49944928,+	p1@Tbc1d9b
Mm9::chr14:63741287..63741296,+	p4@Ctsb
Mm9::chr14:63741303..63741314,+	p3@Ctsb
Mm9::chr2:155644932..155645005,-	p1@BC029722
Mm9::chr8:13288173..13288220,+	p1@Tmco3

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:0004213	cathepsin B activity	0.0426800538728488
GO:0005764	lysosome	0.0426800538728488
GO:0000323	lytic vacuole	0.0426800538728488
GO:0005773	vacuole	0.0426800538728488
GO:0008047	enzyme activator activity	0.0426800538728488
GO:0030814	regulation of cAMP metabolic process	0.0426800538728488
GO:0008191	metalloendopeptidase inhibitor activity	0.0426800538728488
GO:0030799	regulation of cyclic nucleotide metabolic process	0.0426800538728488
GO:0050790	regulation of catalytic activity	0.0426800538728488
GO:0005385	zinc ion transmembrane transporter activity	0.0426800538728488
GO:0006140	regulation of nucleotide metabolic process	0.0426800538728488
GO:0065009	regulation of a molecular function	0.0478674488936791
GO:0015299	solute:hydrogen antiporter activity	0.0478674488936791
GO:0009966	regulation of signal transduction	0.0478674488936791
GO:0043408	regulation of MAPKKK cascade	0.0485669984857689
GO:0006885	regulation of pH	0.0485669984857689
GO:0015298	solute:cation antiporter activity	0.0485669984857689
GO:0046058	cAMP metabolic process	0.0485669984857689
GO:0015300	solute:solute antiporter activity	0.0485669984857689
GO:0005178	integrin binding	0.0485669984857689
GO:0006829	zinc ion transport	0.0485669984857689
GO:0046915	transition metal ion transmembrane transporter activity	0.0485669984857689
GO:0008324	cation transmembrane transporter activity	0.0485669984857689
GO:0045664	regulation of neuron differentiation	0.0485669984857689
GO:0032313	regulation of Rab GTPase activity	0.0485669984857689
GO:0032483	regulation of Rab protein signal transduction	0.0485669984857689
GO:0032482	Rab protein signal transduction	0.0485669984857689

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
non-terminally differentiated cell	9.97e-13	49
ectodermal cell	2.24e-10	44
neurectodermal cell	2.24e-10	44
neural cell	3.95e-10	43
electrically responsive cell	4.11e-08	39
electrically active cell	4.11e-08	39
embryonic cell	1.30e-07	70

Uber Anatomy

Ontology term	p-value	n
nervous system	3.21e-22	75
central nervous system	1.62e-21	73
ectoderm-derived structure	1.17e-17	95
ectoderm	1.17e-17	95
presumptive ectoderm	1.17e-17	95
regional part of nervous system	2.17e-17	54
neural tube	2.45e-16	52
neural rod	2.45e-16	52
future spinal cord	2.45e-16	52
neural keel	2.45e-16	52
brain	3.01e-14	47
future brain	3.01e-14	47
regional part of brain	7.85e-14	46
structure with developmental contribution from neural crest	5.61e-13	92
neurectoderm	2.75e-12	64
neural plate	2.75e-12	64
presumptive neural plate	2.75e-12	64
gray matter	1.59e-11	34
ecto-epithelium	3.23e-11	73
anterior neural tube	6.23e-11	40
regional part of forebrain	2.18e-10	39
forebrain	2.18e-10	39
future forebrain	2.18e-10	39
brain grey matter	8.73e-10	29
regional part of telencephalon	8.73e-10	29
telencephalon	8.73e-10	29
anatomical conduit	3.75e-09	122
tube	3.68e-08	114
pre-chordal neural plate	9.32e-08	49
regional part of cerebral cortex	1.20e-07	17
cerebral cortex	2.51e-07	21
cerebral hemisphere	2.51e-07	21
pallium	2.51e-07	21
occipital lobe	5.02e-07	10
visual cortex	5.02e-07	10
neocortex	5.02e-07	10
adult organism	5.76e-07	51

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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