MCL coexpression mm9:1286

Phase1 CAGE Peaks

	Short description
Mm9::chr11:4060221..4060234,-	p2@Ccdc157
Mm9::chr11:4060235..4060285,-	p1@Ccdc157
Mm9::chr11:4060289..4060308,-	p3@Ccdc157
Mm9::chr12:88488099..88488151,+	p2@Gstz1
Mm9::chr14:58042931..58042948,+	p2@Ift88
Mm9::chr4:154460687..154460719,+	p1@Morn1

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:0016034	maleylacetoacetate isomerase activity	0.0101745724047251
GO:0016853	isomerase activity	0.0101745724047251
GO:0042487	regulation of odontogenesis of dentine-containing teeth	0.0162606022548207
GO:0045862	positive regulation of proteolysis	0.0162606022548207
GO:0006572	tyrosine catabolic process	0.0162606022548207
GO:0006559	L-phenylalanine catabolic process	0.0162606022548207
GO:0006558	L-phenylalanine metabolic process	0.0162606022548207
GO:0005932	basal body	0.0162606022548207
GO:0009074	aromatic amino acid family catabolic process	0.0162606022548207
GO:0006570	tyrosine metabolic process	0.0162606022548207
GO:0030162	regulation of proteolysis	0.0162606022548207
GO:0019439	aromatic compound catabolic process	0.0162606022548207
GO:0042733	embryonic digit morphogenesis	0.0162606022548207
GO:0005930	axoneme	0.0249192623318852
GO:0004364	glutathione transferase activity	0.0249192623318852
GO:0009072	aromatic amino acid family metabolic process	0.0253904864530803
GO:0007224	smoothened signaling pathway	0.0263858473302257
GO:0007368	determination of left/right symmetry	0.0263858473302257
GO:0016859	cis-trans isomerase activity	0.0263858473302257
GO:0009855	determination of bilateral symmetry	0.0263858473302257
GO:0009799	determination of symmetry	0.0263858473302257
GO:0042475	odontogenesis of dentine-containing teeth	0.0263858473302257
GO:0042476	odontogenesis	0.0263858473302257
GO:0019861	flagellum	0.0263858473302257
GO:0009953	dorsal/ventral pattern formation	0.027922280024024
GO:0009063	amino acid catabolic process	0.0287167623369693
GO:0016765	transferase activity, transferring alkyl or aryl (other than methyl) groups	0.0301337658028662
GO:0005815	microtubule organizing center	0.0301337658028662
GO:0009310	amine catabolic process	0.0302816543141528
GO:0044270	nitrogen compound catabolic process	0.0302816543141528
GO:0030326	embryonic limb morphogenesis	0.0319254226005781
GO:0035113	embryonic appendage morphogenesis	0.0319254226005781
GO:0044463	cell projection part	0.0334058050564833
GO:0051247	positive regulation of protein metabolic process	0.0336828146193963
GO:0035107	appendage morphogenesis	0.0336828146193963
GO:0035108	limb morphogenesis	0.0336828146193963
GO:0048736	appendage development	0.0336828146193963
GO:0060173	limb development	0.0336828146193963
GO:0009952	anterior/posterior pattern formation	0.0390185070273834
GO:0006725	aromatic compound metabolic process	0.0456849239475597

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><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
ecto-epithelium	6.77e-11	73
neurectoderm	7.08e-11	64
neural plate	7.08e-11	64
presumptive neural plate	7.08e-11	64
pre-chordal neural plate	4.91e-10	49
ectoderm-derived structure	9.48e-10	95
ectoderm	9.48e-10	95
presumptive ectoderm	9.48e-10	95
neural tube	5.85e-09	52
neural rod	5.85e-09	52
future spinal cord	5.85e-09	52
neural keel	5.85e-09	52
central nervous system	7.08e-09	73
regional part of nervous system	1.30e-08	54
brain	3.61e-08	47
future brain	3.61e-08	47
regional part of brain	4.02e-08	46
nervous system	4.59e-08	75
structure with developmental contribution from neural crest	8.87e-08	92
multi-cellular organism	1.35e-07	333
anterior neural tube	3.08e-07	40
regional part of forebrain	4.94e-07	39
forebrain	4.94e-07	39
future forebrain	4.94e-07	39
anatomical conduit	6.60e-07	122
tube	8.99e-07	114

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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