MCL coexpression mm9:643

Phase1 CAGE Peaks

	Short description
Mm9::chr10:79850331..79850375,-	p1@Mex3d
Mm9::chr12:86114023..86114033,-	p6@Npc2
Mm9::chr12:86114037..86114041,-	p7@Npc2
Mm9::chr15:85166651..85166662,+	p7@Atxn10
Mm9::chr18:35931142..35931212,+	p3@Ube2d2
Mm9::chr19:42160809..42160824,-	p2@Morn4
Mm9::chr2:178062216..178062239,+	p7@Phactr3
Mm9::chr4:40670050..40670064,+	p3@Dnaja1
Mm9::chr5:3927857..3927888,+	p3@Akap9
Mm9::chr8:111775598..111775613,-	p1@ENSMUST00000079189
Mm9::chr8:41596652..41596700,-	p2@Cnot7

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:0032366	intracellular sterol transport	0.0179696488248507
GO:0032367	intracellular cholesterol transport	0.0179696488248507
GO:0030014	CCR4-NOT complex	0.0179696488248507
GO:0032365	intracellular lipid transport	0.0179696488248507
GO:0030521	androgen receptor signaling pathway	0.0239549372912768
GO:0003730	mRNA 3'-UTR binding	0.0239549372912768
GO:0050779	RNA destabilization	0.0307932992010504
GO:0000242	pericentriolar material	0.0448896748248667
GO:0015485	cholesterol binding	0.0487277273992434
GO:0050750	low-density lipoprotein receptor binding	0.0487277273992434
GO:0044265	cellular macromolecule catabolic process	0.0487277273992434
GO:0043285	biopolymer catabolic process	0.0487277273992434
GO:0005515	protein binding	0.0487277273992434
GO:0030518	steroid hormone receptor signaling pathway	0.0487277273992434
GO:0032934	sterol binding	0.0487277273992434
GO:0044450	microtubule organizing center part	0.0487277273992434
GO:0030301	cholesterol transport	0.0487277273992434
GO:0015918	sterol transport	0.0487277273992434
GO:0043487	regulation of RNA stability	0.0487277273992434
GO:0009057	macromolecule catabolic process	0.0487277273992434
GO:0004864	protein phosphatase inhibitor activity	0.0487277273992434
GO:0042632	cholesterol homeostasis	0.0487277273992434
GO:0055088	lipid homeostasis	0.0487277273992434
GO:0055092	sterol homeostasis	0.0487277273992434
GO:0051252	regulation of RNA metabolic process	0.0487277273992434
GO:0030522	intracellular receptor-mediated signaling pathway	0.0496001682551745

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
neuron	4.83e-14	33
neuronal stem cell	4.83e-14	33
neuroblast	4.83e-14	33
electrically signaling cell	4.83e-14	33
ectodermal cell	5.78e-13	44
neurectodermal cell	5.78e-13	44
CNS neuron (sensu Vertebrata)	7.99e-13	23
neuroblast (sensu Vertebrata)	7.99e-13	23
neural cell	1.40e-12	43
electrically responsive cell	2.78e-11	39
electrically active cell	2.78e-11	39
non-terminally differentiated cell	1.64e-10	49

Uber Anatomy

Ontology term	p-value	n
central nervous system	1.70e-22	73
nervous system	4.30e-22	75
neurectoderm	8.40e-22	64
neural plate	8.40e-22	64
presumptive neural plate	8.40e-22	64
ectoderm-derived structure	9.00e-21	95
ectoderm	9.00e-21	95
presumptive ectoderm	9.00e-21	95
ecto-epithelium	6.24e-19	73
neural tube	1.52e-18	52
neural rod	1.52e-18	52
future spinal cord	1.52e-18	52
neural keel	1.52e-18	52
regional part of nervous system	2.79e-18	54
structure with developmental contribution from neural crest	1.39e-17	92
pre-chordal neural plate	6.06e-16	49
brain	2.06e-15	47
future brain	2.06e-15	47
regional part of brain	6.07e-15	46
gray matter	3.99e-13	34
anterior neural tube	4.39e-13	40
regional part of forebrain	1.45e-12	39
forebrain	1.45e-12	39
future forebrain	1.45e-12	39
brain grey matter	3.21e-10	29
regional part of telencephalon	3.21e-10	29
telencephalon	3.21e-10	29
multi-cellular organism	8.90e-07	333

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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