MCL coexpression mm9:602

Phase1 CAGE Peaks

	Short description
Mm9::chr11:4839624..4839635,-	p@chr11:4839624..4839635 -
Mm9::chr11:4839683..4839697,-	p@chr11:4839683..4839697 -
Mm9::chr11:4839712..4839727,-	p@chr11:4839712..4839727 -
Mm9::chr11:4839812..4839821,-	p@chr11:4839812..4839821 -
Mm9::chr11:4839936..4839944,-	p@chr11:4839936..4839944 -
Mm9::chr11:4840044..4840053,-	p@chr11:4840044..4840053 -
Mm9::chr11:4841397..4841408,-	p@chr11:4841397..4841408 -
Mm9::chr11:4843926..4843937,-	p@chr11:4843926..4843937 -
Mm9::chr2:103659822..103659827,-	p1@ENSMUST00000118421 p1@ENSMUST00000167989
Mm9::chr6:90686750..90686771,-	p7@Iqsec1
Mm9::chr6:90686772..90686811,-	p2@Iqsec1
Mm9::chrX:53984619..53984648,+	p8@Fhl1

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:0045110	intermediate filament bundle assembly	0.0135519871096006
GO:0005883	neurofilament	0.0135519871096006
GO:0060052	neurofilament cytoskeleton organization and biogenesis	0.0135519871096006
GO:0060053	neurofilament cytoskeleton	0.0135519871096006
GO:0045109	intermediate filament organization	0.0135519871096006
GO:0032011	ARF protein signal transduction	0.0135519871096006
GO:0005086	ARF guanyl-nucleotide exchange factor activity	0.0135519871096006
GO:0032012	regulation of ARF protein signal transduction	0.0135519871096006
GO:0045104	intermediate filament cytoskeleton organization and biogenesis	0.0186107506779222
GO:0045103	intermediate filament-based process	0.0197022609843965

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)	5.28e-10	23
neuroblast (sensu Vertebrata)	5.28e-10	23

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	5.52e-32	54
neural tube	6.12e-29	52
neural rod	6.12e-29	52
future spinal cord	6.12e-29	52
neural keel	6.12e-29	52
neurectoderm	4.49e-28	64
neural plate	4.49e-28	64
presumptive neural plate	4.49e-28	64
central nervous system	1.32e-25	73
nervous system	1.26e-24	75
ecto-epithelium	2.78e-23	73
ectoderm-derived structure	5.25e-22	95
ectoderm	5.25e-22	95
presumptive ectoderm	5.25e-22	95
brain	7.19e-22	47
future brain	7.19e-22	47
regional part of brain	8.32e-21	46
gray matter	1.40e-19	34
pre-chordal neural plate	3.98e-18	49
structure with developmental contribution from neural crest	2.56e-17	92
anterior neural tube	5.82e-17	40
regional part of forebrain	9.62e-16	39
forebrain	9.62e-16	39
future forebrain	9.62e-16	39
posterior neural tube	1.53e-13	12
chordal neural plate	1.53e-13	12
brain grey matter	3.02e-13	29
regional part of telencephalon	3.02e-13	29
telencephalon	3.02e-13	29
occipital lobe	1.18e-11	10
visual cortex	1.18e-11	10
neocortex	1.18e-11	10
spinal cord	1.19e-10	6
dorsal region element	1.19e-10	6
dorsum	1.19e-10	6
regional part of spinal cord	5.48e-09	5
gray matter of spinal cord	5.48e-09	5
regional part of cerebral cortex	6.76e-09	17
cerebral cortex	4.31e-08	21
cerebral hemisphere	4.31e-08	21
pallium	4.31e-08	21
tube	4.64e-08	114
regional part of midbrain	8.47e-08	4
midbrain	8.47e-08	4
presumptive midbrain	8.47e-08	4
midbrain neural tube	8.47e-08	4
anatomical conduit	5.74e-07	122
basal ganglion	8.05e-07	8
nuclear complex of neuraxis	8.05e-07	8
aggregate regional part of brain	8.05e-07	8
collection of basal ganglia	8.05e-07	8
cerebral subcortex	8.05e-07	8

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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