MCL coexpression mm9:2824

Phase1 CAGE Peaks

	Short description
Mm9::chr13:19711627..19711680,-	p1@Epdr1
Mm9::chr2:131735667..131735684,+	p1@Prnp
Mm9::chr2:131735687..131735715,+	p1@Prnd

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:0006878	cellular copper ion homeostasis	2.00936887370317e-05
GO:0055070	copper ion homeostasis	2.00936887370317e-05
GO:0051260	protein homooligomerization	7.81078619014968e-05
GO:0051259	protein oligomerization	0.000121306222455019
GO:0005507	copper ion binding	0.00031896435691302
GO:0030005	cellular di-, tri-valent inorganic cation homeostasis	0.000700884515879918
GO:0055066	di-, tri-valent inorganic cation homeostasis	0.000700884515879918
GO:0030003	cellular cation homeostasis	0.000700884515879918
GO:0055080	cation homeostasis	0.000700884515879918
GO:0048503	GPI anchor binding	0.000767524049384828
GO:0006461	protein complex assembly	0.000783161993426455
GO:0055082	cellular chemical homeostasis	0.000904389109868064
GO:0006873	cellular ion homeostasis	0.000904389109868064
GO:0035091	phosphoinositide binding	0.00101335011568568
GO:0050801	ion homeostasis	0.00101335011568568
GO:0005543	phospholipid binding	0.0013638582240156
GO:0048878	chemical homeostasis	0.0013638582240156
GO:0019725	cellular homeostasis	0.0013638582240156
GO:0065003	macromolecular complex assembly	0.00287316699102723
GO:0042592	homeostatic process	0.00288700379716113
GO:0008289	lipid binding	0.00331646094962967
GO:0022607	cellular component assembly	0.00343658938090558
GO:0065008	regulation of biological quality	0.00881725972057049
GO:0043169	cation binding	0.0133554956062523
GO:0045121	lipid raft	0.0138335019063751
GO:0046872	metal ion binding	0.0157706284997856
GO:0043167	ion binding	0.0161504046373676
GO:0006979	response to oxidative stress	0.0163375068120297
GO:0007160	cell-matrix adhesion	0.0220620126922838
GO:0031589	cell-substrate adhesion	0.0226757069710698

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	3.88e-13	49
ectodermal cell	3.90e-11	44
neurectodermal cell	3.90e-11	44
neural cell	8.13e-11	43
electrically responsive cell	1.85e-08	39
electrically active cell	1.85e-08	39

Uber Anatomy

Ontology term	p-value	n
ectoderm-derived structure	5.26e-25	95
ectoderm	5.26e-25	95
presumptive ectoderm	5.26e-25	95
nervous system	4.58e-24	75
central nervous system	2.00e-23	73
structure with developmental contribution from neural crest	4.92e-19	92
ecto-epithelium	4.25e-17	73
regional part of nervous system	9.67e-17	54
neural tube	1.10e-15	52
neural rod	1.10e-15	52
future spinal cord	1.10e-15	52
neural keel	1.10e-15	52
neurectoderm	2.03e-15	64
neural plate	2.03e-15	64
presumptive neural plate	2.03e-15	64
brain	3.31e-15	47
future brain	3.31e-15	47
regional part of brain	1.20e-14	46
anatomical conduit	6.65e-12	122
anterior neural tube	1.72e-11	40
tube	5.74e-11	114
regional part of forebrain	6.92e-11	39
forebrain	6.92e-11	39
future forebrain	6.92e-11	39
gray matter	1.45e-10	34
pre-chordal neural plate	1.66e-10	49
brain grey matter	2.67e-10	29
regional part of telencephalon	2.67e-10	29
telencephalon	2.67e-10	29
cerebral cortex	1.37e-07	21
cerebral hemisphere	1.37e-07	21
pallium	1.37e-07	21
regional part of cerebral cortex	2.53e-07	17

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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