MCL coexpression mm9:799

Phase1 CAGE Peaks

	Short description
Mm9::chr11:95574072..95574082,-	p1@ENSMUST00000155531 p1@uc007lao.1
Mm9::chr15:98571806..98571818,-	p@chr15:98571806..98571818 -
Mm9::chr16:4879810..4879836,-	p1@Fam100a
Mm9::chr17:24306359..24306395,-	p1@Atp6v0c
Mm9::chr17:24306593..24306658,-	p2@Atp6v0c
Mm9::chr2:129419264..129419336,+	p2@Sirpa
Mm9::chr5:139960374..139960427,-	p1@Zfand2a
Mm9::chr7:28326103..28326131,+	p@chr7:28326103..28326131 +
Mm9::chr7:28327793..28327828,-	p1@Pld3

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:0007035	vacuolar acidification	0.0157769315378812
GO:0045851	pH reduction	0.0157769315378812
GO:0051452	cellular pH reduction	0.0157769315378812
GO:0051453	regulation of cellular pH	0.0157769315378812
GO:0007042	lysosomal lumen acidification	0.0157769315378812
GO:0030641	cellular hydrogen ion homeostasis	0.0197195436675489
GO:0004630	phospholipase D activity	0.0250893514230226
GO:0033176	proton-transporting V-type ATPase complex	0.0250893514230226
GO:0016471	vacuolar proton-transporting V-type ATPase complex	0.0250893514230226
GO:0030004	cellular monovalent inorganic cation homeostasis	0.0250893514230226
GO:0055067	monovalent inorganic cation homeostasis	0.0250893514230226
GO:0045309	protein phosphorylated amino acid binding	0.0262819222260888
GO:0006910	phagocytosis, recognition	0.0331763951638302
GO:0051219	phosphoprotein binding	0.0331763951638302
GO:0006911	phagocytosis, engulfment	0.0331763951638302
GO:0007040	lysosome organization and biogenesis	0.0331763951638302
GO:0050766	positive regulation of phagocytosis	0.0331763951638302
GO:0050764	regulation of phagocytosis	0.0331763951638302
GO:0005774	vacuolar membrane	0.0331763951638302
GO:0006885	regulation of pH	0.035451443793266
GO:0007033	vacuole organization and biogenesis	0.0356360882026992
GO:0044437	vacuolar part	0.0358036526335401
GO:0045807	positive regulation of endocytosis	0.0359563649399432
GO:0008553	hydrogen-exporting ATPase activity, phosphorylative mechanism	0.0393710703231679
GO:0015985	energy coupled proton transport, down electrochemical gradient	0.0426270730378642
GO:0015986	ATP synthesis coupled proton transport	0.0426270730378642
GO:0051050	positive regulation of transport	0.0426270730378642
GO:0030100	regulation of endocytosis	0.0426270730378642
GO:0006754	ATP biosynthetic process	0.0426270730378642
GO:0006753	nucleoside phosphate metabolic process	0.0426270730378642
GO:0046933	hydrogen ion transporting ATP synthase activity, rotational mechanism	0.0426270730378642
GO:0016469	proton-transporting two-sector ATPase complex	0.0426270730378642
GO:0046961	hydrogen ion transporting ATPase activity, rotational mechanism	0.0426270730378642
GO:0006909	phagocytosis	0.0426270730378642
GO:0007015	actin filament organization	0.0426270730378642
GO:0046034	ATP metabolic process	0.0426270730378642
GO:0008037	cell recognition	0.0426270730378642
GO:0009145	purine nucleoside triphosphate biosynthetic process	0.0426270730378642
GO:0009206	purine ribonucleoside triphosphate biosynthetic process	0.0426270730378642
GO:0009201	ribonucleoside triphosphate biosynthetic process	0.0426270730378642
GO:0004620	phospholipase activity	0.0426270730378642
GO:0019829	cation-transporting ATPase activity	0.0426270730378642
GO:0009142	nucleoside triphosphate biosynthetic process	0.0426270730378642
GO:0009205	purine ribonucleoside triphosphate metabolic process	0.0426270730378642
GO:0009199	ribonucleoside triphosphate metabolic process	0.0426270730378642
GO:0006119	oxidative phosphorylation	0.0426270730378642
GO:0009144	purine nucleoside triphosphate metabolic process	0.0426270730378642
GO:0015992	proton transport	0.0432289395035572
GO:0006752	group transfer coenzyme metabolic process	0.0432289395035572
GO:0009141	nucleoside triphosphate metabolic process	0.0432289395035572
GO:0009152	purine ribonucleotide biosynthetic process	0.0432289395035572
GO:0006818	hydrogen transport	0.0432289395035572
GO:0015662	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism	0.0432289395035572
GO:0009260	ribonucleotide biosynthetic process	0.0432289395035572
GO:0016298	lipase activity	0.0432289395035572
GO:0007160	cell-matrix adhesion	0.0432289395035572
GO:0009150	purine ribonucleotide metabolic process	0.0432289395035572
GO:0008081	phosphoric diester hydrolase activity	0.0432289395035572
GO:0006164	purine nucleotide biosynthetic process	0.0432289395035572
GO:0031589	cell-substrate adhesion	0.0438092038771068
GO:0009259	ribonucleotide metabolic process	0.0450093633137073
GO:0006163	purine nucleotide metabolic process	0.0467984890472701

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	2.30e-10	49
CNS neuron (sensu Vertebrata)	5.75e-09	23
neuroblast (sensu Vertebrata)	5.75e-09	23
neural cell	2.36e-08	43
ectodermal cell	3.62e-08	44
neurectodermal cell	3.62e-08	44
electrically responsive cell	4.28e-08	39
electrically active cell	4.28e-08	39

Uber Anatomy

Ontology term	p-value	n
central nervous system	2.46e-23	73
ectoderm-derived structure	3.06e-23	95
ectoderm	3.06e-23	95
presumptive ectoderm	3.06e-23	95
regional part of nervous system	4.38e-23	54
nervous system	6.54e-23	75
neural tube	7.04e-22	52
neural rod	7.04e-22	52
future spinal cord	7.04e-22	52
neural keel	7.04e-22	52
brain	2.98e-19	47
future brain	2.98e-19	47
regional part of brain	1.34e-18	46
ecto-epithelium	1.82e-18	73
neurectoderm	4.08e-18	64
neural plate	4.08e-18	64
presumptive neural plate	4.08e-18	64
gray matter	6.00e-16	34
anterior neural tube	1.41e-15	40
structure with developmental contribution from neural crest	2.55e-15	92
regional part of forebrain	5.52e-15	39
forebrain	5.52e-15	39
future forebrain	5.52e-15	39
brain grey matter	1.88e-13	29
regional part of telencephalon	1.88e-13	29
telencephalon	1.88e-13	29
anatomical conduit	2.24e-13	122
pre-chordal neural plate	4.46e-13	49
tube	4.52e-12	114
cerebral cortex	1.07e-09	21
cerebral hemisphere	1.07e-09	21
pallium	1.07e-09	21
regional part of cerebral cortex	1.42e-09	17
occipital lobe	8.98e-08	10
visual cortex	8.98e-08	10
neocortex	8.98e-08	10
adult organism	1.29e-07	51
posterior neural tube	4.73e-07	12
chordal neural plate	4.73e-07	12

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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