MCL coexpression mm9:3070

Phase1 CAGE Peaks

	Short description
Mm9::chr16:91931888..91931899,-	p2@Atp5o
Mm9::chr9:50412012..50412057,+	p1@Timm8b
Mm9::chr9:79607562..79607579,-	p2@Cox7a2

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:0022891	substrate-specific transmembrane transporter activity	0.00250991568074336
GO:0015078	hydrogen ion transmembrane transporter activity	0.00250991568074336
GO:0015077	monovalent inorganic cation transmembrane transporter activity	0.00250991568074336
GO:0022857	transmembrane transporter activity	0.00250991568074336
GO:0022892	substrate-specific transporter activity	0.00250991568074336
GO:0005739	mitochondrion	0.00250991568074336
GO:0015399	primary active transmembrane transporter activity	0.00250991568074336
GO:0015405	P-P-bond-hydrolysis-driven transmembrane transporter activity	0.00250991568074336
GO:0022890	inorganic cation transmembrane transporter activity	0.00250991568074336
GO:0005743	mitochondrial inner membrane	0.0057225342407789
GO:0019866	organelle inner membrane	0.0057225342407789
GO:0031966	mitochondrial membrane	0.0057225342407789
GO:0005740	mitochondrial envelope	0.0057225342407789
GO:0042719	mitochondrial intermembrane space protein transporter complex	0.0057225342407789
GO:0007007	inner mitochondrial membrane organization and biogenesis	0.0057225342407789
GO:0045039	protein import into mitochondrial inner membrane	0.0057225342407789
GO:0043681	protein import into mitochondrion	0.0057225342407789
GO:0022804	active transmembrane transporter activity	0.00690195750783833
GO:0044429	mitochondrial part	0.00690195750783833
GO:0045261	proton-transporting ATP synthase complex, catalytic core F(1)	0.00729543162843668
GO:0006626	protein targeting to mitochondrion	0.00768195958890141
GO:0033178	proton-transporting two-sector ATPase complex, catalytic domain	0.00768195958890141
GO:0031975	envelope	0.00768195958890141
GO:0031967	organelle envelope	0.00768195958890141
GO:0006091	generation of precursor metabolites and energy	0.00876348180750257
GO:0005758	mitochondrial intermembrane space	0.0100713616879707
GO:0008324	cation transmembrane transporter activity	0.0100713616879707
GO:0022884	macromolecule transmembrane transporter activity	0.0105338042889815
GO:0015450	P-P-bond-hydrolysis-driven protein transmembrane transporter activity	0.0105338042889815
GO:0007006	mitochondrial membrane organization and biogenesis	0.0105338042889815
GO:0031090	organelle membrane	0.011469811440207
GO:0045259	proton-transporting ATP synthase complex	0.013083604919028
GO:0008320	protein transmembrane transporter activity	0.013083604919028
GO:0015075	ion transmembrane transporter activity	0.013083604919028
GO:0004129	cytochrome-c oxidase activity	0.013083604919028
GO:0031970	organelle envelope lumen	0.013083604919028
GO:0016676	oxidoreductase activity, acting on heme group of donors, oxygen as acceptor	0.013083604919028
GO:0015002	heme-copper terminal oxidase activity	0.013083604919028
GO:0016675	oxidoreductase activity, acting on heme group of donors	0.013083604919028
GO:0006839	mitochondrial transport	0.0133632354221828
GO:0008553	hydrogen-exporting ATPase activity, phosphorylative mechanism	0.014220953171138
GO:0005746	mitochondrial respiratory chain	0.016171419771992
GO:0044444	cytoplasmic part	0.016171419771992
GO:0015985	energy coupled proton transport, down electrochemical gradient	0.016729534515831
GO:0015986	ATP synthesis coupled proton transport	0.016729534515831
GO:0006754	ATP biosynthetic process	0.0179648478012853
GO:0006753	nucleoside phosphate metabolic process	0.0179648478012853
GO:0046933	hydrogen ion transporting ATP synthase activity, rotational mechanism	0.0179648478012853
GO:0016469	proton-transporting two-sector ATPase complex	0.0179648478012853
GO:0046961	hydrogen ion transporting ATPase activity, rotational mechanism	0.0179648478012853
GO:0046034	ATP metabolic process	0.0190375126296127
GO:0044455	mitochondrial membrane part	0.0198541431756748
GO:0009145	purine nucleoside triphosphate biosynthetic process	0.0198541431756748
GO:0009206	purine ribonucleoside triphosphate biosynthetic process	0.0198541431756748
GO:0009201	ribonucleoside triphosphate biosynthetic process	0.0198541431756748
GO:0019829	cation-transporting ATPase activity	0.0202814394360515
GO:0009142	nucleoside triphosphate biosynthetic process	0.0202814394360515
GO:0009205	purine ribonucleoside triphosphate metabolic process	0.0202814394360515
GO:0009199	ribonucleoside triphosphate metabolic process	0.0202814394360515
GO:0006119	oxidative phosphorylation	0.0202814394360515
GO:0009144	purine nucleoside triphosphate metabolic process	0.0202814394360515
GO:0015992	proton transport	0.0204644825670295
GO:0065002	intracellular protein transport across a membrane	0.0204644825670295
GO:0006752	group transfer coenzyme metabolic process	0.0204644825670295
GO:0009141	nucleoside triphosphate metabolic process	0.0208936356106975
GO:0009152	purine ribonucleotide biosynthetic process	0.020943364298783
GO:0006818	hydrogen transport	0.020991568887858
GO:0015662	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism	0.0213937248210542
GO:0009260	ribonucleotide biosynthetic process	0.0214338896913356
GO:0009150	purine ribonucleotide metabolic process	0.0218509542515154
GO:0017038	protein import	0.0218509542515154
GO:0006164	purine nucleotide biosynthetic process	0.0218829475959845
GO:0007005	mitochondrion organization and biogenesis	0.022244838478027
GO:0009259	ribonucleotide metabolic process	0.0229230373481143
GO:0006163	purine nucleotide metabolic process	0.0239045732786988
GO:0042625	ATPase activity, coupled to transmembrane movement of ions	0.0258116144597875
GO:0009108	coenzyme biosynthetic process	0.0261025808848761
GO:0051188	cofactor biosynthetic process	0.0297826186884842
GO:0043492	ATPase activity, coupled to movement of substances	0.0346164408385876
GO:0042626	ATPase activity, coupled to transmembrane movement of substances	0.0346164408385876
GO:0016820	hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances	0.0346164408385876
GO:0009165	nucleotide biosynthetic process	0.0359511133638621
GO:0043234	protein complex	0.0367369378447161
GO:0009055	electron carrier activity	0.0390923774018828
GO:0008565	protein transporter activity	0.040605287285226
GO:0005737	cytoplasm	0.0424474218572633
GO:0006732	coenzyme metabolic process	0.044071881129752
GO:0009117	nucleotide metabolic process	0.0495398307059036

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)	4.60e-10	23
neuroblast (sensu Vertebrata)	4.60e-10	23
ectodermal cell	4.67e-08	44
neurectodermal cell	4.67e-08	44
neural cell	5.72e-08	43
non-terminally differentiated cell	7.93e-07	49

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	2.29e-15	54
structure with developmental contribution from neural crest	2.96e-15	92
central nervous system	8.73e-15	73
nervous system	9.80e-15	75
neural tube	3.95e-14	52
neural rod	3.95e-14	52
future spinal cord	3.95e-14	52
neural keel	3.95e-14	52
gray matter	8.08e-14	34
brain	3.34e-11	47
future brain	3.34e-11	47
brain grey matter	3.65e-11	29
regional part of telencephalon	3.65e-11	29
telencephalon	3.65e-11	29
regional part of brain	5.14e-11	46
neurectoderm	1.82e-09	64
neural plate	1.82e-09	64
presumptive neural plate	1.82e-09	64
anterior neural tube	5.14e-09	40
compound organ	9.58e-09	43
regional part of forebrain	1.35e-08	39
forebrain	1.35e-08	39
future forebrain	1.35e-08	39
cerebral cortex	1.64e-08	21
cerebral hemisphere	1.64e-08	21
pallium	1.64e-08	21
ectoderm-derived structure	2.25e-08	95
ectoderm	2.25e-08	95
presumptive ectoderm	2.25e-08	95
regional part of cerebral cortex	1.29e-07	17
primary circulatory organ	1.41e-07	18
heart	1.41e-07	18
primitive heart tube	1.41e-07	18
primary heart field	1.41e-07	18
anterior lateral plate mesoderm	1.41e-07	18
heart tube	1.41e-07	18
heart primordium	1.41e-07	18
cardiac mesoderm	1.41e-07	18
cardiogenic plate	1.41e-07	18
heart rudiment	1.41e-07	18
tube	2.67e-07	114
anatomical conduit	6.85e-07	122
occipital lobe	8.90e-07	10
visual cortex	8.90e-07	10
neocortex	8.90e-07	10
ecto-epithelium	9.73e-07	73

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)
MA0003.1	0.0699972
MA0004.1	0.801718
MA0006.1	0.60285
MA0007.1	0.784593
MA0009.1	1.27673
MA0014.1	0.416365
MA0017.1	0.635031
MA0019.1	1.08369
MA0024.1	1.23079
MA0025.1	1.51835
MA0027.1	2.9431
MA0028.1	1.49373
MA0029.1	1.20789
MA0030.1	1.21482
MA0031.1	1.17722
MA0038.1	0.963265
MA0040.1	1.28983
MA0041.1	0.714279
MA0042.1	0.69885
MA0043.1	1.3775
MA0046.1	1.31428
MA0048.1	0.353763
MA0050.1	0.845669
MA0051.1	0.973068
MA0052.1	1.29825
MA0055.1	0.190475
MA0056.1	0
MA0057.1	0.337566
MA0058.1	0.690848
MA0059.1	0.705317
MA0060.1	0.502699
MA0061.1	0.5406
MA0063.1	0
MA0066.1	0.951196
MA0067.1	1.63197
MA0068.1	0.343188
MA0069.1	2.89084
MA0070.1	1.28847
MA0071.1	0.844726
MA0072.1	1.2796
MA0073.1	0.00834468
MA0074.1	0.911576
MA0076.1	2.67392
MA0077.1	1.2569
MA0078.1	1.0091
MA0081.1	0.732313
MA0083.1	1.37668
MA0084.1	1.96428
MA0087.1	1.33189
MA0088.1	1.40099
MA0089.1	0
MA0090.1	0.762482
MA0091.1	0.816659
MA0092.1	0.762845
MA0093.1	0.62555
MA0095.1	0
MA0098.1	0
MA0100.1	0.89873
MA0101.1	0.71579
MA0103.1	0.647985
MA0105.1	0.405648
MA0106.1	1.01755
MA0107.1	0.640607
MA0108.2	1.10817
MA0109.1	0
MA0111.1	0.778753
MA0113.1	0.986839
MA0114.1	0.537669
MA0115.1	1.38041
MA0116.1	0.602598
MA0117.1	1.34691
MA0119.1	0.716476
MA0122.1	1.36752
MA0124.1	1.57762
MA0125.1	1.5017
MA0130.1	0
MA0131.1	1.07881
MA0132.1	0
MA0133.1	0
MA0135.1	1.4152
MA0136.1	0.933582
MA0139.1	0.462282
MA0140.1	0.898603
MA0141.1	0.671467
MA0142.1	1.16183
MA0143.1	1.00467
MA0144.1	1.33779
MA0145.1	0.292366
MA0146.1	0.151124
MA0147.1	0.556853
MA0148.1	0.820161
MA0149.1	0.722227
MA0062.2	1.06145
MA0035.2	0.903829
MA0039.2	0.181475
MA0138.2	1.07027
MA0002.2	0.466067
MA0137.2	1.60348
MA0104.2	0.48458
MA0047.2	0.962424
MA0112.2	0.29236
MA0065.2	0.292912
MA0150.1	0.784464
MA0151.1	0
MA0152.1	0.962542
MA0153.1	1.43238
MA0154.1	0.35067
MA0155.1	0.312898
MA0156.1	0.656895
MA0157.1	1.12772
MA0158.1	0
MA0159.1	0.569393
MA0160.1	0.823568
MA0161.1	0
MA0162.1	0.166722
MA0163.1	0.157796
MA0164.1	0.933981
MA0080.2	0.64167
MA0018.2	0.944669
MA0099.2	1.06348
MA0079.2	0.00937321
MA0102.2	2.01714
MA0258.1	0.520639
MA0259.1	0.543506
MA0442.1	0