MCL coexpression mm9:287

Phase1 CAGE Peaks

	Short description
Mm9::chr10:34020647..34020664,+	p@chr10:34020647..34020664 +
Mm9::chr11:33743405..33743416,-	p5@Kcnip1
Mm9::chr14:67423733..67423743,-	p@chr14:67423733..67423743 -
Mm9::chr14:76956449..76956460,-	p4@Serp2
Mm9::chr15:78549275..78549309,-	p5@Elfn2
Mm9::chr17:24625616..24625627,+	p5@Caskin1
Mm9::chr19:47327907..47327937,+	p@chr19:47327907..47327937 +
Mm9::chr1:33964544..33964555,-	p3@Bend6
Mm9::chr2:124962334..124962359,+	p1@Ctxn2
Mm9::chr2:124962484..124962505,+	p2@Ctxn2
Mm9::chr2:181041454..181041465,+	p@chr2:181041454..181041465 +
Mm9::chr3:88552800..88552811,-	p@chr3:88552800..88552811 -
Mm9::chr4:117521906..117521913,+	p15@Slc6a9
Mm9::chr5:137729501..137729520,+	p1@Ache
Mm9::chr6:114081223..114081240,+	p1@Slc6a11
Mm9::chr6:114198039..114198052,+	p@chr6:114198039..114198052 +
Mm9::chr6:114198085..114198112,+	p@chr6:114198085..114198112 +
Mm9::chr6:114198155..114198168,+	p@chr6:114198155..114198168 +
Mm9::chr6:114198339..114198355,+	p@chr6:114198339..114198355 +
Mm9::chr6:114198370..114198396,+	p@chr6:114198370..114198396 +
Mm9::chr6:91107077..91107093,+	p6@Hdac11
Mm9::chr6:91793870..91793909,-	p@chr6:91793870..91793909 -
Mm9::chr7:136400541..136400570,+	p1@Ppapdc1a
Mm9::chr7:26460119..26460206,-	p1@Tmem91
Mm9::chr7:53125597..53125608,-	p@chr7:53125597..53125608 -
Mm9::chr7:58877497..58877512,+	p3@Slc17a6
Mm9::chr8:33760116..33760119,-	p@chr8:33760116..33760119 -
Mm9::chr8:81334120..81334134,-	p6@Lsm6
Mm9::chrX:61750178..61750185,+	p@chrX:61750178..61750185 +

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:0006836	neurotransmitter transport	0.000487893433099392
GO:0005283	sodium:amino acid symporter activity	0.000487893433099392
GO:0005342	organic acid transmembrane transporter activity	0.000487893433099392
GO:0005416	cation:amino acid symporter activity	0.000793169376948295
GO:0005328	neurotransmitter:sodium symporter activity	0.00238250463219786
GO:0005343	organic acid:sodium symporter activity	0.00238250463219786
GO:0005326	neurotransmitter transporter activity	0.00238250463219786
GO:0015179	L-amino acid transmembrane transporter activity	0.00277289081461163
GO:0005275	amine transmembrane transporter activity	0.00544349046617558
GO:0015171	amino acid transmembrane transporter activity	0.00549769167310049
GO:0015370	solute:sodium symporter activity	0.00617884339273634
GO:0015294	solute:cation symporter activity	0.0095865853648283
GO:0046943	carboxylic acid transmembrane transporter activity	0.00977373582424807
GO:0006581	acetylcholine catabolic process	0.00977373582424807
GO:0003990	acetylcholinesterase activity	0.00977373582424807
GO:0022891	substrate-specific transmembrane transporter activity	0.0124562618492223
GO:0008291	acetylcholine metabolic process	0.0154275641646028
GO:0032800	receptor biosynthetic process	0.0154275641646028
GO:0045212	neurotransmitter receptor biosynthetic process	0.0154275641646028
GO:0001505	regulation of neurotransmitter levels	0.0163882840827892
GO:0022857	transmembrane transporter activity	0.016420888300229
GO:0006810	transport	0.0169058882193297
GO:0051234	establishment of localization	0.0169058882193297
GO:0001919	regulation of receptor recycling	0.0169058882193297
GO:0043236	laminin binding	0.0169058882193297
GO:0005332	gamma-aminobutyric acid:sodium symporter activity	0.0169058882193297
GO:0022892	substrate-specific transporter activity	0.0178922045850977
GO:0031623	receptor internalization	0.0188998132089217
GO:0004104	cholinesterase activity	0.0188998132089217
GO:0042439	ethanolamine and derivative metabolic process	0.0188998132089217
GO:0015185	L-gamma-aminobutyric acid transmembrane transporter activity	0.0188998132089217
GO:0008324	cation transmembrane transporter activity	0.0200721206149368
GO:0001881	receptor recycling	0.0217456361305597
GO:0015293	symporter activity	0.0217456361305597
GO:0051179	localization	0.0219577964512983
GO:0050840	extracellular matrix binding	0.0219577964512983
GO:0043621	protein self-association	0.0219577964512983
GO:0045213	neurotransmitter receptor metabolic process	0.0219577964512983
GO:0005313	L-glutamate transmembrane transporter activity	0.0219577964512983
GO:0015172	acidic amino acid transmembrane transporter activity	0.0219577964512983
GO:0001504	neurotransmitter uptake	0.0249850850611956
GO:0051262	protein tetramerization	0.0278661202732491
GO:0015291	secondary active transmembrane transporter activity	0.0296954910337121
GO:0060041	retina development in camera-type eye	0.0299153999596034
GO:0042135	neurotransmitter catabolic process	0.0321993161904013
GO:0007268	synaptic transmission	0.0321993161904013
GO:0015075	ion transmembrane transporter activity	0.0323653279984625
GO:0004407	histone deacetylase activity	0.0357847268869069
GO:0033558	protein deacetylase activity	0.0357847268869069
GO:0019213	deacetylase activity	0.0394701876471836
GO:0042402	biogenic amine catabolic process	0.0394701876471836
GO:0019226	transmission of nerve impulse	0.0394701876471836
GO:0042219	amino acid derivative catabolic process	0.0432429813478802
GO:0006898	receptor-mediated endocytosis	0.0432429813478802

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)	2.16e-22	23
neuroblast (sensu Vertebrata)	2.16e-22	23
neuron	1.62e-13	33
neuronal stem cell	1.62e-13	33
neuroblast	1.62e-13	33
electrically signaling cell	1.62e-13	33
electrically responsive cell	1.93e-10	39
electrically active cell	1.93e-10	39
neural cell	6.85e-09	43
ectodermal cell	1.50e-08	44
neurectodermal cell	1.50e-08	44
non-terminally differentiated cell	4.47e-07	49

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	2.49e-39	54
neural tube	1.98e-36	52
neural rod	1.98e-36	52
future spinal cord	1.98e-36	52
neural keel	1.98e-36	52
neurectoderm	9.42e-35	64
neural plate	9.42e-35	64
presumptive neural plate	9.42e-35	64
central nervous system	5.03e-34	73
nervous system	1.04e-32	75
brain	1.68e-29	47
future brain	1.68e-29	47
gray matter	6.16e-29	34
ecto-epithelium	1.12e-28	73
ectoderm-derived structure	1.20e-28	95
ectoderm	1.20e-28	95
presumptive ectoderm	1.20e-28	95
regional part of brain	2.65e-28	46
pre-chordal neural plate	2.97e-26	49
anterior neural tube	1.49e-25	40
regional part of forebrain	2.63e-24	39
forebrain	2.63e-24	39
future forebrain	2.63e-24	39
brain grey matter	3.72e-22	29
regional part of telencephalon	3.72e-22	29
telencephalon	3.72e-22	29
structure with developmental contribution from neural crest	8.15e-20	92
cerebral cortex	3.34e-13	21
cerebral hemisphere	3.34e-13	21
pallium	3.34e-13	21
occipital lobe	5.37e-12	10
visual cortex	5.37e-12	10
neocortex	5.37e-12	10
regional part of cerebral cortex	9.00e-12	17
posterior neural tube	5.22e-11	12
chordal neural plate	5.22e-11	12
basal ganglion	1.18e-10	8
nuclear complex of neuraxis	1.18e-10	8
aggregate regional part of brain	1.18e-10	8
collection of basal ganglia	1.18e-10	8
cerebral subcortex	1.18e-10	8
tube	1.09e-09	114
spinal cord	1.72e-09	6
dorsal region element	1.72e-09	6
dorsum	1.72e-09	6
anatomical conduit	2.66e-08	122
regional part of spinal cord	2.84e-08	5
gray matter of spinal cord	2.84e-08	5
regional part of midbrain	7.59e-07	4
midbrain	7.59e-07	4
presumptive midbrain	7.59e-07	4
midbrain neural tube	7.59e-07	4

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	3.43156
MA0004.1	0.305832
MA0006.1	1.20095
MA0007.1	0.084375
MA0009.1	0.388771
MA0014.1	3.08692
MA0017.1	0.141194
MA0019.1	0.248074
MA0024.1	0.353393
MA0025.1	1.43891
MA0027.1	1.95996
MA0028.1	0.12595
MA0029.1	0.336166
MA0030.1	0.341346
MA0031.1	0.84229
MA0038.1	0.17284
MA0040.1	0.399043
MA0041.1	0.464369
MA0042.1	0.0533455
MA0043.1	0.469769
MA0046.1	0.418434
MA0048.1	0.67799
MA0050.1	0.111159
MA0051.1	0.178537
MA0052.1	0.405693
MA0055.1	0.378635
MA0056.1	0
MA0057.1	0.830691
MA0058.1	0.189695
MA0059.1	0.203408
MA0060.1	0.0114726
MA0061.1	0.380864
MA0063.1	0
MA0066.1	0.165937
MA0067.1	0.690195
MA0068.1	2.96294
MA0069.1	0.405974
MA0070.1	0.397975
MA0071.1	0.357212
MA0072.1	0.391015
MA0073.1	2.55311
MA0074.1	0.443199
MA0076.1	0.0413193
MA0077.1	0.373365
MA0078.1	0.200156
MA0081.1	0.0645216
MA0083.1	1.18326
MA0084.1	0.999346
MA0087.1	0.432564
MA0088.1	1.80197
MA0089.1	0
MA0090.1	0.942377
MA0091.1	0.32331
MA0092.1	0.555994
MA0093.1	0.314468
MA0095.1	0
MA0098.1	0
MA0100.1	0.137416
MA0101.1	0.0588523
MA0103.1	0.350053
MA0105.1	0.672153
MA0106.1	0.592733
MA0107.1	0.338168
MA0108.2	0.264668
MA0109.1	0
MA0111.1	0.27977
MA0113.1	0.186674
MA0114.1	0.0743624
MA0115.1	0.472164
MA0116.1	0.279815
MA0117.1	0.44472
MA0119.1	0.059082
MA0122.1	0.461557
MA0124.1	0.641584
MA0125.1	0.574947
MA0130.1	0
MA0131.1	0.685442
MA0132.1	0
MA0133.1	0
MA0135.1	0.501131
MA0136.1	0.156089
MA0139.1	0.92028
MA0140.1	0.13735
MA0141.1	1.06715
MA0142.1	0.817195
MA0143.1	0.573785
MA0144.1	0.0765684
MA0145.1	0.087554
MA0146.1	0.392056
MA0147.1	1.00524
MA0148.1	0.327464
MA0149.1	0.220008
MA0062.2	0.00387198
MA0035.2	0.432878
MA0039.2	0.224742
MA0138.2	2.716
MA0002.2	0.114411
MA0137.2	0.0441189
MA0104.2	1.3763
MA0047.2	0.987855
MA0112.2	1.31116
MA0065.2	0.273313
MA0150.1	0.286158
MA0151.1	0
MA0152.1	0.172422
MA0153.1	0.515592
MA0154.1	0.459593
MA0155.1	1.1957
MA0156.1	0.0410387
MA0157.1	0.762276
MA0158.1	0
MA0159.1	1.05755
MA0160.1	0.331527
MA0161.1	0
MA0162.1	0.824796
MA0163.1	1.34258
MA0164.1	0.15631
MA0080.2	0.146586
MA0018.2	0.488272
MA0099.2	0.234689
MA0079.2	2.90175
MA0102.2	1.04989
MA0258.1	0.570617
MA0259.1	0.386929
MA0442.1	0