MCL coexpression mm9:780

Phase1 CAGE Peaks

	Short description
Mm9::chr11:20731012..20731056,-	p1@1110067D22Rik
Mm9::chr11:20731063..20731077,-	p5@1110067D22Rik
Mm9::chr11:79153084..79153137,+	p2@Nf1
Mm9::chr11:86570985..86571074,-	p1@Cltc
Mm9::chr15:81641878..81641921,+	p1@Tef
Mm9::chr18:36440723..36440805,+	p1@Pura
Mm9::chr1:59820262..59820306,+	p@chr1:59820262..59820306 +
Mm9::chr3:7503423..7503503,+	p1@Fam164a
Mm9::chr5:67009875..67009950,-	p1@Apbb2

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:0003690	double-stranded DNA binding	0.0134550899062544
GO:0048522	positive regulation of cellular process	0.0163456878692465
GO:0048518	positive regulation of biological process	0.0163456878692465
GO:0043566	structure-specific DNA binding	0.0163456878692465
GO:0030198	extracellular matrix organization and biogenesis	0.0163456878692465
GO:0046929	negative regulation of neurotransmitter secretion	0.0163456878692465
GO:0021897	forebrain astrocyte development	0.0163456878692465
GO:0021896	forebrain astrocyte differentiation	0.0163456878692465
GO:0043062	extracellular structure organization and biogenesis	0.0163456878692465
GO:0022011	myelination in the peripheral nervous system	0.0163456878692465
GO:0048712	negative regulation of astrocyte differentiation	0.0163456878692465
GO:0032292	ensheathment of axons in the peripheral nervous system	0.0163456878692465
GO:0046907	intracellular transport	0.0163456878692465
GO:0006915	apoptosis	0.0163456878692465
GO:0014065	phosphoinositide 3-kinase cascade	0.0163456878692465
GO:0046580	negative regulation of Ras protein signal transduction	0.0163456878692465
GO:0001937	negative regulation of endothelial cell proliferation	0.0163456878692465
GO:0048715	negative regulation of oligodendrocyte differentiation	0.0163456878692465
GO:0035021	negative regulation of Rac protein signal transduction	0.0163456878692465
GO:0048485	sympathetic nervous system development	0.0163456878692465
GO:0001953	negative regulation of cell-matrix adhesion	0.0163456878692465
GO:0014002	astrocyte development	0.0163456878692465
GO:0035035	histone acetyltransferase binding	0.0163456878692465
GO:0014044	Schwann cell development	0.0163456878692465
GO:0048853	forebrain morphogenesis	0.0163456878692465
GO:0045749	negative regulation of S phase of mitotic cell cycle	0.0163456878692465
GO:0032320	positive regulation of Ras GTPase activity	0.0163456878692465
GO:0012501	programmed cell death	0.0163456878692465
GO:0007399	nervous system development	0.0163456878692465
GO:0008219	cell death	0.0163456878692465
GO:0016265	death	0.0163456878692465
GO:0043525	positive regulation of neuron apoptosis	0.0163456878692465
GO:0048710	regulation of astrocyte differentiation	0.0163456878692465
GO:0001938	positive regulation of endothelial cell proliferation	0.0163456878692465
GO:0051224	negative regulation of protein transport	0.0163456878692465
GO:0048713	regulation of oligodendrocyte differentiation	0.0163456878692465
GO:0046823	negative regulation of nucleocytoplasmic transport	0.0163456878692465
GO:0048854	brain morphogenesis	0.0163456878692465
GO:0042308	negative regulation of protein import into nucleus	0.0163456878692465
GO:0042992	negative regulation of transcription factor import into nucleus	0.0163456878692465
GO:0051932	synaptic transmission, GABAergic	0.0163456878692465
GO:0032228	regulation of synaptic transmission, GABAergic	0.0163456878692465
GO:0048745	smooth muscle development	0.0163456878692465
GO:0022408	negative regulation of cell-cell adhesion	0.0163456878692465
GO:0043065	positive regulation of apoptosis	0.0163456878692465
GO:0043068	positive regulation of programmed cell death	0.0163456878692465
GO:0030029	actin filament-based process	0.0163456878692465
GO:0048731	system development	0.0163456878692465
GO:0051649	establishment of cellular localization	0.0163456878692465
GO:0008284	positive regulation of cell proliferation	0.0163456878692465
GO:0051641	cellular localization	0.0163456878692465
GO:0048844	artery morphogenesis	0.0163456878692465
GO:0031575	G1/S transition checkpoint	0.0163456878692465
GO:0033261	regulation of progression through S phase	0.0163456878692465
GO:0045930	negative regulation of progression through mitotic cell cycle	0.0163456878692465
GO:0030132	clathrin coat of coated pit	0.0163456878692465
GO:0007090	regulation of S phase of mitotic cell cycle	0.0163456878692465
GO:0043409	negative regulation of MAPKKK cascade	0.0163456878692465
GO:0005662	DNA replication factor A complex	0.0163456878692465
GO:0000074	regulation of progression through cell cycle	0.0163456878692465
GO:0048646	anatomical structure formation	0.01699335735862
GO:0008134	transcription factor binding	0.01699335735862
GO:0014014	negative regulation of gliogenesis	0.01699335735862
GO:0045686	negative regulation of glial cell differentiation	0.01699335735862
GO:0001936	regulation of endothelial cell proliferation	0.01699335735862
GO:0007406	negative regulation of neuroblast proliferation	0.01699335735862
GO:0035020	regulation of Rac protein signal transduction	0.01699335735862
GO:0045124	regulation of bone resorption	0.01699335735862
GO:0051058	negative regulation of small GTPase mediated signal transduction	0.01699335735862
GO:0048708	astrocyte differentiation	0.0175351338662379
GO:0051320	S phase	0.0175351338662379
GO:0001540	beta-amyloid binding	0.0175351338662379
GO:0046332	SMAD binding	0.0175351338662379
GO:0000084	S phase of mitotic cell cycle	0.0175351338662379
GO:0030130	clathrin coat of trans-Golgi network vesicle	0.0175351338662379
GO:0048483	autonomic nervous system development	0.0175351338662379
GO:0001952	regulation of cell-matrix adhesion	0.0175351338662379
GO:0014037	Schwann cell differentiation	0.0175351338662379
GO:0048523	negative regulation of cellular process	0.0175794545976659
GO:0000278	mitotic cell cycle	0.0175794545976659
GO:0012510	trans-Golgi network transport vesicle membrane	0.0175794545976659
GO:0021987	cerebral cortex development	0.0175794545976659
GO:0042990	regulation of transcription factor import into nucleus	0.0175794545976659
GO:0045671	negative regulation of osteoclast differentiation	0.0175794545976659
GO:0042991	transcription factor import into nucleus	0.0175794545976659
GO:0050821	protein stabilization	0.0175794545976659
GO:0001935	endothelial cell proliferation	0.0175794545976659
GO:0048856	anatomical structure development	0.0175794545976659
GO:0048519	negative regulation of biological process	0.0175794545976659
GO:0042306	regulation of protein import into nucleus	0.0175794545976659
GO:0043601	nuclear replisome	0.0175794545976659
GO:0045685	regulation of glial cell differentiation	0.0175794545976659
GO:0031647	regulation of protein stability	0.0175794545976659
GO:0002762	negative regulation of myeloid leukocyte differentiation	0.0175794545976659
GO:0014013	regulation of gliogenesis	0.0175794545976659
GO:0022407	regulation of cell-cell adhesion	0.0175794545976659
GO:0030894	replisome	0.0175794545976659
GO:0033157	regulation of intracellular protein transport	0.0175794545976659
GO:0030325	adrenal gland development	0.0175794545976659
GO:0032386	regulation of intracellular transport	0.0175794545976659
GO:0043596	nuclear replication fork	0.0189606964011911
GO:0021782	glial cell development	0.0189606964011911
GO:0048709	oligodendrocyte differentiation	0.0189606964011911
GO:0051223	regulation of protein transport	0.0197054482809939
GO:0004675	transmembrane receptor protein serine/threonine kinase activity	0.0197054482809939
GO:0048169	regulation of long-term neuronal synaptic plasticity	0.0197054482809939
GO:0030660	Golgi-associated vesicle membrane	0.0197054482809939
GO:0005024	transforming growth factor beta receptor activity	0.0197054482809939
GO:0030658	transport vesicle membrane	0.0197054482809939
GO:0022403	cell cycle phase	0.0202095827569335
GO:0016477	cell migration	0.0204644015387217
GO:0046822	regulation of nucleocytoplasmic transport	0.0204644015387217
GO:0051048	negative regulation of secretion	0.0204644015387217
GO:0030140	trans-Golgi network transport vesicle	0.0204644015387217
GO:0009888	tissue development	0.0204644015387217
GO:0007275	multicellular organismal development	0.0204644015387217
GO:0030125	clathrin vesicle coat	0.0204644015387217
GO:0007093	mitotic cell cycle checkpoint	0.0204644015387217
GO:0051349	positive regulation of lyase activity	0.0204644015387217
GO:0030308	negative regulation of cell growth	0.0204644015387217
GO:0045762	positive regulation of adenylate cyclase activity	0.0204644015387217
GO:0007162	negative regulation of cell adhesion	0.0204644015387217
GO:0031281	positive regulation of cyclase activity	0.0204644015387217
GO:0021510	spinal cord development	0.0204644015387217
GO:0021543	pallium development	0.0215144537072125
GO:0030336	negative regulation of cell migration	0.0215144537072125
GO:0048168	regulation of neuronal synaptic plasticity	0.0215144537072125
GO:0045453	bone resorption	0.0220076795855186
GO:0045670	regulation of osteoclast differentiation	0.0220076795855186
GO:0016601	Rac protein signal transduction	0.0220076795855186
GO:0030665	clathrin coated vesicle membrane	0.0220076795855186
GO:0030048	actin filament-based movement	0.0220076795855186
GO:0030199	collagen fibril organization	0.0220076795855186
GO:0048699	generation of neurons	0.0224068643188616
GO:0042127	regulation of cell proliferation	0.0225163873294182
GO:0016525	negative regulation of angiogenesis	0.0227857160623316
GO:0045761	regulation of adenylate cyclase activity	0.0227857160623316
GO:0006928	cell motility	0.0228170981353696
GO:0051674	localization of cell	0.0228170981353696
GO:0048468	cell development	0.023096674058741
GO:0043407	negative regulation of MAP kinase activity	0.023096674058741
GO:0009653	anatomical structure morphogenesis	0.023096674058741
GO:0022008	neurogenesis	0.023096674058741
GO:0030133	transport vesicle	0.023096674058741
GO:0031279	regulation of cyclase activity	0.023096674058741
GO:0048593	camera-type eye morphogenesis	0.023096674058741
GO:0051051	negative regulation of transport	0.023096674058741
GO:0043408	regulation of MAPKKK cascade	0.023096674058741
GO:0051339	regulation of lyase activity	0.023096674058741
GO:0051271	negative regulation of cell motility	0.023096674058741
GO:0002761	regulation of myeloid leukocyte differentiation	0.023096674058741
GO:0046928	regulation of neurotransmitter secretion	0.023096674058741
GO:0051726	regulation of cell cycle	0.0237507957228263
GO:0040013	negative regulation of locomotion	0.0237507957228263
GO:0045792	negative regulation of cell size	0.0237507957228263
GO:0045638	negative regulation of myeloid cell differentiation	0.0237507957228263
GO:0030316	osteoclast differentiation	0.0240709248791205
GO:0050768	negative regulation of neurogenesis	0.0240709248791205
GO:0050804	regulation of synaptic transmission	0.0240709248791205
GO:0051969	regulation of transmission of nerve impulse	0.0240709248791205
GO:0007346	regulation of progression through mitotic cell cycle	0.0240709248791205
GO:0003697	single-stranded DNA binding	0.0240709248791205
GO:0001666	response to hypoxia	0.0248108579845035
GO:0001889	liver development	0.0248108579845035
GO:0048167	regulation of synaptic plasticity	0.0248108579845035
GO:0042981	regulation of apoptosis	0.0251050011782061
GO:0043067	regulation of programmed cell death	0.0253729548010551
GO:0007632	visual behavior	0.0253729548010551
GO:0008542	visual learning	0.0253729548010551
GO:0006886	intracellular protein transport	0.0259086891893655
GO:0007422	peripheral nervous system development	0.0259086891893655
GO:0021537	telencephalon development	0.0259086891893655
GO:0050803	regulation of synapse structure and activity	0.0259086891893655
GO:0007270	nerve-nerve synaptic transmission	0.0265699613075102
GO:0005657	replication fork	0.0265699613075102
GO:0030120	vesicle coat	0.0265699613075102
GO:0001707	mesoderm formation	0.0272087109496776
GO:0001894	tissue homeostasis	0.0272087109496776
GO:0045926	negative regulation of growth	0.0272087109496776
GO:0048332	mesoderm morphogenesis	0.0273748186859302
GO:0030662	coated vesicle membrane	0.0273748186859302
GO:0007405	neuroblast proliferation	0.0273748186859302
GO:0031644	regulation of neurological process	0.0273748186859302
GO:0048871	multicellular organismal homeostasis	0.0273748186859302
GO:0000075	cell cycle checkpoint	0.0273748186859302
GO:0042552	myelination	0.0278214804145908
GO:0001649	osteoblast differentiation	0.0278214804145908
GO:0007088	regulation of mitosis	0.0278214804145908
GO:0001704	formation of primary germ layer	0.0278214804145908
GO:0005798	Golgi-associated vesicle	0.0286953384310088
GO:0007272	ensheathment of neurons	0.0292533937047309
GO:0046850	regulation of bone remodeling	0.0292533937047309
GO:0008366	axon ensheathment	0.0292533937047309
GO:0045765	regulation of angiogenesis	0.0301011951816067
GO:0009790	embryonic development	0.0301363014826384
GO:0007010	cytoskeleton organization and biogenesis	0.0301363014826384
GO:0005905	coated pit	0.03062586274139
GO:0008283	cell proliferation	0.0317820467544107
GO:0032318	regulation of Ras GTPase activity	0.0322634666508231
GO:0030118	clathrin coat	0.0329049836176353
GO:0043523	regulation of neuron apoptosis	0.0329049836176353
GO:0032502	developmental process	0.0332440968863381
GO:0045637	regulation of myeloid cell differentiation	0.0335335459870207
GO:0006469	negative regulation of protein kinase activity	0.034149533003231
GO:0033673	negative regulation of kinase activity	0.034149533003231
GO:0001508	regulation of action potential	0.034922014638442
GO:0051402	neuron apoptosis	0.0351769147734034
GO:0051348	negative regulation of transferase activity	0.0351769147734034
GO:0030659	cytoplasmic vesicle membrane	0.0351769147734034
GO:0010001	glial cell differentiation	0.0351769147734034
GO:0002573	myeloid leukocyte differentiation	0.0368407362901451
GO:0005515	protein binding	0.0370502388151655
GO:0042063	gliogenesis	0.0370531235352101
GO:0051325	interphase	0.0370531235352101
GO:0051329	interphase of mitotic cell cycle	0.0370531235352101
GO:0048592	eye morphogenesis	0.0386679777962139
GO:0007050	cell cycle arrest	0.0397176846146631
GO:0050767	regulation of neurogenesis	0.0397176846146631
GO:0030155	regulation of cell adhesion	0.0397176846146631
GO:0001656	metanephros development	0.0397176846146631
GO:0022402	cell cycle process	0.0399943934116325
GO:0008017	microtubule binding	0.0400475292700703
GO:0004702	receptor signaling protein serine/threonine kinase activity	0.0400475292700703
GO:0043086	negative regulation of catalytic activity	0.0407287675598444
GO:0035270	endocrine system development	0.0414036682275784
GO:0044433	cytoplasmic vesicle part	0.0417032600792224
GO:0007498	mesoderm development	0.0417032600792224
GO:0007612	learning	0.0417032600792224
GO:0007269	neurotransmitter secretion	0.0431004978089489
GO:0050794	regulation of cellular process	0.0431004978089489
GO:0030117	membrane coat	0.0431004978089489
GO:0048475	coated membrane	0.0431004978089489
GO:0030334	regulation of cell migration	0.0431004978089489
GO:0051046	regulation of secretion	0.0431004978089489
GO:0048869	cellular developmental process	0.0441314655668843
GO:0030154	cell differentiation	0.0441314655668843
GO:0015631	tubulin binding	0.0445029206157498
GO:0007188	G-protein signaling, coupled to cAMP nucleotide second messenger	0.0445029206157498
GO:0001764	neuron migration	0.0445029206157498
GO:0065008	regulation of biological quality	0.0445029206157498
GO:0012506	vesicle membrane	0.0446674617431578
GO:0006606	protein import into nucleus	0.0446674617431578
GO:0035023	regulation of Rho protein signal transduction	0.0446674617431578
GO:0051170	nuclear import	0.0452713279105757
GO:0015031	protein transport	0.0455026347024982
GO:0007187	G-protein signaling, coupled to cyclic nucleotide second messenger	0.045683542693465
GO:0051270	regulation of cell motility	0.0462754481709401
GO:0043405	regulation of MAP kinase activity	0.0466741229496561
GO:0019933	cAMP-mediated signaling	0.0466741229496561
GO:0007369	gastrulation	0.0480212347133907
GO:0019935	cyclic-nucleotide-mediated signaling	0.0482043106355067
GO:0007160	cell-matrix adhesion	0.0482043106355067
GO:0040012	regulation of locomotion	0.0482043106355067
GO:0045184	establishment of protein localization	0.0482043106355067
GO:0045055	regulated secretory pathway	0.0482043106355067
GO:0043087	regulation of GTPase activity	0.0482043106355067
GO:0017038	protein import	0.0482043106355067
GO:0021915	neural tube development	0.0487597388117101
GO:0044454	nuclear chromosome part	0.0498570487141844
GO:0031589	cell-substrate adhesion	0.0498570487141844
GO:0043170	macromolecule metabolic process	0.0498574753935555

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><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
ectoderm-derived structure	5.56e-13	95
ectoderm	5.56e-13	95
presumptive ectoderm	5.56e-13	95
ecto-epithelium	4.26e-12	73
multi-cellular organism	4.78e-12	333
structure with developmental contribution from neural crest	5.86e-12	92
anatomical conduit	5.91e-12	122
regional part of nervous system	1.43e-11	54
neurectoderm	8.25e-11	64
neural plate	8.25e-11	64
presumptive neural plate	8.25e-11	64
central nervous system	1.28e-10	73
neural tube	1.42e-10	52
neural rod	1.42e-10	52
future spinal cord	1.42e-10	52
neural keel	1.42e-10	52
tube	1.80e-10	114
nervous system	2.33e-10	75
gray matter	5.58e-10	34
brain	1.06e-08	47
future brain	1.06e-08	47
embryo	1.52e-08	320
regional part of brain	2.97e-08	46
brain grey matter	4.43e-08	29
regional part of telencephalon	4.43e-08	29
telencephalon	4.43e-08	29
occipital lobe	4.62e-08	10
visual cortex	4.62e-08	10
neocortex	4.62e-08	10
pre-chordal neural plate	1.21e-07	49
anterior neural tube	1.55e-07	40
regional part of forebrain	4.80e-07	39
forebrain	4.80e-07	39
future forebrain	4.80e-07	39

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	5.04139
MA0004.1	1.02263
MA0006.1	0.670874
MA0007.1	0.38073
MA0009.1	0.82278
MA0014.1	2.09919
MA0017.1	0.26239
MA0019.1	0.642876
MA0024.1	0.779446
MA0025.1	1.05446
MA0027.1	2.46647
MA0028.1	0.24786
MA0029.1	0.757957
MA0030.1	0.764448
MA0031.1	0.729293
MA0038.1	0.534262
MA0040.1	0.835181
MA0041.1	0.323687
MA0042.1	0.311486
MA0043.1	0.918718
MA0046.1	0.858391
MA0048.1	1.47862
MA0050.1	0.431976
MA0051.1	0.542972
MA0052.1	0.84317
MA0055.1	0.221677
MA0056.1	0
MA0057.1	1.93392
MA0058.1	0.305206
MA0059.1	0.316585
MA0060.1	0.9744
MA0061.1	0.56663
MA0063.1	0
MA0066.1	1.29967
MA0067.1	1.16502
MA0068.1	0.077274
MA0069.1	0.843506
MA0070.1	0.833895
MA0071.1	0.431174
MA0072.1	0.825495
MA0073.1	0.00108891
MA0074.1	0.488775
MA0076.1	0.765781
MA0077.1	0.804033
MA0078.1	0.575205
MA0081.1	0.338098
MA0083.1	0.917931
MA0084.1	1.49188
MA0087.1	0.87515
MA0088.1	0.18495
MA0089.1	0
MA0090.1	0.362551
MA0091.1	0.407455
MA0092.1	0.362847
MA0093.1	0.709711
MA0095.1	0
MA0098.1	0
MA0100.1	0.477594
MA0101.1	0.324888
MA0103.1	0.272167
MA0105.1	0.720048
MA0106.1	0.582805
MA0107.1	0.266586
MA0108.2	0.665343
MA0109.1	0
MA0111.1	0.375908
MA0113.1	0.555251
MA0114.1	0.561811
MA0115.1	0.921497
MA0116.1	0.670446
MA0117.1	0.88947
MA0119.1	0.325434
MA0122.1	0.909168
MA0124.1	1.11203
MA0125.1	1.03833
MA0130.1	0
MA0131.1	0.638414
MA0132.1	0
MA0133.1	0
MA0135.1	0.954884
MA0136.1	0.508047
MA0139.1	0.867077
MA0140.1	0.477483
MA0141.1	0.29014
MA0142.1	0.714976
MA0143.1	0.571221
MA0144.1	0.195095
MA0145.1	0.442138
MA0146.1	3.35461
MA0147.1	1.12076
MA0148.1	0.410398
MA0149.1	0.330018
MA0062.2	0.738221
MA0035.2	0.482026
MA0039.2	1.36306
MA0138.2	0.630612
MA0002.2	0.145685
MA0137.2	0.287486
MA0104.2	0.926067
MA0047.2	0.533516
MA0112.2	0.442124
MA0065.2	0.44341
MA0150.1	0.380623
MA0151.1	0
MA0152.1	0.53362
MA0153.1	0.971406
MA0154.1	0.581988
MA0155.1	0.490492
MA0156.1	0.278949
MA0157.1	0.683365
MA0158.1	0
MA0159.1	0.214506
MA0160.1	0.413266
MA0161.1	0
MA0162.1	3.06145
MA0163.1	1.53225
MA0164.1	0.508398
MA0080.2	0.267388
MA0018.2	1.28741
MA0099.2	0.624421
MA0079.2	5.6867
MA0102.2	1.5442
MA0258.1	0.180934
MA0259.1	1.70624
MA0442.1	0