Supplemental Table 1 List of Genes Associated with Parkinson S Disease

Supplemental table 1List of genes associated with Parkinson’s disease

Gene symbol / Gene name / Reference*
A2M / Alpha-2-macroglobulin / 12133586;20861575
ABCB1 / ATP-binding cassette, sub-family B (MDR/TAP), member 1 / 19196542;15767512; 15121788; 12360103
ACE / Angiotensin I converting enzyme / 12084438; 11015454
ACMSD / Aminocarboxymuconate semialdehyde decarboxylase / 23153929; 21292315
ADH1C / Alcohol dehydrogenase 1C (class I), gamma polypeptide / 15642852
ADH7 / Alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide / 11009184; 15642852
ADORA2A / Adenosine A2a receptor / 21281405
AGER / Advanced glycosylation end product-specific receptor / 24304868
AKT1 / V-akt murine thymoma viral oncogene homolog 1 / 18395980
ANG / Angiogenin, ribonuclease, RNase A family, 5 / 22190368
APEX1 / APEX nuclease (multifunctional DNA repair enzyme) 1 / 22224629
APOE / Apolipoprotein E / 24504617; 21782446; 21741729; 21360299; 20037210; 19308307; 17230455; 16904828; 10353349; 19321880; 16462203; 15184605; 12811635; 11992569; 10746597; 10319883; 9328263; 7916421
ARHGAP27 / Rho GTPase activating protein 27 / 21248740
ASCL1 / Achaete-scute family bHLH transcription factor 1 / 20097173; 16021468
ATG5 / Autophagy related 5 / 23384565
ATG7 / Autophagy related 7 / 23295909
ATP13A2 / ATPase type 13A2 / 19015489
ATXN2 / Ataxin 2 / 24534762
ATXN8 / Ataxin 8 / 22577844
BDNF / Brain-derived neurotrophic factor / 21510922; 19538209; 15120095; 14579123; 11782995
BRINP1 / Bone morphogenetic protein/retinoic acid inducible neural-specific 1 / 20070850
BST1 / Bone marrow stromal cell antigen 1 / 23820587; 22786590; 22438815; 21248740; 21084426; 21044948; 19915576; 23853107; 20697102; 21812969; 20711177; 22658533
BTNL2 / Butyrophilin-like 2 / 20711177; 21248740
C6orf10 / Chromosome 6 open reading frame 10 / 21248740
C9orf72 / Chromosome 9 open reading frame 72 / 23845100
CALB1 / Calbindin 1, 28kDa / 18568448
CAST / Calpastatin / 20127884
CCDC62 / Coiled-coil domain containing 62 / 24335092; 23153929; 22438815; 21292315
CCK / Cholecystokinin / 10668930
CD14 / CD14 molecule / 16337421
CDCP2 / CUB domain containing protein 2 / 16252231
CDK5R1 / Cyclin-dependent kinase 5, regulatory subunit 1 (p35) / 21130530
CDNF / Cerebral dopamine neurotrophic factor / 21320571
CHP1 / Calcineurin-like EF-hand protein 1 / 21085126
CHRNA5 / Cholinergic receptor, nicotinic, alpha 5 (neuronal) / 22884254
CHRNB3 / Cholinergic receptor, nicotinic, beta 3 (neuronal) / 24731518
CLU / Clusterin / 21912625
COMT / Catechol-O-methyltransferase / 24389856; 24772965; 22890010; 21781348; 18698234; 9121699; 9503277; 11171904; 15753616; 14673217
CP / Ceruloplasmin (ferroxidase) / 15557511
CRHR1 / Corticotropin releasing hormone receptor 1 / 15459824; 21248740; 21084426; 20711177; 18985386
CRHR1-IT1 / CRHR1 intronic transcript 1 / 19915575; 21248740; 21084426; 20711177; 18985386
CTSD / Cathepsin D / 12811635
CXCL8 / Chemokine (C-X-C motif) ligand 8 / 15120188
CYP1A1 / Cytochrome P450, family 1, subfamily A, polypeptide 1 / 24389856; 8872868
CYP2D6 / Cytochrome P450, family 2, subfamily D, polypeptide 6 / 24376807; 20364044; 10353349; 10208640; 9455978; 18327668; 15061826; 11097352; 8581363; 7697946; 7823053; 7916091; 8291573; 7903297; 8420147; 1350805; 1349052; 25101650
CYP2E1 / Cytochrome P450, family 2, subfamily E, polypeptide 1 / 19381774; 18327668
DBH / Dopamine beta-hydroxylase (dopamine beta-monooxygenase) / 20498626; 14991826
DCC / DCC netrin 1 receptor / 21085126
DDRGK1 / DDRGK domain containing 1 / 25064009
DGKQ / Diacylglycerol kinase, theta 110kDa / 23618683; 22438815; 21248740; 18985386
DLST / Dihydrolipoamide S-succinyltransferase (E2 component of 2-oxo-glutarate complex) / 9450778
DRD2 / Dopamine receptor D2 / 24772965; 11104188; 10634251; 9191771; 16816977; 10534246
DRD3 / Dopamine receptor D3 / 16816977
DRD4 / Dopamine receptor D4 / 16816977; 9727737
EIF2B3 / Eukaryotic translation initiation factor 2B, subunit 3 gamma, 58kDa / 15986317
ELAVL4 / ELAV like neuron-specific RNA binding protein 4 / 18587682; 17230446
EN1 / Engrailed homeobox 1 / 19345444; 17905480
EN2 / Engrailed homeobox 2 / 19270442
EPHB1 / EPH receptor B1 / 21085126
EPHX1 / Epoxide hydrolase 1, microsomal (xenobiotic) / 10720475
ERBB2 / Erb-b2 receptor tyrosine kinase 2 / 23332978
ESR1 / Estrogen receptor 1 / 24595449
ESR2 / Estrogen receptor 2 (ER beta) / 24595449; 15219649; 15635591
FBXO7 / F-box protein 7 / 25029497
FBXO41 / F-box protein 41 / 23777664
FBXO42 / F-box protein 42 / 24063688
FGF20 / Fibroblast growth factor 20 / 23153929; 22342445; 21738488; 18568448; 17515805; 15122513; 18252210; 18205889
FHIT / Fragile histidine triad / 23793441
FRAXE / Fragile site, folic acid type, rare, fra(X)(q28) E / 15342126
GAK / Cyclin G associated kinase / 24080174; 24039160; 23618683; 23153929; 22786590; 22438815; 22198721; 21738487; 21248740; 21044948; 20711177; 18985386; 21258085; 21058943
GALNT3 / Polypeptide N-acetylgalactosaminyltransferase 3 / 16252231
GBA / Glucosidase, beta, acid / 24756352; 24243800; 24126159; 23676350; 23227814; 22812582; 22438815; 22387070; 22192918; 21915911; 21738487; 21338444; 21812969; 22658533; 21837367; 21745757; 20947659; 20816920; 20528910; 20004703; 19858467; 19846850; 19433656; 19383421; 19286695; 18987351; 18332251; 18160183; 18074383; 17875915; 17703984; 17702778; 15525722; 24842889
GCH1 / GTP cyclohydrolase 1 / 25064009; 24993959
GFPT2 / Glutamine-fructose-6-phosphate transaminase 2 / 20070850
GIGYF2 / GRB10 interacting GYF protein 2 / 22115759; 20178831
GLA / Galactosidase, alpha / 21683120
GLIS1 / GLIS family zinc finger 1 / 22759478
GPNMB / Glycoprotein (transmembrane) nmb / 23153929; 21738488
GPRIN3 / GPRIN family member 3 / 18985386
GRIN2A / Glutamate receptor, ionotropic, N-methyl D-aspartate 2A / 24915238; 21876681
GSK3B / Glycogen synthase kinase 3 beta / 24779391; 22815195; 21130530; 20039940; 16315267
GSTM1 / Glutathione S-transferase mu 1 / 17403576; 10720475; 10215103; 17250723; 15061826
GSTO1 / Glutathione S-transferase omega 1 / 22494505; 22016051
GSTP1 / Glutathione S-transferase pi 1 / 17250723; 25101650
GSTT1 / Glutathione S-transferase theta 1 / 10953187; 10215103; 18327668; 9872254
HCG23 / HLA complex group 23 (non-protein coding) / 20711177; 21248740
HFE / Hemochromatosis / 16824219; 12902032; 12098643
HIP1R / Huntingtin interacting protein 1 related / 24080174; 23153929; 22786590; 22438815; 21292315
HIVEP3 / Human immunodeficiency virus type I enhancer binding protein 3 / 17388942; 15986317
HLA-C / Major histocompatibility complex, class I, C / 24183452
HLA-DQA2 / Major histocompatibility complex, class II, DQ alpha 2 / 20711177
HLA-DQB1 / Major histocompatibility complex, class II, DQ beta 1 / 12944708
HLA-DRA / Major histocompatibility complex, class II, DR alpha / 24511991; 24183452; 23083294; 22096524; 21791235; 20711177
HLA-DRB1 / Major histocompatibility complex, class II, DR beta 1 / 24183452; 23139797; 22807207; 20462916
HLA-DRB5 / Major histocompatibility complex, class II, DR beta 5 / 20711177
HMOX1 / Heme oxygenase 1 / 20039940
HMOX2 / Heme oxygenase 2 / 21709601
HNMT / Histamine N-methyltransferase / 21794955; 17985251
HP / Haptoglobin / 17918239
HSD3B7 / Hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 7 / 23238920
HSPA1A / Heat shock 70kDa protein 1A / 14605873
HTR2A / 5-hydroxytryptamine (serotonin) receptor 2A, G protein-coupled / 16876316
HTR6 / 5-hydroxytryptamine (serotonin) receptor 6, G protein-coupled / 11889255
HTRA2 / HtrA serine peptidase 2 / 21701785
IGF2 / Insulin-like growth factor 2 / 18085551
IL10 / Interleukin 10 / 22387064
IL18 / Interleukin 18 / 21241672
IL1A / Interleukin 1, alpha / 18760325; 17458495
IL1B / Interleukin 1, beta / 20427258; 17562931; 17458495; 12070246; 12052541; 12052540; 20880267
IL1RN / Interleukin 1 receptor antagonist / 22384497
IL6 / Interleukin 6 / 22384497; 15635591
INPP5F / Inositol polyphosphate-5-phosphatase F / 25064009
INS / Insulin / 18085551
ITGA8 / Integrin, alpha 8 / 22438815
KANSL1 / KAT8 regulatory NSL complex subunit 1 / 15459824; 20711177; 19915575; 21248740; 21084426
LAMP3 / Lysosomal-associated membrane protein 3 / 24631562; 23496138; 23153929; 22786590; 22438815; 21292315; 21812969; 24842889
LINGO1 / Leucine rich repeat and Ig domain containing 1 / 21752692; 21506150; 20600614; 20369371; 19720553
LINGO2 / Leucine rich repeat and Ig domain containing 2 / 21287203; 20369371
LMX1A / LIM homeobox transcription factor 1, alpha / 19189040
LMX1B / LIM homeobox transcription factor 1, beta / 19189040
LRPAP1 / Low density lipoprotein receptor-related protein associated protein 1 / 24504617
LRRK1 / Leucine-rich repeat kinase 1 / 24241507
LRRK2 / Leucine-rich repeat kinase 2 / 24559644; 24339985; 24046064; 24014121; 23820587; 23624603; 23182315; 23115130; 22981185; 22842796; 22786590; 22575062; 22438815; 22418733; 21738487; 21268244; 11891824; 23651603; 20697102; 18704525; 21812969; 20711177; 19915576; 19915575; 23962496; 22658533; 22575234; 21924942; 21885347; 21159540; 20673920; 20629711; 19854095; 19699188; 19672984; 18781329; 18716801; 18412265; 18213618; 18201824; 18201193; 17938369; 17314670; 17187665; 17050822; 17019612; 16633828; 16436782; 16436781; 16269443; 25243190; 24842889
MAOA / Monoamine oxidase A / 14962671; 9642149; 7913737; 25066260
MAOB / Monoamine oxidase B / 24772965; 21781348; 17044053; 14962671; 11171904; 10953187; 7913737; 18327668; 18205889; 10091612; 8489207; 25066260
MAPT / Microtubule-associated protein tau / 24511991; 24559644; 24779391; 23830801; 23153929; 22786590; 22438815; 21738487; 21248740; 21044948; 19912324; 15459824; 14966169; 21812969; 21084426; 20711177; 20070850; 19915575; 18985386; 23962496; 23238920; 22221882; 22104010; 21425343; 21063069; 21058943; 19879020; 19558713; 19450659; 18509094; 18210157; 18162161; 17683088; 17637803; 17514749; 17192721; 16552760; 16315267; 15732111; 15627775; 15297935; 15201350; 14991810; 14600827; 11958849; 11710889; 10665497; 24842889
MAPT-AS1 / MAPT antisense RNA 1 / 20711177; 21248740; 21084426
MCCC1 / Methylcrotonoyl-CoA carboxylase 1 (alpha) / 24631562; 23496138; 23153929; 22438815; 21738487; 21292315; 24842889
MEGF10 / Multiple EGF-like-domains 10 / 23793441
MIR4697 / MicroRNA 4697 / 25064009
MMP9 / Matrix metallopeptidase 9 / 24040066
MMRN1 / Multimerin 1 / 18985386
MT-ATP6 / Mitochondrially encoded ATP synthase 6 / 17357825
MT-CO1 / Mitochondrially encoded cytochrome c oxidase I / 19076426
MT-CYB / Mitochondrially encoded cytochrome b / 15786469; 12391595
MT-ND1 / Mitochondrially encoded NADH dehydrogenase 1 / 12670626; 16784756
MT-ND3 / Mitochondrially encoded NADH dehydrogenase 3 / 15975594; 15827561; 12618962; 15488317; 17357825; 17174475
MT-ND4 / Mitochondrially encoded NADH dehydrogenase 4 / 23645593
MT-ND5 / Mitochondrially encoded NADH dehydrogenase 5 / 15786469; 12618962; 17357825; 18810306
MT-RNR2 / Mitochondrially encoded 16S RNA / 23645593
MT-TL2 / Mitochondrially encoded tRNA leucine 2 (CUN) / 15786469; 15827561; 19076426
MT-TQ / Mitochondrially encoded tRNA glutamine / 15975594; 15488317; 10953187; 9292870; 17174475
MT-TT / Mitochondrially encoded tRNA threonine / 9113500
MTHFR / Methylenetetrahydrofolate reductase (NAD(P)H) / 24064257; 23916622; 21070756
MTIF3 / Mitochondrial translational initiation factor 3 / 20887776; 17267121
MTR / 5-methyltetrahydrofolate-homocysteine methyltransferase / 21070756
MTRR / 5-methyltetrahydrofolate-homocysteine methyltransferase reductase / 24686188; 21070756
MTX1 / Metaxin 1 / 21837367
NAT2 / N-acetyltransferase 2 (arylamine N-acetyltransferase) / 20364044; 16141799; 12654968; 11936704; 10953187; 10634239; 22878430; 20461808; 10928584; 9855506; 9343502
NCAPD2 / Non-SMC condensin I complex, subunit D2 / 25166511
NDUFV2 / NADH dehydrogenase (ubiquinone) flavoprotein 2, 24kDa / 16784756; 9570948
NEDD9 / Neural precursor cell expressed, developmentally down-regulated 9 / 18063669
NFE2L2 / Nuclear factor, erythroid 2-like 2 / 20196834; 25496089
NOD2 / Nucleotide-binding oligomerization domain containing 2 / 23651603; 17174426
NOS1 / Nitric oxide synthase 1 (neuronal) / 19326438; 18663495; 12490535; 11809160
NOS2 / Nitric oxide synthase 2, inducible / 18663495; 16823855; 14981185; 12490535
NOS3 / Nitric oxide synthase 3 (endothelial cell) / 18663495
NPAS3 / Neuronal PAS domain protein 3 / 20070850
NQO1 / NAD(P)H dehydrogenase, quinone 1 / 22016051
NQO2 / NAD(P)H dehydrogenase, quinone 2 / 11688992; 18314446
NR4A2 / Nuclear receptor subfamily 4, group A, member 2 / 22827504; 12756136; 11914402; 12496759
NSF / N-ethylmaleimide-sensitive factor / 21812969; 20711177; 19915575; 21248740
NUCKS1 / Nuclear casein kinase and cyclin-dependent kinase substrate 1 / 19915576; 23747047; 21268244; 21172849; 20934365; 20697102; 21812969; 19915575
P2RX7 / Purinergic receptor P2X, ligand gated ion channel, 7 / 23648388
PARK10 / Parkinson disease 10 (susceptibility) / 12402251; 25663231
PARK16 / Parkinson disease 16 (susceptibility) / 23820587; 22438815; 24842889
PARK2 / Parkin RBR E3 ubiquitin protein ligase / 23436552; 23275044; 21829596; 20146068; 18704525; 17766365; 12975291; 12584415; 12374768; 11710888; 10511432; 10319889
PARK7 / Parkinson protein 7 / 20146068; 19968671
PARP1 / Poly (ADP-ribose) polymerase 1 / 17362997
PASD1 / PAS domain containing 1 / 16252231
PCGF3 / Polycomb group ring finger 3 / 21248740
PDXK / Pyridoxal (pyridoxine, vitamin B6) kinase / 20035503
PGLYRP2 / Peptidoglycan recognition protein 2 / 24838182
PGLYRP3 / Peptidoglycan recognition protein 3 / 24838182
PGLYRP4 / Peptidoglycan recognition protein 4 / 24838182
PHACTR2 / Phosphatase and actin regulator 2 / 19429005
PHOX2B / Paired-like homeobox 2b / 16021468
PINK1 / PTEN induced putative kinase 1 / 20146068; 18704525; 17084972; 16969854; 16769864
PITX3 / Paired-like homeodomain 3 / 22429667; 22411443; 21524731; 21469209; 21138504; 19394114; 19345444; 18420308; 17905480
PLA2G6 / Phospholipase A2, group VI (cytosolic, calcium-independent) / 23182313; 21812034
PLEKHM1 / Pleckstrin homology domain containing, family M (with RUN domain) member 1 / 19915575; 18985386; 20070850; 21248740
PM20D1 / Peptidase M20 domain containing 1 / 19915576; 23747047; 21840748; 20697102
POLG / Polymerase (DNA directed), gamma / 23251356; 20399836; 17846414; 22963882
POMC / Proopiomelanocortin / 16876316
PON1 / Paraoxonase 1 / 22704918; 15368102; 12210872; 11239953; 9739148
PON2 / Paraoxonase 2 / 22016051; 22704918
PPARGC1A / Peroxisome proliferator-activated receptor gamma, coactivator 1 alpha / 21595954
PRDM2 / PR domain containing 2, with ZNF domain / 21469201; 24335092; 16252231
RAB25 / RAB25, member RAS oncogene family / 22438815
RAB29 / RAB29, member RAS oncogene family / 22232350; 21738488; 19915576; 20683486; 22658533
RAI1 / Retinoic acid induced 1 / 21738487
RFX4 / Regulatory factor X, 4 (influences HLA class II expression) / 21084426
RIT2 / Ras-like without CAAX 2 / 24080174; 22451204; 21738487
RRAS2 / Related RAS viral (r-ras) oncogene homolog 2 / 21085126
SCARB2 / Scavenger receptor class B, member 2 / 23408458; 22223122; 21738487
SEMA5A / Sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A / 18950607; 16252231; 16685660
SERPINA3 / Serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3 / 9219874; 15542006
SHMT1 / Serine hydroxymethyltransferase 1 (soluble) / 24686188
SIPA1L2 / Signal-induced proliferation-associated 1 like 2 / 25064009
SLC11A2 / Solute carrier family 11 (proton-coupled divalent metal ion transporter), member 2 / 21777657
SLC18A2 / Solute carrier family 18 (vesicular monoamine transporter), member 2 / 23369548
SLC25A48 / Solute carrier family 25, member 48 / 21812969
SLC2A13 / Solute carrier family 2 (facilitated glucose transporter), member 13 / 19915576
SLC2A9 / Solute carrier family 2 (facilitated glucose transporter), member 9 / 20589538
SLC41A1 / Solute carrier family 41 (magnesium transporter), member 1 / 19915576; 23747047; 22232350; 21268244; 20697102; 21738487
SLC45A3 / Solute carrier family 45, member 3 / 19915576; 21840748; 21268244; 20697102
SLC6A3 / Solute carrier family 6 (neurotransmitter transporter), member 3 / 16963468; 12210886; 10983695; 10762168; 9380062; 12686408
SLC6A4 / Solute carrier family 6 (neurotransmitter transporter), member 4 / 24684793; 19521089; 20861575
SLCO3A1 / Solute carrier organic anion transporter family, member 3A1 / 21812969
SMPD1 / Sphingomyelin phosphodiesterase 1, acid lysosomal / 23871123; 23535491
SNCA / Synuclein, alpha (non A4 component of amyloid precursor) / 24511991; 24080174; 24005725; 23853107; 23830801; 23820587; 23737253; 23182315; 23153929; 22786590; 22438815; 22425546; 22349157; 22076805; 21953863; 21738487; 21268244; 21248740; 21044948; 19915576; 20697102; 18704525; 18568448; 21812969; 21084426; 20711177; 20070850; 19915575; 18985386; 23962496; 22878430; 22658533; 22104010; 21425343; 21060011; 20513365; 19890971; 18606870; 18485051; 18404644; 18210157; 17872362; 17683088; 17531291; 17292657; 16896109; 16500997; 15786467; 15732111; 15670652; 15455394; 14718715; 12185186; 11532993; 10720300; 10319883; 24842889
SOD2 / Superoxide dismutase 2, mitochondrial / 8806673; 18327668
SPPL2C / Signal peptide peptidase like 2C / 20711177; 19915575; 21084426; 18985386
SPR / Sepiapterin reductase (7,8-dihydrobiopterin:NADP+ oxidoreductase) / 16443856
SREBF1 / Sterol regulatory element binding transcription factor 1 / 21738487
ST8SIA4 / ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4 / 22003392
STBD1 / Starch binding domain 1 / 21738488
STH / Saitohin / 15459824; 14966169; 19912324; 20711177; 18985386
STK39 / Serine threonine kinase 39 / 24080174; 23153929; 22786590; 22438815; 21292315; 21812969
STX1B / Syntaxin 1B / 23153929; 21738488
SYT11 / Synaptotagmin XI / 23153929; 22786590; 22438815; 21292315
TF / Transferrin / 24121126; 12140659
TFAM / Transcription factor A, mitochondrial / 24184878; 19925850
TFR2 / Transferrin receptor 2 / 24121126
TH / Tyrosine hydroxylase / 18085551
TMEM175 / Transmembrane protein 175 / 21248740
TNF / Tumor necrosis factor / 22384497; 18362084; 17562931; 17192953; 11585553; 20880267
TNFRSF1A / Tumor necrosis factor receptor superfamily, member 1A / 11072751
TREM2 / Triggering receptor expressed on myeloid cells 2 / 23800361
UCHL1 / Ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase) / 22839974; 17287139; 16941465; 15882803; 15048890; 14579123; 11782995; 20302855; 22878430; 20861575; 12210873; 11535241; 10923647; 10563640
UNC13B / Unc-13 homolog B (C. elegans) / 21812969
USP24 / Ubiquitin specific peptidase 24 / 20302855; 18854859; 16917932; 15986317
USP25 / Ubiquitin specific peptidase 25 / 21738487
USP37 / Ubiquitin specific peptidase 37 / 22003392
USP40 / Ubiquitin specific peptidase 40 / 16917932; 20302855
VDR / Vitamin D (1,25- dihydroxyvitamin D3) receptor / 24595449; 23880018; 22842395; 21309754; 22213340; 15953876
VPS13C / Vacuolar protein sorting 13 homolog C (S. cerevisiae) / 25064009
WFS1 / Wolfram syndrome 1 (wolframin) / 16876316
WNT3 / Wingless-type MMTV integration site family, member 3 / 21812969; 19915575; 20711177
XRCC1 / X-ray repair complementing defective repair in Chinese hamster cells 1 / 22224629
XRCC3 / X-ray repair complementing defective repair in Chinese hamster cells 3 / 22224629
ZNF385D / Zinc finger protein 385D / 21812969

*References are designated by PMIDs, which are the identifiers of PubMed. PMIDs in each gene term are equal and there’re not priorities in the permutation of the

corresponding PMIDsofspecified genes.

Supplemental table 2Gene Ontology Biological Process terms enriched in PD-related genes

GO Biological Process Termsa / No. ofgenesb / P-valuec / PBH-valued
GO:0042493 / response to drug / 33 / 3.1810-17 / 5.5810-15
GO:0001666 / response to hypoxia / 23 / 1.1610-12 / 3.9610-11
GO:0001975 / response to amphetamine / 10 / 1.3010-12 / 4.1210-11
GO:0045471 / response to ethanol / 15 / 1.8410-11 / 4.1110-10
GO:0042220 / response to cocaine / 8 / 1.3810-9 / 1.9010-8
GO:0014073 / response to tropane / 8 / 1.3810-9 / 1.9010-8
GO:0003001 / generation of a signal involved in cell-cell signaling / 22 / 4.7610-9 / 5.3610-8
GO:0007613 / memory / 11 / 4.9410-9 / 5.5110-8
GO:0035094 / response to nicotine / 8 / 9.3710-9 / 9.1310-8
GO:0032225 / regulation of synaptic transmission, dopaminergic / 6 / 2.2210-8 / 1.8910-7
GO:0055093 / response to hyperoxia / 7 / 2.2910-8 / 1.9110-7
GO:0006805 / xenobiotic metabolic process / 14 / 2.3310-8 / 1.9210-7
GO:0051583 / dopamine uptake involved in synaptic transmission / 5 / 3.1410-8 / 2.3710-7
GO:0042416 / dopamine biosynthetic process / 5 / 3.1410-8 / 2.3710-7
GO:0034312 / diol biosynthetic process / 6 / 3.6610-8 / 2.6610-7
GO:0032689 / negative regulation of interferon-gamma production / 7 / 4.3910-8 / 3.0810-7
GO:0043271 / negative regulation of ion transport / 9 / 7.8210-8 / 5.0310-7
GO:0016045 / detection of bacterium / 6 / 1.3110-7 / 7.9610-7
GO:0042053 / regulation of dopamine metabolic process / 5 / 1.3810-7 / 8.3510-7
GO:0044117 / growth of symbiont in host / 6 / 1.8910-7 / 1.1110-6
GO:0008344 / adult locomotory behavior / 9 / 2.6410-7 / 1.4710-6
GO:0045429 / positive regulation of nitric oxide biosynthetic process / 7 / 2.8210-7 / 1.5510-6
GO:0002437 / inflammatory response to antigenic stimulus / 7 / 3.5410-7 / 1.8710-6
GO:0001659 / temperature homeostasis / 7 / 3.5410-7 / 1.8710-6
GO:0007568 / aging / 15 / 3.8910-7 / 2.0110-6
GO:0051000 / positive regulation of nitric-oxide synthase activity / 5 / 4.2410-7 / 2.1510-6
GO:0009408 / response to heat / 9 / 5.8610-7 / 2.8910-6
GO:0033555 / multicellular organismal response to stress / 8 / 5.9110-7 / 2.8910-6
GO:0050830 / defense response to Gram-positive bacterium / 7 / 6.6610-7 / 3.1910-6
GO:0035176 / social behavior / 7 / 6.6610-7 / 3.1910-6
GO:0010039 / response to iron ion / 6 / 6.7110-7 / 3.1910-6
GO:0010042 / response to manganese ion / 5 / 6.8110-7 / 3.2310-6
GO:0043524 / negative regulation of neuron apoptotic process / 10 / 7.0010-7 / 3.2910-6
GO:0050709 / negative regulation of protein secretion / 7 / 9.8310-7 / 4.5110-6
GO:0042136 / neurotransmitter biosynthetic process / 5 / 1.0510-6 / 4.7410-6
GO:0042033 / chemokine biosynthetic process / 5 / 1.0510-6 / 4.7410-6
GO:0032355 / response to estradiol stimulus / 10 / 1.4010-6 / 6.1410-6
GO:0002028 / regulation of sodium ion transport / 7 / 1.6910-6 / 7.1610-6
GO:0014048 / regulation of glutamate secretion / 5 / 2.2310-6 / 9.2210-6
GO:0032309 / icosanoid secretion / 6 / 2.3610-6 / 9.6010-6
GO:0014059 / regulation of dopamine secretion / 5 / 3.1210-6 / 1.2410-5
GO:0030431 / sleep / 6 / 3.6310-6 / 1.4110-5
GO:0017085 / response to insecticide / 10 / 3.7110-6 / 1.4310-5
GO:0070374 / positive regulation of ERK1 and ERK2 cascade / 9 / 4.2410-6 / 1.5910-5
GO:0001964 / startle response / 5 / 4.2810-6 / 1.6010-5
GO:0019233 / sensory perception of pain / 8 / 4.4310-6 / 1.6510-5
GO:0006953 / acute-phase response / 7 / 5.0810-6 / 1.8510-5
GO:0006879 / cellular iron ion homeostasis / 8 / 5.5710-6 / 2.0110-5
GO:0071222 / cellular response to lipopolysaccharide / 9 / 5.6310-6 / 2.0310-5
GO:0043270 / positive regulation of ion transport / 10 / 6.0210-6 / 2.1610-5
GO:0032755 / positive regulation of interleukin-6 production / 6 / 6.5310-6 / 2.3310-5
GO:0044704 / single-organism reproductive behavior / 8 / 6.9410-6 / 2.4710-5
GO:0050728 / negative regulation of inflammatory response / 8 / 7.7310-6 / 2.7410-5
GO:0002698 / negative regulation of immune effector process / 7 / 1.0010-5 / 3.4510-5
GO:0045840 / positive regulation of mitosis / 6 / 1.1110-5 / 3.7710-5
GO:0051953 / negative regulation of amine transport / 5 / 1.2510-5 / 4.1810-5
GO:0050715 / positive regulation of cytokine secretion / 7 / 1.2910-5 / 4.2910-5
GO:0006509 / membrane protein ectodomain proteolysis / 6 / 1.5310-5 / 5.0110-5
GO:0051588 / regulation of neurotransmitter transport / 6 / 1.7910-5 / 5.8010-5
GO:0043255 / regulation of carbohydrate biosynthetic process / 7 / 2.0610-5 / 6.5010-5
GO:0009895 / negative regulation of catabolic process / 8 / 2.0710-5 / 6.5210-5
GO:0042593 / glucose homeostasis / 9 / 2.3210-5 / 7.1910-5
GO:0051954 / positive regulation of amine transport / 5 / 2.4410-5 / 7.4710-5
GO:0032094 / response to food / 5 / 2.4410-5 / 7.4710-5
GO:0021955 / central nervous system neuron axonogenesis / 5 / 2.4410-5 / 7.4710-5
GO:0014074 / response to purine-containing compound / 9 / 3.3410-5 / 9.8810-5
GO:0007631 / feeding behavior / 8 / 3.4910-5 / 0.0001
GO:0043407 / negative regulation of MAP kinase activity / 7 / 3.5310-5 / 0.0001
GO:0042312 / regulation of vasodilation / 5 / 3.6310-5 / 0.0001
GO:0001836 / release of cytochrome c from mitochondria / 6 / 4.7310-5 / 0.0001
GO:0021549 / cerebellum development / 7 / 4.7610-5 / 0.0001
GO:0042558 / pteridine-containing compound metabolic process / 5 / 5.2110-5 / 0.0001
GO:0048168 / regulation of neuronal synaptic plasticity / 6 / 5.3510-5 / 0.0001
GO:0048660 / regulation of smooth muscle cell proliferation / 7 / 5.7710-5 / 0.0002
GO:0051602 / response to electrical stimulus / 5 / 6.1810-5 / 0.0002
GO:0032680 / regulation of tumor necrosis factor production / 7 / 6.3310-5 / 0.0002
GO:0032642 / regulation of chemokine production / 6 / 6.8110-5 / 0.0002
GO:0002673 / regulation of acute inflammatory response / 6 / 6.8110-5 / 0.0002
GO:0030901 / midbrain development / 5 / 7.2810-5 / 0.0002
GO:0008542 / visual learning / 5 / 8.5310-5 / 0.0002
GO:0002699 / positive regulation of immune effector process / 8 / 8.8210-5 / 0.0002
GO:0040014 / regulation of multicellular organism growth / 7 / 9.0510-5 / 0.0002
GO:0009581 / detection of external stimulus / 8 / 9.4710-5 / 0.0002
GO:0051971 / positive regulation of transmission of nerve impulse / 6 / 9.5610-5 / 0.0002
GO:0045944 / positive regulation of transcription from RNA polymerase II promoter / 23 / 0.0001 / 0.0002
GO:0045732 / positive regulation of protein catabolic process / 7 / 0.0001 / 0.0002
GO:0031331 / positive regulation of cellular catabolic process / 8 / 0.0001 / 0.0002
GO:0009612 / response to mechanical stimulus / 9 / 0.0001 / 0.0002
GO:0001764 / neuron migration / 8 / 0.0001 / 0.0002
GO:1901606 / alpha-amino acid catabolic process / 7 / 0.0002 / 0.0004
GO:1900117 / regulation of execution phase of apoptosis / 10 / 0.0002 / 0.0004
GO:0051384 / response to glucocorticoid stimulus / 9 / 0.0002 / 0.0004
GO:0042542 / response to hydrogen peroxide / 7 / 0.0002 / 0.0004
GO:0042129 / regulation of T cell proliferation / 8 / 0.0002 / 0.0004
GO:0010676 / positive regulation of cellular carbohydrate metabolic process / 5 / 0.0002 / 0.0004
GO:0090316 / positive regulation of intracellular protein transport / 7 / 0.0003 / 0.0006
GO:0043525 / positive regulation of neuron apoptotic process / 5 / 0.0003 / 0.0006
GO:0032611 / interleukin-1 beta production / 5 / 0.0003 / 0.0006
GO:0015909 / long-chain fatty acid transport / 5 / 0.0003 / 0.0006
GO:0014823 / response to activity / 5 / 0.0003 / 0.0006
GO:0010043 / response to zinc ion / 5 / 0.0003 / 0.0006
GO:0001974 / blood vessel remodeling / 5 / 0.0003 / 0.0006
GO:2001233 / regulation of apoptotic signaling pathway / 6 / 0.0004 / 0.0008
GO:0050768 / negative regulation of neurogenesis / 7 / 0.0004 / 0.0008
GO:0046889 / positive regulation of lipid biosynthetic process / 5 / 0.0004 / 0.0008
GO:0033138 / positive regulation of peptidyl-serine phosphorylation / 5 / 0.0004 / 0.0008
GO:0006801 / superoxide metabolic process / 5 / 0.0004 / 0.0008
GO:0006120 / mitochondrial electron transport, NADH to ubiquinone / 5 / 0.0004 / 0.0008
GO:0002455 / humoral immune response mediated by circulating immunoglobulin / 6 / 0.0004 / 0.0008
GO:0002381 / immunoglobulin production involved in immunoglobulin mediated immune response / 5 / 0.0004 / 0.0008
GO:0046683 / response to organophosphorus / 7 / 0.0005 / 0.0010
GO:0034614 / cellular response to reactive oxygen species / 6 / 0.0005 / 0.0010
GO:0033013 / tetrapyrrole metabolic process / 5 / 0.0005 / 0.0010
GO:0031295 / T cell costimulation / 6 / 0.0005 / 0.0010
GO:0050729 / positive regulation of inflammatory response / 6 / 0.0006 / 0.0012
GO:0021987 / cerebral cortex development / 6 / 0.0006 / 0.0012
GO:0007269 / neurotransmitter secretion / 7 / 0.0006 / 0.0012
GO:0071363 / cellular response to growth factor stimulus / 12 / 0.0007 / 0.0014
GO:0060333 / interferon-gamma-mediated signaling pathway / 6 / 0.0007 / 0.0014
GO:0050806 / positive regulation of synaptic transmission / 5 / 0.0007 / 0.0014
GO:0046328 / regulation of JNK cascade / 8 / 0.0007 / 0.0014
GO:0022898 / regulation of transmembrane transporter activity / 6 / 0.0007 / 0.0014
GO:0071407 / cellular response to organic cyclic compound / 5 / 0.0008 / 0.0015
GO:0051092 / positive regulation of NF-kappaB transcription factor activity / 7 / 0.0008 / 0.0015
GO:0050796 / regulation of insulin secretion / 8 / 0.0008 / 0.0015
GO:0051899 / membrane depolarization / 6 / 0.0009 / 0.0017
GO:0031018 / endocrine pancreas development / 5 / 0.0009 / 0.0017
GO:0010906 / regulation of glucose metabolic process / 6 / 0.0009 / 0.0017
GO:0045761 / regulation of adenylate cyclase activity / 5 / 0.001 / 0.0018
GO:0043200 / response to amino acid stimulus / 6 / 0.001 / 0.0018
GO:0006721 / terpenoid metabolic process / 5 / 0.001 / 0.0018
GO:0051896 / regulation of protein kinase B signaling cascade / 6 / 0.0011 / 0.0020
GO:0043123 / positive regulation of I-kappaB kinase/NF-kappaB cascade / 8 / 0.0011 / 0.0020
GO:0031623 / receptor internalization / 5 / 0.0011 / 0.0020
GO:0070664 / negative regulation of leukocyte proliferation / 5 / 0.0012 / 0.0022
GO:0045833 / negative regulation of lipid metabolic process / 5 / 0.0012 / 0.0022
GO:0045766 / positive regulation of angiogenesis / 6 / 0.0012 / 0.0022
GO:0010001 / glial cell differentiation / 8 / 0.0012 / 0.0022
GO:0008284 / positive regulation of cell proliferation / 20 / 0.0012 / 0.0022
GO:0006914 / autophagy / 7 / 0.0012 / 0.0022
GO:0043467 / regulation of generation of precursor metabolites and energy / 5 / 0.0013 / 0.0023
GO:0007565 / female pregnancy / 8 / 0.0013 / 0.0023
GO:0051924 / regulation of calcium ion transport / 7 / 0.0015 / 0.0027
GO:0045926 / negative regulation of growth / 9 / 0.002 / 0.0034
GO:0061351 / neural precursor cell proliferation / 6 / 0.0021 / 0.0036
GO:0019886 / antigen processing and presentation of exogenous peptide antigen via MHC class II / 6 / 0.0021 / 0.0036
GO:0045598 / regulation of fat cell differentiation / 5 / 0.0022 / 0.0037
GO:0044259 / multicellular organismal macromolecule metabolic process / 5 / 0.0022 / 0.0037
GO:0042306 / regulation of protein import into nucleus / 7 / 0.0022 / 0.0037
GO:0042035 / regulation of cytokine biosynthetic process / 6 / 0.0022 / 0.0037
GO:0003073 / regulation of systemic arterial blood pressure / 5 / 0.0022 / 0.0037
GO:0031669 / cellular response to nutrient levels / 8 / 0.0023 / 0.0038
GO:0032368 / regulation of lipid transport / 5 / 0.0024 / 0.0040
GO:0006767 / water-soluble vitamin metabolic process / 5 / 0.0024 / 0.0040
GO:0002700 / regulation of production of molecular mediator of immune response / 5 / 0.0024 / 0.0040
GO:0050821 / protein stabilization / 5 / 0.0027 / 0.0044
GO:0006672 / ceramide metabolic process / 5 / 0.0027 / 0.0044
GO:0048489 / synaptic vesicle transport / 5 / 0.0029 / 0.0047
GO:0015992 / proton transport / 5 / 0.0029 / 0.0047
GO:0070555 / response to interleukin-1 / 5 / 0.0031 / 0.0050
GO:0050868 / negative regulation of T cell activation / 5 / 0.0031 / 0.0050
GO:0006576 / cellular biogenic amine metabolic process / 7 / 0.0032 / 0.0051
GO:0051259 / protein oligomerization / 12 / 0.0035 / 0.0055
GO:0051100 / negative regulation of binding / 5 / 0.0035 / 0.0055
GO:0032846 / positive regulation of homeostatic process / 5 / 0.0035 / 0.0055
GO:2000021 / regulation of ion homeostasis / 7 / 0.0039 / 0.0061
GO:0071356 / cellular response to tumor necrosis factor / 5 / 0.004 / 0.0063
GO:0031396 / regulation of protein ubiquitination / 8 / 0.0041 / 0.0064
GO:0030168 / platelet activation / 9 / 0.0043 / 0.0067
GO:0008361 / regulation of cell size / 5 / 0.0044 / 0.0068
GO:0002706 / regulation of lymphocyte mediated immunity / 5 / 0.0044 / 0.0068
GO:0006417 / regulation of translation / 9 / 0.0045 / 0.0070
GO:0048813 / dendrite morphogenesis / 5 / 0.0047 / 0.0073
GO:0042594 / response to starvation / 6 / 0.0048 / 0.0074
GO:0033189 / response to vitamin A / 6 / 0.0048 / 0.0074
GO:0043254 / regulation of protein complex assembly / 8 / 0.006 / 0.0091
GO:0071248 / cellular response to metal ion / 5 / 0.0065 / 0.0098
GO:0043648 / dicarboxylic acid metabolic process / 5 / 0.0065 / 0.0098
GO:0019217 / regulation of fatty acid metabolic process / 5 / 0.0065 / 0.0098
GO:0017157 / regulation of exocytosis / 5 / 0.0065 / 0.0098
GO:0002822 / regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains / 5 / 0.0065 / 0.0098
GO:0050673 / epithelial cell proliferation / 9 / 0.0066 / 0.0099
GO:0060402 / calcium ion transport into cytosol / 5 / 0.0068 / 0.0102
GO:0002685 / regulation of leukocyte migration / 5 / 0.0068 / 0.0102
GO:0050731 / positive regulation of peptidyl-tyrosine phosphorylation / 6 / 0.0071 / 0.0106
GO:0006813 / potassium ion transport / 6 / 0.0071 / 0.0106
GO:0007623 / circadian rhythm / 5 / 0.0072 / 0.0107
GO:0051129 / negative regulation of cellular component organization / 11 / 0.0075 / 0.0111
GO:0008202 / steroid metabolic process / 10 / 0.0075 / 0.0111
GO:0006575 / cellular modified amino acid metabolic process / 8 / 0.0076 / 0.0113
GO:0043473 / pigmentation / 5 / 0.0079 / 0.0116
GO:0002285 / lymphocyte activation involved in immune response / 5 / 0.0083 / 0.0122
GO:0009791 / post-embryonic development / 5 / 0.0087 / 0.0127
GO:0042445 / hormone metabolic process / 7 / 0.0089 / 0.0129
GO:0051235 / maintenance of location / 8 / 0.0091 / 0.0131
GO:0006909 / phagocytosis / 5 / 0.0091 / 0.0131
GO:0010951 / negative regulation of endopeptidase activity / 6 / 0.0097 / 0.0139
GO:0000187 / activation of MAPK activity / 6 / 0.0097 / 0.0139
GO:0000041 / transition metal ion transport / 5 / 0.01 / 0.0143
GO:0032886 / regulation of microtubule-based process / 5 / 0.0104 / 0.0148
GO:0030307 / positive regulation of cell growth / 5 / 0.0104 / 0.0148
GO:0016042 / lipid catabolic process / 9 / 0.0107 / 0.0152
GO:0034765 / regulation of ion transmembrane transport / 5 / 0.0109 / 0.0154
GO:0022602 / ovulation cycle process / 5 / 0.0119 / 0.0167
GO:0048872 / homeostasis of number of cells / 7 / 0.0121 / 0.0169
GO:0006732 / coenzyme metabolic process / 8 / 0.0125 / 0.0173
GO:0050852 / T cell receptor signaling pathway / 5 / 0.0129 / 0.0178
GO:0032526 / response to retinoic acid / 5 / 0.0129 / 0.0178
GO:0050808 / synapse organization / 6 / 0.0133 / 0.0183
GO:0050920 / regulation of chemotaxis / 5 / 0.014 / 0.0192
GO:0001649 / osteoblast differentiation / 6 / 0.0146 / 0.0200
GO:0042638 / exogen / 7 / 0.0148 / 0.0202
GO:0007411 / axon guidance / 11 / 0.0148 / 0.0202
GO:0050770 / regulation of axonogenesis / 5 / 0.0164 / 0.0222
GO:0045619 / regulation of lymphocyte differentiation / 5 / 0.0164 / 0.0222
GO:0030335 / positive regulation of cell migration / 8 / 0.0165 / 0.0223
GO:0019932 / second-messenger-mediated signaling / 6 / 0.0172 / 0.0231
GO:0008277 / regulation of G-protein coupled receptor protein signaling pathway / 5 / 0.0176 / 0.0236
GO:0015758 / glucose transport / 5 / 0.0197 / 0.0261
GO:0048565 / digestive tract development / 5 / 0.0211 / 0.0278
GO:0043280 / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / 5 / 0.0211 / 0.0278
GO:0022612 / gland morphogenesis / 5 / 0.0211 / 0.0278
GO:0019439 / aromatic compound catabolic process / 19 / 0.0211 / 0.0278
GO:0006638 / neutral lipid metabolic process / 5 / 0.0211 / 0.0278
GO:0006790 / sulfur compound metabolic process / 8 / 0.0213 / 0.0280
GO:0035303 / regulation of dephosphorylation / 5 / 0.0219 / 0.0287
GO:0009749 / response to glucose stimulus / 5 / 0.0219 / 0.0287
GO:0044743 / intracellular protein transmembrane import / 8 / 0.0222 / 0.0290
GO:0001763 / morphogenesis of a branching structure / 7 / 0.0232 / 0.0301
GO:0007188 / adenylate cyclase-modulating G-protein coupled receptor signaling pathway / 5 / 0.0234 / 0.0302
GO:0006511 / ubiquitin-dependent protein catabolic process / 11 / 0.0234 / 0.0302
GO:0030522 / intracellular receptor mediated signaling pathway / 8 / 0.0248 / 0.0320
GO:0043433 / negative regulation of sequence-specific DNA binding transcription factor activity / 5 / 0.025 / 0.0322
GO:0030324 / lung development / 6 / 0.0251 / 0.0323
GO:2000241 / regulation of reproductive process / 7 / 0.0255 / 0.0327
GO:0048839 / inner ear development / 6 / 0.0258 / 0.0330
GO:0030595 / leukocyte chemotaxis / 5 / 0.0259 / 0.0331
GO:0002274 / myeloid leukocyte activation / 5 / 0.0267 / 0.0340
GO:0051146 / striated muscle cell differentiation / 7 / 0.028 / 0.0353
GO:0014706 / striated muscle tissue development / 9 / 0.0289 / 0.0364
GO:0008286 / insulin receptor signaling pathway / 6 / 0.0327 / 0.0407
GO:0048592 / eye morphogenesis / 5 / 0.0352 / 0.0437
GO:0030100 / regulation of endocytosis / 5 / 0.0352 / 0.0437
GO:0030879 / mammary gland development / 5 / 0.0383 / 0.0474

a Only the leaf GO Biological Process terms containing 5 or more PD-related genes are shown.

b Number of genes in the 242PD-related genes and also in the category

c P-values were calculated by hypergeometric test

d PBH-values were adjusted by Benjamini & Hochberg (BH) method