Integrative analyses of proteomics and RNA transcriptomics implicate mitochondrial processes, protein folding pathways and GWAS loci in Parkinson disease

Table 2 Significant genes with evidence from GWAS analysis

Mega-meta GWAS loci^a	Implicated gene	Description	Additional evidence	Potential PD-relevant biological functions^b
No rs# available (chr4:816756) intronic	CPLX1	complexin 1	Proteomics	Synaptic vesicle exocytosis
rs2263418 (chr12:40582993) upstream	SLC2A13	solute carrier family 2 (facilitated glucose transporter), member 13	Proteomics	N/A
rs356182 (chr4:90626111) downstream	SNCA	synuclein, alpha (non A4 component of amyloid precursor)	Proteomics	Presynaptic signaling and membrane trafficking
rs8118008 (chr20:3168166) downstream	SLC4A11	solute carrier family 4, sodium borate transporter, member 11	RNA-Seq	N/A
rs4889620 (chr16:31131174) intronic	KAT8	K(lysine) acetyltransferase 8	RNA-Seq	Histone acetyltransferase activity, transcription factor binding
rs6812193 (chr4:77198986) intronic	FAM47E	family with sequence similarity 47, member E	RNA-Seq	Transcription cofactor activity
rs823118 (chr1:205723572) upstream	NUCKS1	nuclear casein kinase and cyclin-dependent kinase substrate 1	RNA-Seq	N/A
rs1375131 (chr2:135954797) UTR3	ZRANB3	zinc finger, RAN-binding domain containing 3	RNA-Seq	DNA annealing helicase and endonuclease activities
rs11724635 (chr4:15737101) upstream	CD38	CD38 molecule	RNA-Seq	Signal transduction, calcium signaling
rs34195153 (chr1:154913723) downstream	PYGO2	pygopus family PHD finger 2	RNA-Seq	Signal transduction

^aSince some genes have multiple SNPs within 100 kb of their start and end sites showing association to PD status at p-values < 5E-8 [7], only the SNP with the lowest p-value is shown for each implicated gene. SNP coordinates are based on the hg19 (GRCh37.p13) human reference. SNP annotations: downstream/outstream = outside the gene boundaries, within 100 kb from the start or end site of the gene, intronic = located in the gene intron, UTR3 = located in the 3′-UTR of the gene
^bBased on gene information from GeneCards (http://www.genecards.org/), accessed in January 2015

ISSN: 1755-8794