ProSim: A Method for Prioritizing Disease Genes Based on Protein Proximity and Disease Similarity

Table 2

Top ten genes predicted for ProSim, PRINCE, RWR, and DADA.

Breast cancer				Colorectal cancer
ProSim	PRINCE	RWR	DADA	ProSim	PRINCE	RWR	DADA
ATM	NBN	PIK3R1	PIK3R1	TP53	BRCA1	TP53	TP53
PPP1R13L	TIE1	HTT	FNTA	JUN	MSH2	AKT1	AURKA
FOSL2	BRCA1	CD44	ATM	PIK3R1	MLH1	AKT	RHOA
ERBB4	MSH2	CALM1	HTT	HTT	EP300	IL3	RET
BRIP1	PATZ1	JUN	SHOC2	NRAS	AKT1	NRAS	NTRK1
HIP1	DGCR2	MAPK3	RASSF2	PSEN1	BUB1B	BRCA2	CCND1
UBE2K	ATM	TPX2	CD44	CTNNB1	OGG1	BUB1B	BUB1B
RALGDS	MRE11A	SVIL	CALM1	CBL	RNF139	LYN	BRCA2
FOXG1	H2AFX	RAF1	JUN	AKT1	APC	AURKA	EP300
PLK1	TERF2	PSEN1	RAF1	VAV1	EXO1	HNF1A	GABRB1
Lung cancer				Diabetes mellitus
ProSim	PRINCE	RWR	DADA	ProSim	PRINCE	RWR	DADA
PPP1R13L	TP53	PPP1R13L	IMPDH2	TP53	RHOA	AKT1	AKT1
ERBB4	VRK1	MAP3K8	APLP2	JUN	MAFA	PLN	INS
PLK1	TP53RK	IGF1R	PLK1	PIK3R1	BSCL2	PSEN1	PSEN1
BRD7	ERBB4	BRD7	ICMT	HTT	SLC2A2	LYN	JUN
UBE2K	CDKN2A	UBE2K	GSTM4	HNF1A	HNF4A	HNF1A	HNF1A
EGFR	TP53INP1	HUWE1	RAD17	PSEN1	INS	PCBD1	TP53
TAPBP	TAG	TAPBP	KLF4	LYN	IAPP	CASP8	ALB
UHMK1	EGFR	UHMK1	CASP8	CBL	NEUROD1	PIK3R1	NEUROD1
MAP3K8	RRM2	DGCR2	PIAS1	AKT1	GATA5	HTT	CEBPA
HIP1	CUL9	HIP1	FOSL2	VAV1	MAP3K13	EP300	RAC3
Prostate cancer				Alzheimer’s disease
ProSim	PRINCE	RWR	DADA	ProSim	PRINCE	RWR	DADA
TP53	NBN	TP53	TP53	TP53	HSD17B10	AKT1	AKT1
JUN	BRIP1	RNASEL	RNASEL	JUN	BACE2	PAX2	SFRP2
HTT	JUN	PAX2	AR	HTT	TP53	CASP8	PAX2
CD44	BRCA1	ERBB2	ABCE1	APBB2	JUN	PSEN1	CASP8
BARD1	HTT	CD19	AKT1	PSEN1	HADHB	APBB3	WT1
CD82	RAD50	BACE2	ERBB2	LYN	NAE1	BLMH	PSEN1
ERBB2	TP53	CASP8	CASP8	VAV1	APLP2	MAPK8	RAC3
REL	MRE11A	TSG101	BUB1B	CCND1	BLMH	WT1	RB1
SLPI	ATM	ATM	CCNE1	CASP8	APBB1	SFRP2	MAPK8
JUNB	BRCA2	CCND1	STAT5A	KIT	F12	RAC3	RHOA