GWGGI: software for genome-wide gene-gene interaction analysis

BMC Genomic Data

Table 2 Comparison of GWGGI with other software on the T1D dataset

	LRMW	TAMW	Plink	BOOST	MDR	RJ
Memory usage	7 Mb	7 Mb	7 Mb	5 Mb	56 Mb	110 Mb
Time	1.5 min	3 min	5.5 hr	14’s	2 min	12 min
Model	7 SNPs	472 SNPs	2 SNPs	2 SNPs	2 SNPs	1674 SNPs^*
P-value	1.12e-268	3.06e-138	1.74e-30	3.31e-62	1.27e-20	1.27e-103
Selected SNPs^**	rs3957146	rs9273363	rs9272723	rs9270986	rs9273363	rs9273363
	rs377763	rs3957146	rs9469220	rs9469220	rs9275418	rs3957146
	rs9270986	rs9270986				rs9275523
	rs9273363	rs3135377				rs9275418
	rs3177928	rs9275523				rs9469220

^*For Random Jungle, we choose the SNPs with permutation importance scores larger than 0.
^**SNPs chosen by the methods. If the number is larger than 5, we list the top 5 SNPs.

ISSN: 2730-6844