Bag of Naïve Bayes: biomarker selection and classification from genome-wide SNP data

BMC Bioinformatics

Table 1 SNPs selected as attributes for at least 5% of the Naïve Bayes Classifiers by BoNB on the WTCCC T1D dataset, with B = 200 Bootstrap samples and classifiers.

SNP	Chr	Gene	Relation	%NBCs	MU (median)
rs6679677	1	RSBN1	downstream	7	0.033
rs9266774	6	MICA	upstream	5.5	0.011
rs805301	6	BAT3	intron	17.5	0.043
rs492899	6	SKIV2L	intron	8.5	0.025
rs9273363	6	HLA-DQB1	downstream	100	0.835
rs9275418	6	HLA-DQB1	upstream	80	0.160
rs6936863	6	HLA-DQA2	upstream	8	0.08
rs9784858	6	TAP2	intron	5	0.008
rs3101942	6	LOC100294145	exon	21.5	0.045

First column: dbSNP RS ID. Second column: SNP chromosome. Third and fourth column: annotated gene and relation with the SNP. Fifth column: percentage of Naïve Bayes Classifiers that included the SNP as attribute. Sixth column: median of the marginal utility of the SNP. SNPs selected as genetic biomarkers by the permutation procedure are marked in bold.

ISSN: 1471-2105