XHM: A system for detection of potential cross hybridizations in DNA microarrays

BMC Bioinformatics

Table 1 Extent of potential cross-hybridizations in DNA microarray probes.

Clone set	DB	Type A (%)				Type B (%)			CHS(A,B)
		= 0	= 1	≥ 2	≥ 2*	= 0	= 1	≥ 2
Rn 14	RefSeq	63.3	30.7	6.0	16.3	91.3	6.6	1.7	70/200,25
Rn 14	TIGR RGI	5.2	74.6	20.2	21.3	87.7	8.5	3.8	70/200,25
Rn 14	UniGeneUnique	15.9	63.0	21.2	25.2	84.7	11.1	4.2	70/200,25
Rn 14	BeGIn	26.2	62.8	11.1	15.0	82.3	15.4	2.3	70/200,25
Mm 15	RefSeq	34.3	43.2	22.5	34.2	84.5	5.8	9.7	70/200,25
Mm 15	TIGR MGI	47.3	21.5	31.3	59.0	79.5	8.5	12.1	70/200,25
Mm 15	UniGeneUnique	9.9	49.1	40.1	45.0	76.2	11.6	12.3	70/200,25
Mm 15	BeGIn	5.3	57.0	37.8	40.0	78.7	11.5	9.8	70/200,25
Hs 40	RefSeq	13.1	59.5	27.4	31.5	93.3	4.0	2.7	70/200,25
Hs 40	TIGR HGI	1.0	30.8	68.2	68.9	72.5	18.2	9.3	70/200,25
Hs 40	UniGeneUnique	10.9	60.7	28.4	31.8	87.4	7.7	4.9	70/200,25
Mm Oligo	RefSeq	32.5	64.4	3.2	4.7	97.7	1.9	0.3	70/69,20
Mm Oligo	TIGR MGI	59.6	26.2	14.2	35.1	95.8	3.2	1.0	70/69,20
Mm Oligo	UniGeneUnique	9.6	77.7	12.7	14.0	94.8	4.3	0.9	70/69,20
Mm Oligo	BeGIn	15.6	77.1	7.3	8.6	95.7	3.6	0.6	70/69,20

Three cDNA probe sets, human (Hs 40), rat (Rn 14) and mouse (Mm 15), and one mouse oligonucleotide set (Mm Oligo) were checked against cDNA databases (DB). In most cases, a single hit shows that the probe is represented in the DB. Two or more hits indicate potential cross-hybridization. If a hit qualifies as a type A hit, it is not considered to be type B, even if it satisfies the criteria. The percentages represent the number of probes having the given number of hits, relative to the total number of probes in the probe set. The column ≥ 2* shows the number of probes with two or more hits, relative to the total number of the probes that were found in the database. Default BLAST settings were used, except for word-size (9), and mismatch penalty (-1). The column CHS(A,B) shows the Cross-Hybridization Settings used for type A and type B search. Total number of probes: Hs 40: 40000, Rn 14:13447, Mm 15:13797 and Mm Oligo:16463.

ISSN: 1471-2105