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

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

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
  1. 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.