Predicting Splice Variant from DNA Chip Expression Data

Table 2.

Splice Variant Prediction from 10 Normal Rat Tissues

Bladder Eye Heart Kidney Large intestine Small intestine Liver Pancreas Placenta Testis Total
Gene 113  85  96 123 102  69 143 186 141 168  268
Probe 185 129 190 189 134 101 254 433 214 314 1218

  • Total RNA of 10 different rat tissues (bladder, eye, heart, kidney, large intestine, small intestine, liver, pancreas, placenta, and testis) were extracted, labeled, and hybridized to the Rat1600 chip using standard and identical procedures. Individual feature hybridization data were collected and normalized as described in Methods. Potential splice variants were predicted by SPLICE and NEIGHBORHOOD algorithm. The number of predictions for each tissue type was calculated separately. The selection ratio (R) was set at 10 and other default cutoff values were applied.

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  1. Genome Res. 11: 1237-1245

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