Transcript profiling of common bean using the Soybean Genome Array: optimizing analysis by masking biased probes

ABSTRACT: Common bean (Phaseolus vulgaris) and soybean (Glycine max) both belong to the Phaseoleae tribe and share significant coding sequence homology. To evaluate the utility of the soybean GeneChip for transcript profiling of common bean, we hybridized cRNAs purified from nodule, leaf, and root of common bean and soybean in triplicate to the soybean GeneChip. Initial data analysis showed a decreased sensitivity and specificity in common bean cross-species hybridization (CSH) GeneChip data compared to that of soybean. We employed a method that masked putative probes targeting inter-species variable (ISV) regions between common bean and soybean. A masking signal intensity threshold was selected that optimized both sensitivity and specificity. After masking for ISV regions, the number of differentia

ORGANISM(S): Glycine max

SUBMITTER: S Yang 

PROVIDER: E-GEOD-18822 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress