These results support the argument that it is more reliable to interpret microarray data at transcript level than at gene level. The inferiority of the Affy-protein level annotation to our annotation could be attributed to the technical details in their alignment and association procedures [26] . First, they used the representative mRNA sequence ('consensus' or 'exemplar' sequence of each probeset), instead of the probe sequences themselves, as the query sequence in the alignment. Second, they aligned against the GenBank non-redundant protein database, rather than a comprehensive pool of mRNA sequences. In microarray experiment hybridization takes place between the probe sequences immobilized on the array and the cDNA sequences from the sample, so one can deduce that the alignment between the representative mRNA sequences and the protein sequences cannot precisely simulate the hybridization between probes and mRNAs. Finally, NetAffx filtered the blast results according to a cut- off of E-value, which indicates the likelihood of the observed alignment by chance [27] . Although frequently adopted for sequence homology analysis in closely related species, E-value is not sensitive enough to grade the many well aligned targets from the same species. In our practice, we took the probe sequences as the query and the mRNA sequences as the alignment targets, and adopted the matching nucleotide proportion as the filtering criterion (see Methods).