BlastProDom, Coil, FPrintScan, HMMPIR, HMMPfam, HMMSmart, HMMTigr, ProfileScan, ScanRegExp, and Seg superfamily were selected as the database methods.
Research costs for the questionnaire-based method were less than one-third of the costs for the databases method.
The abundance within the EST database method, on the other hand, while growing in popularity, has only recently been proposed for estimation of expression levels [ 22].
In Figure 4, we show the ratio of the expression level estimated by the abundance within the EST database method [ 22] to that measured by the microarray method [ 24, 25].
To analyze the abundance within the EST database method for expression analysis, we use the complete original EST data set [ 22].
We suggest that this discrepancy is due to the indirect way in which the abundance within the EST database method estimates expression levels.
But the GOA database method achieves the best accuracy for a protein when the single-genome PON of the same species is used.
The recall rate of the domain-based method (36.6%) is significantly lower than that of the GOA database method (47.5%) since the InterPro database used for the domain-based method is only one of information sources to build the GOA database and the predicted GO terms are often less than the annotations in GOA database.
We cannot exclude, however, that the observed bias of expression rates with length may substantially arise from the microarray, rather than abundance within the EST database, method.
