Avoiding inconsistencies over time and tracking difficulties in Applied Biosystems AB1700？/Panther？ probe-to-gene annotations

We report here similar inconsistencies in the probe-to-gene annotation of Applied Biosystems AB1700 data, demonstrating that this is not an isolated concern. Moreover, the online information source PANTHER does not provide information required to track such inconsistencies, hence, even correctly annotated datasets, when resubmitted after PANTHER was updated to a new probe-to-gene annotation release, will generate differing results without any feedback on the origin of the change.The importance of unequivocal annotation of microarray experiments can not be underestimated. Inconsistencies greatly diminish the usefulness of the technology. Novel methods in the analysis of transcriptome profiles often rely on large disparate datasets stemming from multiple sources. The predictive and analytic power of such approaches rapidly diminishes if only least-common subsets can be used for analysis. We present here the information that needs to be provided together with the raw AB1700 data, and the information required together with the biologic interpretation of such data to avoid inconsistencies and tracking difficulties.Studying the cellular transcriptome and its dynamics using microarray technology has become a common place application in modern biomedical research [1]. Dedicated databases [i.e. [2-4]] store several hundreds of individual microarray datasets and are growing exponentially. Many different commercial and research originating microarray formats and platforms are being used [2-4]. Since microarray technology currently can not be used to determine absolute expression levels of genes, comparative analysis of transcriptome data across different biological conditions is challenging. Cross-platform comparisons can only be carried out if coherent mapping of genes between the platforms and their particular probe-to-gene and gene-to-genome annotations can be achieved. The public microarray databases are very valuable as here standard formatting and annotation procedures a