annotationTools

The "annotationTools," an R package compliant with Bioconductor, is designed to facilitate the annotation of microarray experiments and the integration of gene expression profiles from diverse datasets. This tool addresses the challenges of cross-platform and cross-species analyses, which are pivotal for leveraging the vast array of DNA microarray formats and datasets available for comparative studies. Such comparisons are crucial for identifying conserved molecular processes across different species or validating discoveries using public data, often involving studying across various microarray platforms.

One of the annotationTools' core functionalities is its ability to match probes across different microarray formats by utilizing microarray annotations alongside molecular biology databases, such as orthology databases. Despite the modern database models in which these annotations are typically stored, they are frequently distributed as flat file databases—a format that annotation tools adeptly navigate.

By systematically providing a set of specialized functions for mining information from these flat file databases, annotationTools simplifies the process of annotating microarray experiments. Moreover, it enables users to conduct cross-species analyses of gene expression data by integrating information from multiple databases, including orthology databases, for mapping orthologous probes across species.

Through its practical applications, such as cross-platform probe mapping and cross-species analysis leveraging orthology databases, annotationTools demonstrates its utility in facilitating explorative comparisons of transcriptional changes across different technological platforms and species, including comparing disease-related transcriptional changes between human patients and genetic mouse models.