Chinese Hamster Ovary cells are one of the most important cell lines for the production of therapeutically proteins. Due to the high homology of the recombinant glycoproteins to the native human molecules optimal therapeutic efficiency is provided. To improve the overall performance of Chinese hamster cell systems for producing medical proteins, transcriptome analysis is very helpful. Since only limited sequence information about the Chinese hamster cells is available, a species-specific microarray for public access has not yet been developed. Alternatively, existing microarray platforms for closely genetically related, well-annotated organisms, such as mouse, have been proven to yield valuable expression data in cross-species transcriptome analysis. In previous works, the application of mouse microarrays for analysing Chinese hamster cells has already been evaluated. In this project additional hamster sequence data that became available more recently, were used to add more confidence to the data derived from previous studies. Sequences from other mammals were also used to obtain a set of probes conserved amongst several species, to support the approach of developing a generic microarray chip in the future. Furthermore, the usage of sequence alignment programs, a custom global alignment algorithm (iMAT) and automated annotation resulted in a distinct subset of probes derived from iMAT analysis results. These probes were investigated using signal intensity values from heat shock studies on CHO cells. Finally, the differences in the correlation coefficient values, which were calculated from the experimental signal intensities obtained from these heat shock experiments, were used to create a novel reliability scale based on three parameters (iMAT score, % sequence homology and consecutive number of matching base pairs). This scale, along with software, delivered in this project, are invaluable new items to the field of inter-species microarray analysis, and will support the application of microarray chips for their feasibility in inter-species experiments.