hMiDas and hMitChip: new opportunities in mitochondrial bioinformatics and genomic medicine

We developed a human mitochondria-focused gene database (hMiDas) and customized cDNA microarray chip (hMitChip) to help biomedical research in mitochondrial genomics. The current version of hMiDas contains 1,242 gene entries (including mtDNA genes, nuclear genes related to mitochondria structure and junctions, predicted loci and experimental genes), organized in 15 categories and 24 subcategories. The database interface allows keyword-based searches as well as advanced field and/or case-sensitive searches. Each gene record includes 19 fields, mostly hyperlinked to the corresponding source. Moreover, for each gene, the user is given the option to run literature search using PubMed, and gene/protein homology search using BLAST and FASTA. The hMitChip was constructed using hMiDas as a reference. Currently, it contains a selection of 501 mitochondria-related nuclear genes and 192 control elements, all spotted in duplicate on glass slides. Slide quality was checked by microarray hybridization with 50 μg of Cy3-labeled sample cDNA and Cy5-labeled comparing cDNA, followed by array scan and image analysis. The hMitChip was tested in vitro using RNA extracted from cancer cell lines. Gene expression changes detected by hMitChip were confirmed by quantitative real-time RT-PCR analysis.