LDGIdb: a database of gene interactions inferred from long-range strong linkage disequilibrium between pairs of SNPs
1 Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
2 Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Miaoli County, 350, Taiwan
3 Department of Life Science, National Chiao-Tung University, Hsinchu, 300, Taiwan
4 Department of Dentistry, China Medical University, Taichung, 404, Taiwan
5 Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-yi County, 600, Taiwan
BMC Research Notes 2012, 5:212 doi:10.1186/1756-0500-5-212Published: 2 May 2012
Complex human diseases may be associated with many gene interactions. Gene interactions take several different forms and it is difficult to identify all of the interactions that are potentially associated with human diseases. One approach that may fill this knowledge gap is to infer previously unknown gene interactions via identification of non-physical linkages between different mutations (or single nucleotide polymorphisms, SNPs) to avoid hitchhiking effect or lack of recombination. Strong non-physical SNP linkages are considered to be an indication of biological (gene) interactions. These interactions can be physical protein interactions, regulatory interactions, functional compensation/antagonization or many other forms of interactions. Previous studies have shown that mutations in different genes can be linked to the same disorders. Therefore, non-physical SNP linkages, coupled with knowledge of SNP-disease associations may shed more light on the role of gene interactions in human disorders. A user-friendly web resource that integrates information about non-physical SNP linkages, gene annotations, SNP information, and SNP-disease associations may thus be a good reference for biomedical research.
Here we extracted the SNPs located within the promoter or exonic regions of protein-coding genes from the HapMap database to construct a database named the
The LDGIdb is a user-friendly resource that integrates non-physical SNP linkages and SNP-disease associations for studies of gene interactions in human diseases. With the help of the LDGIdb, it is plausible to infer population-specific SNP linkages for more focused studies, an avenue that is potentially important for pharmacogenetics. Moreover, by referring to disease-association information such as the GWAS data, the LDGIdb may help identify previously uncharacterized disease-associated gene interactions and potentially lead to new discoveries in studies of human diseases.
Gene interaction, SNP, Linkage disequilibrium, Systems biology, Bioinformatics