A novel tissue-specific meta-analysis approach for gene expression predictions, initiated with a mammalian gene expression testis database
- Equal contributors
1 Institute of Bioinformatics and Applied Biotechnology (IBAB), Biotech Park, Electronic City, Bangalore - 560100, Karnataka state, India
2 Shodhaka Life Sciences Pvt. Ltd., IBAB, Biotech Park, Bangalore - 560100, India
BMC Genomics 2010, 11:467 doi:10.1186/1471-2164-11-467Published: 11 August 2010
In the recent years, there has been a rise in gene expression profiling reports. Unfortunately, it has not been possible to make maximum use of available gene expression data. Many databases and programs can be used to derive the possible expression patterns of mammalian genes, based on existing data. However, these available resources have limitations. For example, it is not possible to obtain a list of genes that are expressed in certain conditions. To overcome such limitations, we have taken up a new strategy to predict gene expression patterns using available information, for one tissue at a time.
The first step of this approach involved manual collection of maximum data derived from large-scale (genome-wide) gene expression studies, pertaining to mammalian testis. These data have been compiled into a
Manual compilation of gene expression data, which can be a painstaking process, followed by a consensus expression status determination for specific locations and conditions, can be a reliable way of making use of the existing data to predict gene expression patterns. MGEx-Tdb provides expression information for 14 different combinations of specific locations and conditions in humans (25,158 genes), 79 in mice (22,919 genes) and 23 in rats (14,108 genes). It is also the first system that can predict expression of genes with a 'reliability-score', which is calculated based on the extent of agreements and contradictions across gene-sets/studies. This new platform is publicly available at the following web address: http://resource.ibab.ac.in/MGEx-Tdb/ webcite