Kinexus Bioinformatics Corporation, a world-leader in molecular intelligence research, announced the launch of its TranscriptoNET KnowledgeBase (http://126.96.36.199) for the study of human gene expression in over 300 types of human tissues and organs as well as over 300 human cancer cell lines. This open-access resource for the biomedical research community features comprehensive information on the mRNA expression levels for almost ~23,000 human genes. The original data was retrieved from the National Center for Biotechnology Information Gene Expression Omnibus (NCBI GEO), which serves as a repository of experimental gene microarray results submitted by researchers from around the world. Kinexus and its academic collaborators normalized the data from over 900 different studies with more than 6000 biological specimens to permit investigations of gene expression and potential interactions that can only be undertaken with such a large dataset of over 125 million separate gene expression measurements. This normalization process was based on the identification of 60 genes that were commonly and highly expressed in all of the biological samples.
When genes are activated by transcription factors, they are transcribed into intermediate messenger-RNA (mRNA) copies. These mRNAs are subsequently translated with the aid of protein synthesis machinery in ribosomes to make the unique proteins encoded by these genes. Measurement of mRNA levels for specific genes reveals whether the proteins specified by these genes are actively produced in the diverse cell types found in the human body. The differential expression of genes determines the structures and biochemical activities in cells that account for their special physiological functions.
TranscriptoNET is a powerful tool for discovery of genes that are uniquely or commonly expressed throughout the human body, and can be used to uncover possible functional interactions amongst the 23,000 proteins encoded by the human genome based on their co-expression patterns. In the selection of human specimens for inclusion in TranscriptoNET, special emphasis was placed on human tumours and cancer cell lines to identify the differential regulation of genes in cancer. TranscriptoNET can be used to uncover new potential oncogenes and tumour suppressor genes that may encode cancer protein biomarkers and drug targets.
"While all human cells carry the same genes, the production of proteins from these genes is markedly different and dynamically changing in the various cell types found in the tissues and organs of the body" commented Dr. Steven Pelech, President and Chief Scientific Officer of Kinexus and a professor in the Department of Medicine at the University of British Columbia. "While gene microarray data has been available for nearly a decade from the NCBI GEO database, TranscriptoNET now enables researchers to compare the results from thousands of human specimens directly with each other and conduct meta-analyses."
Kinexus Bioinformatics Corporation