Lab-Less Research
18/07/12 12:56 Filed in: GenomeWeb Daily Scan
Submitted by S. Pelech - Kinexus on Wed, 07/18/2012 - 15:38.
The NCBI's GEO database is a wonderful resource for examination of the changes in gene expression within individual studies, but it is difficult to compare the data across different studies, which were often performed with different gene chip platforms. At Kinexus Bioinformatics Corporation, we retrieved from the GEO database the human gene expression data from over 900 different studies with over 6000 biological specimens and systematically normalized the results. This normalization process was based on the identification of 60 genes that were commonly and highly expressed in all of the biological samples. We then created the open-access website TranscriptoNET (www.transcriptonet.ca) to permit users to investigate gene expression patterns and potential interactions that can only be undertaken with such a large dataset of over 125,000,000 gene expression measurements. TranscriptoNET features comprehensive information on the mRNA expression levels of about 23,000 genes in about 600 types of human organs, tissues and cells as measured with gene microarrays.
In the selection of human specimens for inclusion in TranscriptoNET, we paid special attention to human tumours and cancer cell lines to identify the differential regulation of genes in cancer. We believe that this can uncover new potential oncogenes and tumour suppressor genes that may encode cancer protein biomarkers and drug targets. We invite the biomedical research community to freely use TranscriptoNET as a powerful tool for discovery of genes that are uniquely or commonly expressed throughout the human body, and to uncover possible functional interactions amongst the 23,000 proteins encoded by the human genome based on their co-expression patterns. The differential expression of genes determines the structures and biochemical activities in cells that define their physiological functions. TranscriptoNET could also be used to aid researchers in understanding how the body’s diverse organs, tissues and cells may be developmentally related. Ultimately, the TrancriptoNET resource provides for hypotheses generation that can lead to better designed and fruitful experimental follow up.
Link to the original blog post
The NCBI's GEO database is a wonderful resource for examination of the changes in gene expression within individual studies, but it is difficult to compare the data across different studies, which were often performed with different gene chip platforms. At Kinexus Bioinformatics Corporation, we retrieved from the GEO database the human gene expression data from over 900 different studies with over 6000 biological specimens and systematically normalized the results. This normalization process was based on the identification of 60 genes that were commonly and highly expressed in all of the biological samples. We then created the open-access website TranscriptoNET (www.transcriptonet.ca) to permit users to investigate gene expression patterns and potential interactions that can only be undertaken with such a large dataset of over 125,000,000 gene expression measurements. TranscriptoNET features comprehensive information on the mRNA expression levels of about 23,000 genes in about 600 types of human organs, tissues and cells as measured with gene microarrays.
In the selection of human specimens for inclusion in TranscriptoNET, we paid special attention to human tumours and cancer cell lines to identify the differential regulation of genes in cancer. We believe that this can uncover new potential oncogenes and tumour suppressor genes that may encode cancer protein biomarkers and drug targets. We invite the biomedical research community to freely use TranscriptoNET as a powerful tool for discovery of genes that are uniquely or commonly expressed throughout the human body, and to uncover possible functional interactions amongst the 23,000 proteins encoded by the human genome based on their co-expression patterns. The differential expression of genes determines the structures and biochemical activities in cells that define their physiological functions. TranscriptoNET could also be used to aid researchers in understanding how the body’s diverse organs, tissues and cells may be developmentally related. Ultimately, the TrancriptoNET resource provides for hypotheses generation that can lead to better designed and fruitful experimental follow up.
Link to the original blog post