John Walker, Ph.D.
Group Leader
Thanks to genomic research, the last few years have witnessed an explosion of information that is one of the unrivaled advances in the history of science - a wealth of new genomic data and genomic technologies in such abundance that there is now a tremendous need to manage the data and make the tools more widely available.
In our Gene Expression Core, we provide numerous services for scientists at GNF and for our outside collaborators, including advice on experimental design, preparation of samples, acquisition of data, and analysis of results. For further analyses, we provide comparisons with reference datasets including the Gene Expression Atlas and our own in-house data, and we train users in various software analysis packages.
Over the past several years, we have designed and analyzed hundreds of microarray experiments and prepared over 7,000 samples. We have been involved in the beta testing of multiple products for Affymetrix and for microarray software companies. We are also active members of the gene expression community with our contributions to Symatlas. We provide full support for the GeneAtlas data on our website, Symatlas.gnf.org. The GeneAtlas data provides baseline expression data for all protein-encoding transcripts across more than 60 murine tissues, and over 100 human tissues. Also available on the website is expression data from over 80 cell lines, including the NCI60 dataset, as well as baseline data from other rodent tissues. We provide the raw data to the public upon request, add additional samples when requested, and field all questions relating to data acquisition and sample characteristics. Our in-house gene expression database provides data from hundreds of microarray experiments, and gives GNF and Novartis scientists the ability to organize, analyze, and visualize the data. Each of the over 7,000 samples in this database have been fully annotated with respect to characteristics such as tissue type, genotype/age/gender of donor, drug treatment conditions, etc. This dataset covers expression projects over a wide range of biology, from cancer to neurodegenerative diseases to metabolic disorders. Careful mining of this dataset is likely to identify more potential drug targets for a variety of human diseases. We also provide raw data from these datasets, analyze the data in other software packages, and use other algorithms upon request.
Selected Publications
