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Frequently Asked Questions1. What is GenoMesh? GenoMesh is a genome-wide analysis of gene-to-gene relationships and pathways based on the association between individual genes and MeSH terms obtained from literature. 2. Who are primary GenoMesh users? Biologists and bioinformaticians who are interested in genetic interactions and biological pathways. 3. What literature information have you used for your GenoMesh calcuation? We downloaded all possible E. coli and Brucella-related publications from PubMed, including their titles, abstracts, and MeSH terms. Specific E. coli and Brucella genes are retrieved from the downloaded items. The matrices between these genes and their associated MeSH terms collected from corresponding papers are then generated. 4. Why the gene-MeSH matrices are important in your GenoMesh system? The gene-MeSH matrices described above are the essential data used for later calculation of gene-to-Mesh and gene-to-gene relationships. These matrices can be considered similar to DNA microarray data (intensity of gene x condition). Each MeSH term is like a condition in a microarray experiment, and the number of the occurrences of each MeSH term in a gene-MeSH matrix is like the intensity of a gene under one condition detected by microarray. 5. How do you ensure your method of calculating the gene-to-gene relationships based on the gene-MeSH matrices has high specificity and sensitivity? We have compared many different formulas of distance or dissimilarity calculation based on the gene-MeSH matrices. Gold standards of gene-to-gene relationships have been used to find out which method is most specific and sensitive. 6. Is GenoMesh novel? Yes. As far as we know, GenoMesh is the first algorithm and web-based system to investigate genome-wide gene-to-gene relationships and pathways. The formula we developed for calculating the dissimilarity between any two genes in this setting is the most specific and sensitive and has not been used in existing publications. 7. Why is your GenoMesh approach significant? GenoMesh is expected to have significant impacts in literature mining and bioinformatics. It is the first approach to study genome-wide gene-to-gene interactions and pathways using a microarray-type of analysis based on published papers. Our studies show that GenoMesh can not only retrieve known gene-to-gene relationships publised in literature, but it can also predict unknown gene-to-gene relationships and pathways. 8. Has GenoMesh been published? Not yet. A manuscript is almost finished and being submitted to a peer-reviewed journal. 9. Are you going to study other organisms using GenoMesh? Yes. Currently we are using E. coli and Brucella spp. as our two user cases. E. coli is a well-studied model organism. Brucella is a less-studied bacterium. Based on the results of these two user cases, we will then further expand the GenoMesh system to other organisms, including other bacteria and even eukaryotic organisms (e.g., human and mouse). 10. How can we get help? Please contact us by emails, phone, or by filling our our online feedback form.
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