New approach for understanding genome variations in KEGG.
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TLDR
This work has introduced a new approach where human gene variants are explicitly incorporated into what it calls ‘network variants’ in the recently released KEGG NETWORK database, which allows accumulation of knowledge about disease-related perturbed molecular networks caused not only by gene variants, but also by viruses and other pathogens, environmental factors and drugs.Abstract:
KEGG (Kyoto Encyclopedia of Genes and Genomes; https://www.kegg.jp/ or https://www.genome.jp/kegg/) is a reference knowledge base for biological interpretation of genome sequences and other high-throughput data. It is an integrated database consisting of three generic categories of systems information, genomic information and chemical information, and an additional human-specific category of health information. KEGG pathway maps, BRITE hierarchies and KEGG modules have been developed as generic molecular networks with KEGG Orthology nodes of functional orthologs so that KEGG pathway mapping and other procedures can be applied to any cellular organism. Unfortunately, however, this generic approach was inadequate for knowledge representation in the health information category, where variations of human genomes, especially disease-related variations, had to be considered. Thus, we have introduced a new approach where human gene variants are explicitly incorporated into what we call 'network variants' in the recently released KEGG NETWORK database. This allows accumulation of knowledge about disease-related perturbed molecular networks caused not only by gene variants, but also by viruses and other pathogens, environmental factors and drugs. We expect that KEGG NETWORK will become another reference knowledge base for the basic understanding of disease mechanisms and practical use in clinical sequencing and drug development.read more
Citations
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g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update).
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KEGG: integrating viruses and cellular organisms.
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Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0)
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TL;DR: The authors provide an update to their 2013 protocol for using the PANTHER classification system, detailing how to analyze genome-wide experimental data with the newest version of PANTHER (v.14.0), with improvements in the areas of data quality, data coverage, statistical algorithms and user experience.
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