BioCyc: A Genomic and Metabolic Web Portal with Multiple Omics Analytical Tools

Abstract

BioCyc.org is a web portal that contains Pathway/Genome Databases for over 14,500 organisms, including 2400 human microbiome members. The BioCyc databases are unique in integrating a diverse range of data and providing a high level of curation for important microbes as well as model eukaryotic organisms and Homo sapiens. Each Pathway/Genome Database describes the genome and proteome of an organism, as well as its biochemical pathways and (for a small number of organisms) its regulatory network. BioCyc bioinformatics tools combine unparalleled breadth and user friendliness and include a unique set of visualization tools to speed comprehension of its extensive and complex data. BioCyc also includes MetaCyc, the largest collection of metabolic pathways and enzymes currently available, with over 2600 pathways. It contains the equivalent of about 9,400 textbook-pages of mini-review summaries for enzymes and pathways. The data in MetaCyc has been manually curated from over 58,000 published papers. Analysis tools in BioCyc include comparisons of pathways and genomes among multiple organisms, alignment of orthologous genes in a multi-genome browser, and searching for minimal-cost metabolic network routes that connect two substrates. Tools are also provided for visualizing omics data – such as metabolomics and gene expression data – on individual pathway diagrams, on personalized groups of multiple pathway diagrams called pathway collages, and on diagrams depicting the full metabolic network of an organism. A new visualization tool in BioCyc is the Omics Dashboard, an interactive tool for exploration and analysis of gene-expression and metabolomics datasets through a hierarchy of cellular systems and subsystems. This highly visual tool enables the user to survey their data at a very high level of abstraction, and to drill down to examine details at the pathway, subsystem, and gene levels. Patterns in the data can often be perceived quickly and easily. Another new tool is the MultiOmics Explainer, which helps researchers understand and interpret the results of their omics experiments in the context of what is known about an organism's metabolic and regulatory network. At this time this tool is not available online and requires installation of the software on a local computer. Another recent addition to BioCyc involves manual curation of databases for important pathogens. So far, the project includes Mycobacterium tuberculosis (H37Rv), Staphylococcus aureus (NCTC 8325) and Salmonella enterica (14028S) The BioCyc databases can be accessed through the BioCyc.org web site and can be downloaded. In addition, the Pathway Tools software can be downloaded and installed locally to create BioCyc-like databases for more genomes, curate existing databases, or perform additional analyses that are not available online. Access to MetaCyc and EcoCyc is unrestricted. Unlimited access to other databases requires a subscription. Support or Funding Information National Institute of General Medical Sciences of the National Institutes of Health (NIH) [GM080746, GM077678, GM75742] A portion of the initial display of the Omics Dashboard, showing the average gene expression levels of genes, at different time points, in pathways from different subsystems. Another example output of the Omics Dashboard, showing gene-expression profiles at the regulon level. A typical pathway diagram from a BioCyc database. The Multi-Genome Browser enables comparison of orthologous regions from different organisms. Genes in the Genome Browser are color-coded to indicate transcription units. Reaction diagrams provide color-coded atom mapping between reactants and products. This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.