The BioCyc Web Portal for Microbial Genomes and Metabolic Pathways

About this Class

BioCyc.org [1] is an extensive web portal containing 17,000 microbial genomes and associated metabolic pathways. BioCyc databases are created through a process that combines computational inferences with imported and curated data from multiple sources. The first step in the creation of BioCyc databases is to run prediction algorithms for metabolic pathways, operons, PFam domains, and orthologs. We next run programs that import data from related databases (such as UniProt) including regulatory network data, protein features, subcellular locations, and Gene Ontology assignments. Curated databases next receive intensive review and updating by a Ph.D. biologist that includes reviewing the computationally predicted metabolic pathways, entering new gene functions and metabolic pathways from the experimental literature, and defining protein complexes. The resulting databases are high-quality reference sources for the latest gene and pathway information. Overall the BioCyc databases have been curated from 95,000 publications. The BioCyc website provides extensive bioinformatics tools for searching and analyzing these databases, and leveraging them for analysis of omics datasets. Genome-related tools include a genome browser, sequence searching and alignment, and extraction of sequence regions. Pathway-related tools include pathway diagrams, a tool for navigating zoomable organism-specific metabolic map diagrams, and a tool for searching for metabolic routes that transform a starting metabolite into a product metabolite. Regulation tools depict operons and regulatory sites, as well as showing full organism regulatory networks. Comparative analysis tools enable comparisons of genome organization, of orthologs, and of pathway complements. Omics data analysis tools support enrichment analysis and painting of transcriptomics and metabolomics data onto individual pathway diagrams and onto zoomable metabolic map diagrams. A new Omics Dashboard tool enables interactive exploration of omics datasets through a hierarchy of cellular systems. SmartTables enable users to construct tables of genes, metabolites, or pathways, and to perform analysis such as transforming a set of pathways to all genes within the pathway set.