Pathway/Genome Web Portal for 20,000 Organisms

BioCyc has 20,000 databases including 70 curated databases. For a listing of databases, click here.

Each BioCyc PGDB describes the genome of an organism, as well as its biochemical pathways and, for a small fraction of organisms, its regulatory network.

Manually Curated Databases

• EcoCyc: The data in this Escherichia coli K-12 MG1655 database have been gathered during two decades of literature-based curation from more than 43,000 articles. EcoCyc describes the metabolic, transport, and regulatory machinery of E. coli. EcoCyc curators have authored the equivalent of 3,600 textbook-pages of mini-review summaries for E. coli genes and pathways.
• MetaCyc: Contains 3,006 metabolic pathways and 17,800 biochemical reactions from all domains of life. MetaCyc data and commentary were gathered from 71,000 publications to provide a comprehensive metabolic encyclopedia whose mini-review summaries encompass the equivalent of 10,079 textbook pages.

Computationally Generated Databases with some Manual Curation

• YeastCyc: This highly curated metabolic network for Saccharomyces cerevisiae was curated from 47,000 publications.
• HumanCyc: This database was derived from a computational pathway analysis of the human genome, followed by literature-based curation of human pathways and enzymes.
• BsubCyc: The curated metabolic and regulatory networks for this Bacillus subtilis database cite 7,000 publications. Included are 180 regulatory genes controlling 1,200 regulated genes.
• Mycobacterium tuberculosis, Corynebacterium glutamicum, Peptoclostridium difficile, Bacillus anthracis, Francisella tularensis, Helicobacter pylori, Vibrio cholerae, and others.

Computationally Generated Databases

Eukaryotic databases in BioCyc include Rattus norvegicus, Mus musculus, Caenorhabditis elegans, Drosophila melanogaster, and Arabidopsis thaliana.

All PGDBs include the genome, predicted metabolic pathways, and predicted pathway hole fillers (genes coding for missing enzymes in metabolic pathways). Bacterial PGDBs include predicted operons. The exact types of data present in different databases will vary. Many databases also include:

• Protein subcellular locations, enzyme kinetics data, protein features, Gene Ontology terms, predicted Pfam domains
• Curated regulatory information including promoters, operons, transcription-factor binding sites
• Reaction atom mappings (map atoms from reactants to products)
• Ortholog relationships to other BioCyc genomes, organism phenotypes
• Database links

For an overview of BioCyc, visit http://bioinformatics.ai.sri.com/ptools/webinars/2020webinars/2020INTROBIOCYC01.mp4

A sample of the most popular BioCyc informatics tools:

• Comprehensive search options (Genes, Proteins, RNAs, Compounds, Reactions, Pathways, Articles and more)
• Omics Data Analysis
• Genome Browser
• Metabolic-map and regulatory-network viewers
• Run Metabolic Model
• Metabolic route search
• BLAST and sequence pattern searches
• Browse Pathway Ontology
• Comparative Analysis
• SmartTables

Curated Genome and Metabolic Pathway Data Derived from 130,000 Publications

BioCyc curators summarize and synthesize information from thousands of publications, saving scientists time in literature research, and integrating data for large-scale computational analyses.

BioCyc data include:

• Genomes
• Gene essentiality data
• Regulatory networks
• Gene Ontology terms
• Orthologs
• Protein features (e.g., enzyme active sites)
• Protein functions
• Metabolic pathways
• Metabolites
• Growth media and growth observations

Extensive Genome Informatics and Comparative Genomics Tools

BioCyc provides a powerful and comprehensive set of features for querying, visualization, and analysis of BioCyc data and user data. Some of our more popular tools are listed here.

Genome Browser (above)

Genome browser depiction of a region of the E. coli chromosome.

Gene colors indicate operon organization. Promoters and terminators are depicted when known. Pseudogenes are marked with X’s.

Comparative Genome Browser

Aligns genome regions around orthologous genes.

Regulatory Network Viewer

The Regulatory Overview depicts the transcriptional regulatory network in a PGDB. Here, the E. coli regulatory network is highlighted to show genes that regulate the gntR gene (blue lines), and the genes that are regulated by gntR (purple lines). The inner two rings are populated by transcription factors and sigma factors; the outer ring contains other genes.

Omics Data Analysis Tools

Cellular Omics Viewer

The BioCyc Cellular Omics Viewer enables the user to paint omics datasets onto organism-specific metabolic network diagrams . Scientists can interpret high-throughput datasets in a pathway context, including animation of time-course or comparative datasets. Reaction lines can be colored with gene expression, proteomics, or reaction flux data; compound nodes can be colored with metabolomics data. Multi-omics data can be analyzed by coloring data onto reactions and metabolites simultaneously. Omics pop-ups graph omics data values using bar graphs, heat maps, or X-Y plots.

Omics Dashboard

The BioCyc Omics Dashboard enables the user to rapidly survey how all cellular systems are responding to a given stimulus. Scientists can quickly view the response of genes within one or more specific systems of interest, and can gauge the relative activity levels of different cellular systems. The Dashboard also enables comparison of expression levels of a cellular system with those of its known regulators. The Dashboard consists of a set of panels, each representing a system of cellular function. Each panel shows a graph depicting omics data for each of a set of subsystems. Multiple timepoints or experimental conditions are plotted as separate data series within the graphs. Clicking on a panel drills down into its component subsystems.

Advanced Database Access

• Extensive query tools available under Tools > Search menu
• Author advanced queries: The Structured Advanced Query Form enables intuitive construction of database queries of SQL power using a Web-based interface
• Extensive web services APIs provided
• SmartTables enable table-based data analyses