Expansion of the BioCyc collection of pathway/genome databases to 160 genomes - PubMed (original) (raw)
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes
Peter D Karp et al. Nucleic Acids Res. 2005.
Abstract
The BioCyc database collection is a set of 160 pathway/genome databases (PGDBs) for most eukaryotic and prokaryotic species whose genomes have been completely sequenced to date. Each PGDB in the BioCyc collection describes the genome and predicted metabolic network of a single organism, inferred from the MetaCyc database, which is a reference source on metabolic pathways from multiple organisms. In addition, each bacterial PGDB includes predicted operons for the corresponding species. The BioCyc collection provides a unique resource for computational systems biology, namely global and comparative analyses of genomes and metabolic networks, and a supplement to the BioCyc resource of curated PGDBs. The Omics viewer available through the BioCyc website allows scientists to visualize combinations of gene expression, proteomics and metabolomics data on the metabolic maps of these organisms. This paper discusses the computational methodology by which the BioCyc collection has been expanded, and presents an aggregate analysis of the collection that includes the range of number of pathways present in these organisms, and the most frequently observed pathways. We seek scientists to adopt and curate individual PGDBs within the BioCyc collection. Only by harnessing the expertise of many scientists we can hope to produce biological databases, which accurately reflect the depth and breadth of knowledge that the biomedical research community is producing.
Figures
Figure 1
Distribution of BioCyc pathways across species. (a) Frequency analysis: the _x_-axis shows the number of detected pathways and the _y_-axis the number of species containing those pathways. (b) Completeness analysis: the _x_-axis shows the percentage of pathway completeness and the _y_-axis the frequency of pathways with the corresponding degree of completeness—more than 60% of pathways are more than 50% complete in the BioCyc collection of PGDBs.
Figure 2
Relationship between number of pathways (_x_-axis) and number of genes (_y_-axis) for all species in the BioCyc collection. Bacterial species are shown in light grey, archaeal species in open-grey squares and eukaryotes in black. The fitted line—a linear regression curve—refers to Bacteria only; most Archaea exhibit a similar relationship. The two outlier bacterial species with fewer than 25 pathways can be seen on the left part of the graph: Mycobacterium avium paratuberculosis and Ralstonia solanacearum GMI1000. The three largest eukaryotic genomes with >10 000 genes show a significant underrepresentation of pathways for their genome size.
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