These releases include a complete set of reactions whose presence can be inferred over thousands of complete genomes (bacteria and archaea) integrated with data from the first release, and an initial set of 10 tested constraint-based models.. The source for this data is (i) genome sequence and protein-coding gene annotations submitted to the international nucleotide archives (ii) InterPro annotations of the protein sequences (iii) curated associations of InterPro entries (indicating protein domains) and gene ontology terms (indicating protein functions) (iv) curated associations of Gene Ontology (GO) functions to reactions (as defined in the RhEA database) and (v) curated and predicted genome-protein-reaction associations imported from the Microscope platform.
The genome-reaction associations are periodically updated on a monthly basis. Read here to know more about the methodology, and to access the most up-to-date statistics.
New! Explore the Genome-Reaction Matrix Browser, a prototype visual interface to the reactions and pathways inferred in the genomes.
This first Microme release integrates reactions and pathways for E. coli K-12 into a Reactome knowledge-base, combining data from EcoCyc with reactions derived from the iAF1260 model (Feist AM et al). The two reaction sets have been matched and integrated, corrected for errors and discrepencies and cross-referenced to other resources including ChEBI and RhEA. The above reference data has been projected to 23 target priority species. Homologies between gene products, used to support the inference, are constructed using the Ensembl Gene Tree Algorithm (Vilella et al.). The whole set of pathways and reactions can be accessed using our Reactome-based pathway browser.
- Species: 24
- Small molecules: 1386
- Polypeptides: 17368
- Protein Complexes: 7910
- Reactions: 29660
- Pathways: 5723