Addition of Escherichia coli K – 12 1 2 Growth-Observations and Gene Essentiality Data to 2 3 the EcoCyc Database

14 The set of compounds that can support growth of an organism is defined by the presence 13 15 of transporters and metabolic pathways that convert nutrient sources into cellular com14 16 ponents and energy for growth. A collection of known nutrient sources can therefore serve 15 17 both as an impetus for investigating new metabolic pathways and transporters, and as a 16 18 reference for computational modeling of known metabolic pathways. To establish such a 17 19 collection for Escherichia coli K–12, we have integrated data on the growth or non-growth 18 20 of E. coli K–12 obtained from published observations using a variety of individual me19 21 dia, and from high-throughput Phenotype Microarrays (PMs), into the EcoCyc database. 20 22 The assembled collection revealed a substantial number of discrepancies between the high21 23 throughput datasets, which we investigated where possible using low-throughput growth 22 24 assays on soft agar and in liquid culture. We also integrated six datasets describing 16,119 23 25 observations of the growth of single-gene knock-out mutants of E. coli K–12 into EcoCyc, 24 26 which are relevant to anti-microbial drug design, provide clues regarding the roles of genes 25 27 of unknown function, and are useful for validating metabolic models. To make this infor26 28 mation easily accessible to EcoCyc users, we developed software for capturing, querying, 27 29 and visualizing cellular growth assays and gene-essentiality data. 28