title: PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools.
abstract: PortEco (http://porteco.org) aims to collect, curate and provide data and analysis tools to support basic biological research in Escherichia coli (and eventually other bacterial systems). PortEco is implemented as a 'virtual' model organism database that provides a single unified interface to the user, while integrating information from a variety of sources. The main focus of PortEco is to enable broad use of the growing number of high-throughput experiments available for E. coli, and to leverage community annotation through the EcoliWiki and GONUTS systems. Currently, PortEco includes curated data from hundreds of genome-wide RNA expression studies, from high-throughput phenotyping of single-gene knockouts under hundreds of annotated conditions, from chromatin immunoprecipitation experiments for tens of different DNA-binding factors and from ribosome profiling experiments that yield insights into protein expression. Conditions have been annotated with a consistent vocabulary, and data have been consistently normalized to enable users to find, compare and interpret relevant experiments. PortEco includes tools for data analysis, including clustering, enrichment analysis and exploration via genome browsers. PortEco search and data analysis tools are extensively linked to the curated gene, metabolic pathway and regulation content at its sister site, EcoCyc.
authors.affiliation: Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA, Department of Genetics, Stanford University, Stanford, CA 94305, USA, Department of Biology, Texas A&M University, College Station, TX, 77843, USA, Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA and Deptartment of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA.
authors.forename: James C
authors.initials: JC
authors.lastname: Hu
authors.forename: Gavin
authors.initials: G
authors.lastname: Sherlock
authors.forename: Deborah A
authors.initials: DA
authors.lastname: Siegele
authors.forename: Suzanne A
authors.initials: SA
authors.lastname: Aleksander
authors.forename: Catherine A
authors.initials: CA
authors.lastname: Ball
authors.forename: Janos
authors.initials: J
authors.lastname: Demeter
authors.forename: Sushanth
authors.initials: S
authors.lastname: Gouni
authors.forename: Timothy A
authors.initials: TA
authors.lastname: Holland
authors.forename: Peter D
authors.initials: PD
authors.lastname: Karp
authors.forename: John E
authors.initials: JE
authors.lastname: Lewis
authors.forename: Nathan M
authors.initials: NM
authors.lastname: Liles
authors.forename: Brenley K
authors.initials: BK
authors.lastname: McIntosh
authors.forename: Huaiyu
authors.initials: H
authors.lastname: Mi
authors.forename: Anushya
authors.initials: A
authors.lastname: Muruganujan
authors.forename: Farrell
authors.initials: F
authors.lastname: Wymore
authors.forename: Paul D
authors.initials: PD
authors.lastname: Thomas
authors.forename: Tomer
authors.initials: T
authors.lastname: Altman
mesh_terms: D000483:Alleles; D004268:DNA-Binding Proteins / Q000378:metabolism; D030541:Databases, Genetic; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000378:metabolism; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D020407:Internet; D010641:Phenotype; D012333:RNA, Messenger / Q000378:metabolism; D012270:Ribosomes / Q000378:metabolism; D012984:Software
chemical_list: D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D012333:RNA, Messenger