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.

Figure 1.

Main workflows supported for retrieving and analyzing high-throughput data sets at PortEco. There are three entry points (blue text at top), and at each intermediate step the user can choose between several different paths for further analysis and exploration.

Figure 2.

(A) EcoliWiki pages for publications related to track data include a user-editable table listing relevant track data, with links to genome browsers and data files. These pages can be tagged to place them into EcoliWiki Categories. (B) A tag extension on the appropriate Category page creates a summary table aggregating all available high-throughput tracks from Category members. (C) The table can be sorted and searched for keywords and used to launch GBrowse views with the selected tracks enabled. Custom track lists can be created based on (D) keyword matches or (E) lists of PubMed IDs.