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.
Nucleic Acids Res. 2014 Jan;42(Database issue):D677-84. doi: 10.1093/nar/gkt1203. Epub 2013 Nov 26.
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.
PortEco（http://porteco.org）旨在收集、整理和提供数据和分析工具，以支持大肠杆菌（最终也包括其他细菌系统）的基础生物学研究。PortEco 被实现为一个“虚拟”的模式生物数据库，为用户提供了一个单一的统一接口，同时整合了来自各种来源的信息。PortEco 的主要重点是能够广泛利用现有的大量大肠杆菌高通量实验，并通过 EcoliWiki 和 GONUTS 系统利用社区注释。目前，PortEco 包括来自数百项全基因组 RNA 表达研究的精心整理的数据，来自数百个注释条件下的单基因敲除高通量表型研究的数据，来自数十种不同 DNA 结合因子的染色质免疫沉淀实验的数据，以及来自核糖体分析实验的数据，这些数据深入了解了蛋白质表达。条件已经用一致的词汇进行了注释，并且数据已经被一致地标准化，以使用户能够找到、比较和解释相关的实验。PortEco 包括数据分析工具，包括聚类、富集分析和通过基因组浏览器进行探索。PortEco 的搜索和数据分析工具与姐妹站点 EcoCyc 中精心整理的基因、代谢途径和调控内容广泛链接。
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