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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

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Published on: December 7, 2021

PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools.

James C Hu¹, Gavin Sherlock, Deborah A Siegele

¹Department 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 Research

|November 29, 2013

Summary

PortEco is a virtual model organism database for Escherichia coli research, integrating diverse high-throughput experimental data and analysis tools. It enhances biological research by providing a unified interface for accessing and interpreting complex datasets.

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Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

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Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Published on: November 12, 2012

Area of Science:

Microbiology
Bioinformatics
Systems Biology

Background:

Escherichia coli is a key model organism for biological research.
High-throughput experiments generate vast amounts of data for E. coli.
Integrating and analyzing this data is challenging for researchers.

Purpose of the Study:

To develop a centralized resource for E. coli data.
To provide tools for analyzing high-throughput experimental data.
To support basic biological research in E. coli and other bacteria.

Main Methods:

Implementation of a virtual model organism database.
Integration of data from multiple sources, including genome-wide expression, phenotyping, ChIP-seq, and ribosome profiling.
Development of consistent data normalization and annotation vocabularies.
Leveraging community annotation systems (EcoliWiki, GONUTS).

Main Results:

PortEco provides a unified interface to curated data from hundreds of studies.
Data includes RNA expression, single-gene knockout phenotypes, DNA-binding factor interactions, and protein expression.
Consistent annotation and normalization enable data comparison and interpretation.
Integrated analysis tools include clustering, enrichment analysis, and genome browsers.

Conclusions:

PortEco serves as a valuable resource for E. coli research.
The platform facilitates the use of high-throughput data for biological discovery.
It supports comparative analysis across different experimental conditions and data types.