PortEco

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Link/URL:	PortEco
What:	A next-generation resource for knowledge and data about the biology of Escherichia coli laboratory strains, its bacteriophages, plasmids and mobile genetic elements.
Who:	PI: Paul Thomas, USC
Updates:
Upcoming events:
Web Services:
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About PortEco

PortEco is a next generation resource for everything about laboratory strains of Escherichia coli, its phages, plasmids and mobile genetic elements.

For more information about PortEco, please click here.

PortEco Leadership Team

• Paul D. Thomas, University of Southern California, PI
• Jim Hu, Texas A&M University, PI
• Gavin Sherlock, Stanford University, PI
• Peter D. Karp, SRI International
• Deborah Siegele, Texas A&M University

PortEco Steering Committee

• Carol Gross, University of California, San Francisco, chair
• Richard Gourse, University of Wisconsin, co-chair
• Carol Bult, The Jackson Laboratory
• Rex Chisholm, Northwestern University
• Roger Hendrix, University of Pittsburgh
• Terence Hwa, University of California, San Diego
• Arkady Khodursky, University of Minnesota
• Tricia Kiley, University of Wisconsin
• Robert Landick, University of Wisconsin
• Philip Matsumura, University of Illinois-Chicago
• Amy Vollmer, Swarthmore College

Content

PortEco search simultaneously searches many different web resources, displaying summary information and providing links to more detailed information at each of these resources.

Gene product information

• Displays summary information from "gene pages" and/or "protein pages" at several different resources.
• Sources:
  • EcoCyc, a database of E. coli K-12 genes and metabolic pathways
  • EcoGene, a database of E. coli genes
  • UniProt, a database of protein information
  • EcoliWiki, an editable information resource

Gene expression

• Displays information about how a gene is expressed.
• Sources:
  • EcoCyc: operons, genes that are co-transcribed
  • Omics/Stanford Microarray Database: performs four different searches at SMD
  • GenExpDB, E. coli Community's Gene Expression Database

Pathways and Interactions

• Displays information about metabolic pathways and physical and functional interactions between gene products.
• Sources:
  • EcoCyc: metabolic pathways
  • Pathway Commons: protein-protein interactions derived from experiments assaying physical interactions (from the IntAct and MINT databases)
  • STRING: protein-protein "functional" interactions inferred from a number of different types of evidence

Protein 3D structure

• Displays information about the three-dimensional molecular structure of proteins.
• Source:
  • RSCB Protein Data Bank, models based on direct experimental data such as X-ray crystallography
  • Protein Model Portal, computed models based on a homologous experimental structure

Evolution

• Displays information about homologous genes (genes that evolved from a common ancestor) and the evolutionary relationships between them.
• Source:
  • PANTHER, a database of protein phylogenetic trees, orthologs, and functional evolution of genes

Community

• Search results of PortEco community features:
  • Forum, open posting of E. coli related discussions
  • Calendar, E. coli related events

Publications

• Search results of curated E. coli publications stored at EcoliWiki.

Using PortEco

Browsing

• PortEco:Expression holds post-publication microarray gene expression data from E. coli experiments. Our goal is to provide free access to all published E. coli expression data.
• Chemical Genomics Data can be viewed for data from Nichols et al. (2010) Phenotypic Landscape of a Bacterial Cell. Cell 143, 1097–1109.

Searching

PortEco search simultaneously searches many different web resources, displaying summary information and providing links to more detailed information at each of these resources. You can enter a topic, gene, etc. in the search bar at the top of the page of PortEco site to search. For more information, see PortEco Search Help.

Usage examples

Add links to additional pages describing success stories here.

Other sites with related content

• About PortEco
• EcoliWiki
• EcoCyc

References

See Help:References for how to manage references in EcoliWiki.

External Links

PortEco URL:http://porteco.org