Chloroplast 2010 Phenotypic Analysis Overview
The Chloroplast 2010 Project is running a variety of phenotypic assays on thousands of mutants in experimentally validated or computationally predicted chloroplast targeted genes. The phenotypic data and sample tracking information are stored in a relational database and can be queried using a set of tools that can be accessed through this website. You can use these software tools by clicking here; these tools allow the user to see whether there are data for mutants of a gene (use AGI query), or search for mutants with a specific allele designation [use Search by Query Term(s)]. Alternatively, it is possible to do an in silico mutant screen [use Search by Assay Results]. User beware: queries return all genes that have a mutant with one or more individuals exhibiting the queried characteristic. These are first-pass-mutant-screening data and you should scrutinize the data carefully to evaluate the consistency of the results.
Simple Boolean logic is supported for phenotypic queries. Note that we only include data for insertion alleles if a homozygous mutant is found; those mutants with no homozygous mutants should not be returned in searches. It is also possible to link to external sites for more information about the gene or allele of interest (currently TAIR at Carnegie Institution and BAR at University of Toronto).
The software is designed to work with Explorer 7.0 and higher and Mozilla Firefox 2.0 and higher. If you use other browsers and discover unexpected behavior, please let Matt Larson (larsonm@msu.edu) know. Beginning users are encouraged to access the help document from each page of the database tools.
These tools are still works in progress and we seek your feedback. Please report software bugs to Matt Larson (larsonm@msu.edu) - note that the more specific you can be about exactly what happened or why you think a tool is not working the more likely it is that we can rapidly fix the problem. Questions about the project or suggestions about new search tools should be directed to Rob Last (lastr@msu.edu). If you have general questions about the software being used in this project please contact Curtis Wilkerson (wilker13@msu.edu).
If you publish results that are enabled by the data from this project, please site Ajjawi et al (2010) Plant Physiology 152:529-540. If you use protocols or approaches from this project, please cite Lu et al (2008) Plant Physiology 146:1482-1500. The database and query tools accessible from this site are described in Lu et al (2011) Chloroplast 2010: A database for large-scale phenotypic screening of Arabidopsis mutants. Plant Physiol. 155: 1589-1900. The work is supported by NSF 2010 grant MCB-0519740 and DBI-0619489 (for Mass Spectrometry equipment used for the amino acid assay). Please let Rob Last (lastr@msu.edu) know if you make an interesting discovery so that we can tell NSF.