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Open Access Software

PARE: A tool for comparing protein abundance and mRNA expression data

Eric Z Yu1, Anne E Counterman Burba1 and Mark Gerstein123*

Author Affiliations

1 Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA

2 Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA

3 Department of Computer Science, Yale University, New Haven, CT 06520, USA

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BMC Bioinformatics 2007, 8:309  doi:10.1186/1471-2105-8-309

Published: 24 August 2007

Abstract

Background

Techniques for measuring protein abundance are rapidly advancing and we are now in a situation where we anticipate many protein abundance data sets will be available in the near future. Since proteins are translated from mRNAs, their expression is expected to be related to their abundance, to some degree.

Results

We have developed a web tool, called PARE (Protein Abundance and mRNA Expression; http://proteomics.gersteinlab.org webcite), to correlate these two quantities. In addition to globally comparing the quantities of protein and mRNA, PARE allows users to select subsets of proteins for focused study (based on functional categories and complexes). Furthermore, it highlights correlation outliers, which are potentially worth further examination.

Conclusion

We anticipate PARE will facilitate comparative studies on mRNA and protein abundance by the proteomics community.