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

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), 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.