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

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.We anticipate PARE will facilitate comparative studies on mRNA and protein abundance by the proteomics community.Quantifying mRNA expression is currently one of the most exciting and active areas in genomics, and as a result there are copious amounts of data available. However, mRNA does not directly arbitrate biological function; that role is filled by proteins, which are translated from mRNA and connect mRNA to biological processes by acting on the latter as a regulator. In contrast to the abundance of mRNA expression data, considerably fewer quantitative protein expression datasets are available due to the comparatively recent advent of methods for measuring protein abundance on a large scale (such as the use of ICAT and iTRAQ with mass spectrometry) and the difficulty of these experiments relative to chip-based mRNA studies. Also, for many studies, protein abundance data has not been published and is not available via public databases. Because protein levels are linked to mRNA expression by the process of translation, we expect a relationship between these abundances. Moreover, if a high correlation is found, we can use mRNA expression data to directly model protein expression. Conversely, a low correlation indicates that the abundance of a particular protein is somewhat independent of mRNA expression. Similar to the first-order kinetics theory of chemical reactions, the theory governing the relation between mRNA and protein considers the protein synthesis rate to be proportional to the corresponding mRNA concentration and the p