ProtPlot Data Mining Tool for Virtual Protein Expression Patterns

Introduction

ProtPlot is a Java-based data-mining software tool for virtual 2D gels. It may be downloaded and run as a stand-alone application on your computer. Its exploratory data analysis environment provides tools for the data-mining of quantified virtual 2D gel (pIe, Mw, expression) data of estimated expression from the CGAP EST mRNA tissue expression database. This lets you look at the aggregated data in new ways: for example, which estimated "proteins" are in a specified range of (pI,Mw)? Or which sets of estimated "proteins" are up or down regulated or missing between cancer samples and normal samples? Which sets or "proteins" cluster together across different types of cancers or normals? Here, one may aggregate several different normal and several different cancers as well as specify other filtering criteria.

As is well known, mRNA expression generally does not correlate well with protein expression as seen in 2D-PAGE gels (Ideker et.al., Science 292: 929-934, 2001). However, some new insights may occur by viewing the transcription data in the protein domain. If actual protein expression data is available for some of these tissues, it might be useful to compare mRNA estimated expression and actual protein expression. This tool may helps find those proteins with similar expression and those that have quite different expression. This might be useful in thinking about new hypotheses for protein post-modifications or mRNA post-transcription processing.

ProtPlot generates an interactive virtual protein 2D-gel Map scatterplot based on a database of derived maximum EST expression over a variety of tissue types from data obtained from the NCI-NCBI CGAP EST database of human cancer, precancer and cancer mRNA expression (CGAP is the NCI's Cancer Genome Anatomy Project http://cgap.nci.nih.gov/. EST is the Expressed Sequence Tag of a mRNA found in particular tissues). The EST hit rate is a rough estimate of gene expression. These ESTs were mapped to SWISS-PROT (expasy.ch) accession numbers and Ids, the Mw and pI estimates were computed and used as estimates for corresponding proteins in a pseudo 2D-gel.

ProtPlot data is contained in a set of tissue- and histology-specific .prp (i.e., PRotPlot) files described in the data format documentation. These are kept in the PRP directory that comes with ProtPlot when you install it. You will be able to update these .prp files from the ProtPlot Web server http://www.lecb.ncifcrf.gov/TMAP.

The ProtPlot Web site and program Help menu provide additional information:

NOTE: this software is undergoing Beta-testing so full functionality may not be available.

Contacts: Djamel Medjahed, LMT, SAIC-Frederick.
Peter Lemkin, LECB, NCI-Frederick.

Hosted at tmap.sourceforge.net

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Revised: 08-26-2004