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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:
Contacts:
Djamel Medjahed,
LMT, SAIC-Frederick.
Revised: 08-26-2004
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.
Peter Lemkin,
LECB, NCI-Frederick.