AbMiner: A bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for
genomic,
proteomic, and immunologic studies
Sylvia M Major, Satoshi Nishizuka, Daisaku Morita, Rick Rowland, Margot Sunshine, Uma Shankavaram, Frank
Washburn, Daniel Asin, Hosein Kouros-Mehr, David Kane and John N Weinstein, BMC Bioinformatics 2006, 7:192
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Abstract
Background
Monoclonal antibodies are used extensively throughout the biomedical sciences for detection of antigens, either
in vitro or in vivo. We, for example, have used them for quantitation of proteins on "reverse-phase" protein
lysate
arrays. For those studies, we quality-controlled > 600 available monoclonal antibodies and also needed to develop
precise information on the genes that encode their antigens. Translation among the various protein and gene
identifier
types proved non-trivial because of one-to-many and many-to-one relationships. To organize the antibody,
protein,
and gene information, we initially developed a relational database in Filemaker for our own use. When it became
apparent that the information would be useful to many other researchers faced with the need to choose or
characterize
antibodies, we developed it further as AbMiner, a fully relational web-based database under MySQL, programmed
in Java.
Description
AbMiner is a user-friendly, web-based bioinformatics program package and relational
database
of information on > 600 commercially available antibodies that we validated by Western blot for protein
microarray
studies. It includes many types of information on the antibody, the immunogen, the vendor, the antigen, and the
antigen's gene. Multiple gene and protein identifier types provide links to corresponding entries in a variety
of
other public databases, including resources for phosphorylation-specific antibodies. AbMiner also includes our
quality-control data against a pool of 60 diverse cancer cell types (the NCI-60) and also protein expression
levels
for the NCI-60 cells measured using our high-density "reverse-phase" protein lysate microarrays for a selection
of the listed antibodies. Some other available database resources give information on antibody specificity for
one
or a couple of cell types. In contrast, the data in AbMiner indicate specificity with respect to the antigens in
a
pool of 60 diverse cell types from nine different tissues of origin.
Conclusions
AbMiner is a relational database that provides extensive information from our own laboratory and other sources
on more than 600 available antibodies and the genes that encode the antibodies' antigens.
