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ARTICLE WATCH
utility of the method, and the stabilization of maltosebinding
protein on binding to maltose is also demonstrated.
MICROARRAYS
Lee MT, Kuo FC,Whitmore GA, Sklar J. Importance of
replication in microarray gene expression studies: statistical
methods and evidence from repetitive cDNA
hybridizations. Proc Natl Acad Sci USA 2000;97:9834–
9839
This study investigates the inherent variability in
gene expression data and assess the extent to which
replication in an experiment produces more consistent
and reliable findings. The results show that any
single microarray output is subject to substantial variability,
even though, by design, variability as a result
of multiple preparations of probe, arrays on different
slides, or arrays generated at different times is not
admitted. A single output yields numerous misclassifications.
Replications are not consistent and therefore
produce different lists of expressed genes. Modeling
the random variation in gene expression indicates
that the probability that mRNA in the sample tissue
184 JOURNAL OF BIOMOLECULAR TECHNIQUES, VOLUME 11, ISSUE 4, DECEMBER 2000
either fails to be represented as probe or fails to
hybridize to the cDNAs on the slide may be as large
as 5% (false-negatives). The probability that ghost
genes are expressed may be as large as 10% (falsepositives).
When microarray data from several replicates
are combined, however, a more accurate picture
of gene expression is produced. It is recommended
that at least three replicates be included in the design
of experiments using cDNA microarrays.
BIOINFORMATICS
Fenyö D. Identifying the proteome: software tools. Curr
Opin Biotechnol 2000;11:391–395.
This article reviews the various software tools that
are available on the internet for searching protein
sequence databases using mass spectral information.
Both peptide mapping data listing the mass values of
proteolytic peptides and fragment ion data derived by
collisional dissociation of peptides to yield sequenceinformative
ions are included. Attention is paid to the
methods used by the various tools to rank protein
candidates and the methods by which the quality of
identifications are assessed.