different genes. Alignments are also given in the
case of BLAST searches.
17.4.3 Final Analyses
The LjGEA Web server not only provides a plat-
form for gene expression data retrieval, but also
serves as a tool for further analysis. The server
indicates whether the gene is legume-specific,
whether it falls in a known common pathway, or
whether it has a homolog in other related legumes
(i.e., Medicago and soybean). Two other very
useful tools are co- and differential expression
analysis. The server enables batch retrieval of
genes, whose expression profiles are highly cor-
related with that of a chosen gene. This can be
performed for a subset of experiments or the entire
data set from all experiments. For each co-
expression analysis session, users customize the
co-expression calculation method (currently
Pearson’s correlation coefficient or cosine corre-
lation; Rodgers and Nicewander 1988 ) and set a
correlation threshold and the maximum number of
transcripts to be returned. As described earlier, the
multi-transcript viewer enables visual comparison
of expression profiles. On the other hand, the
differential expression tool allows the user to
retrieve all the genes whose expression is changed
between two user-chosen conditions. The user can
also determine the threshold of change (fold-
change). Altogether, this server can be very
helpful for both forward and reverse genetic
studies.Fig. 17.3 The result page: thefirst page of result
contains the probe set number and the values of transcript
level in each condition. The clickable‘magnifying glass’
symbol opens another window, where the transcript levels
under different conditions are represented graphically194 J. Verdier et al.