The soybean EST database is a very large one and contains a wide range of expression information (from ca. 80 different libraries).  Several of the soybean EST libraries of particular relevance to the work proposed here include those for hypocotyl response to an incompatible race of P. sojae (Gm-c1084), cotyledon response to the glucan elicitor (Gm-c1076) and leaf response to an incompatible infection with Psg (Gm-c1074).

To complement our cataloging of soybean defense genes and results from preliminary analyses, we undertook a thorough comparative analysis of the defense-related libraries at the TIGR Soybean Gene Index.  Analyses available at TIGR include electronic comparisons of expression in two libraries of choice. The output of such an analysis is analogous to data generated in an experimental expression array. Thus, by comparing expression in the defense-related libraries to suitable control libraries, we were able to essentially do a subtraction electronically and define those genes selectively up-regulated by the treatment. To rule out false positives, we limited our search to those genes that were expressed at least at the 0.1% level and which were up-regulated when compared to the appropriate control library with a confidence of at least 95% or a "Group R Value" of at least 4.0. While hits in these analyses included genes for the phenylpropanoid pathways, due to our extensive characterization of these elsewhere, we have excluded them from this description. Within these various constraints, the analyses led to the definition of over 40 genes that were selectively up-regulated in one or all three of the defense-related libraries (Table 1). Expression is given as a percent of all ESTs in that library. The most significant increases in expression are shown in red, those with an intermediate increase in expression in green and those with no statistical difference from controls in grey. The expression levels marked with an asterisk denote responses that were the highest (ranked either 1 or 2) in this library when compared to all other (ca. 80) EST libraries.

While some of the genes in Table 1 are already on our list of genes of immediate interest, several potentially new candidates were suggested.

Note added December, 2004:  Please note that since this table was developed, the TC designations for many of the genes listed here have changed.  Searching for them at the TIGR database will give you their new designations.

Table 1. Electronic Expression Analysis of Up-regulated Genes in Defense-Related EST Libraries

Abbreviations: PR, pathogenesis-related protein genes; PR-L, other PR-like protein genes; Redox, redox related genes; PCD, genes related to programmed cell death; SIG, signaling genes; STR, signal transduction genes; TF, transcription factors; Wall, cell wall related genes; UNK, unknown function. Control libraries used for comparison were: Gm-c1032 for Gm-c1076 (glucan elicitor), Gm-c1045 for Gm-c1084 (P. sojae infected), Gm-c1037 for Gm-c1074 (Pseudomonas infected).