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Selected genes comprised those identified from the sequenced genomes of Xanthomonas strains (17 from X. axonopodis pv. vesicatoria strain CFBP5618, 8 from X. campestris pv. campestris strain CFBP5241 and 7 from X. axonopodis pv. citri strain 306) [64] [64].
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The first class of AS genes comprise those that are both alternatively spliced and differentially expressed (AS+DE).
The second class of AS genes comprise those that are alternatively spliced but constitutively expressed (AS+CE) as a function of activation (Table 1).
By so doing, it is also possible to examine the genes comprising those factors with strong links to clinical phenotypes which will lead to biological insights into this association.
b Partial genes comprise those sequences that fail one of the first three criteria (above) but meet the fourth.
The final category of highly expressed genes comprises those involved in immune function, e.g. thymosin β [ 68], α macroglobulin and a mannan-binding lectin associated serine protease, which is a complement control module.
We used the Genevestigator Clustering Analysis tool to look for relationships between a collection of Arabidopsis genes comprising those listed in Table 1 and a further group that includes the results of a search of the TAIR database for senescence-related genes.
The first inclusion benchmark for potential target genes comprised the prediction by more than one of the three used publically available miRNA target gene analysis tools (targetscan, MiRanda, EimMo3).
Thus, twenty-six genes comprised the 'refined' model (Table 2).
Merged clusters of genes comprised the core response.
We then noted whether these recurring genes comprised the highest connected genes of any networks.
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