Modulation of gene expression in Leishmania cells resistant to methotrexate. DNA microarrays were analyzed as described in Materials and methods and the software GeneSpring version GX3.1 was used to represent fold modulation either on a chromosome by chromosome basis (1 to 36) or as a scatter plot (inserts) for both (a) L. infantum MTX20.5 and (b) L. major MTX60.4. Vertical bars refer to individual genes on each chromosome and their location above or below the strand represents the transcribed strand. Transcription in Leishmania leads to polycistronic RNAs. Red (increased expression) and blue (decreased expression) dashed lines in the scatter plots indicate 1.5-fold differences in gene expression, with the y-axis representing the expression ratios between the mutant and wild-type cells and the x-axis the signal intensity in the mutant. The color scale indicates the modulation of hybridization signals in the resistant mutants compared to wild-type cells. The spots corresponding to genes that are part of the DHFR-TS amplicons are circled in the scatter plots. The entire data set was deposited in GEO under the accession number series GSE9949.