Transcript relative abundances for selected functional groups agree with published protein expression data. Shown are mean transcript log2 ratios (stage/reference) from T. cruzi oligonucleotide microarray analyses for A) ribosomal protein genes in metacyclic trypomastigotes, B) genes in the histidine-to-glutamate pathway in epimastigotes, C) mucin genes in trypomastigotes, and D) flagellum-associated genes in amastigotes. The ribosomal genes were selected based on their having the term 'ribosomal' in their annotation and their having either proteome or transcriptome data associated with them. Gene ID's in panels B and D are official gene symbols (prefix Tc00.1047053 is truncated) assigned to annotated genes in the reference CL Brener T. cruzi genome. In panels A and C the y-axis scale is provided as a reference for gene order for the genes in Additional files 9 and 10, respectively, which show the mean microarray ratios for three biological replicates for each life cycle stage and their standard deviations. Error bars in panels A, B, and D are standard deviations for three biological replicates and reflect biological, not technical variation.