Figure 1

Two-way clustering of normalized RNA-seq and microarray log ₂ transformed read counts or probe fluorescent intensities for all genes, respectively, for C. thermocellum grown on switchgrass or Populus 12 hours and 37 hours postinoculation. RNA-seq read counts normalized by RPM, RPKM, KDMM, UQS, or TMM in the JMP Genomics 6 software suite were plotted with the microarray probe fluorescent intensities normalized by the LOESS method. Genes were clustered into a default of ten clusters based on similarity of expression patterns across all transcriptomic platforms and normalization techniques. KDMM, kernel density mean of M component; RNA-seq, RNA sequencing; RPKM, reads per kilobase per million; RPM, reads per million; TMM, trimmed mean of M component; UQS, upper quartile scaling.