Global transcriptome analysis of Clostridium thermocellum ATCC 27405 during growth on dilute acid pretreated Populus and switchgrass

Table 3 Summary of genes passing significance and 2-fold differential expression thresholds

Analysis, normalization strategy	Total number of genes FDR <0.05	Total number of genes differentially expressed (± 2-fold)
Microarray	2,351	315
RNA-seq, KDMM	280	192
RNA-seq, UQS	249	104
RNA-seq, RPM	147	117
RNA-seq, RPKM	21	7
RNA-seq, TMM	10	10

FDR <0.05 used for significance criteria. FDR, false discovery rate; KDMM, kernel density mean of M component; RPKM, reads per kilobase per million; RPM, reads per million; TMM, trimmed mean of M component; UQS, upper quartile scaling.

ISSN: 2731-3654