Adomas et al. BMC Genomics 2010, 11:477 http://www.biomedcentral.com/1471-2164/11/477 Page 5 of 16 Table 2 Comparison of oligo(dT) and MTP priming in terms of number of genes significantly differentially expressed in specific biological processes and metabolic pathways with the highest number of genes significantly differentially expressed (P ≤ 0.05) in S. cerevisiae and N. crassa Process/pathway* Oligo(dT) MTP Additional genes identified by MTP Improvement (%) Carbohydrate Metabolism Amino Acid Metabolism Lipid Metabolism Metabolism of Cofactors and Vitamins Energy Metabolism Glycan Biosynthesis and Metabolism Xenobiotics Biodegradation and Metabolism Nucleotide Metabolism Signalling Metabolism of Other Amino Acids Cell cycle Biosynthesis of Secondary Metabolites Folding, Sorting and Degradation Replication and repair Translation Transcription Carbohydrate metabolism Translation Amino acid metabolism Lipid metabolism Xenobiotics biodegradation and metabolism Metabolism of other amino acids Metabolism of cofactors and vitamins Energy metabolism Glycan biosynthesis and metabolism Nucleotide metabolism Biosynthesis of secondary metabolites Signalling Protein fate Transcription Saccharomyces cerevisiae, nitrogen depletion 136 208 114 181 55 89 43 67 37 62 28 58 28 52 31 49 19 39 20 36 20 32 9 15 7 12 8 8 2 2 1 1 Neurospora crassa, protoperithecial development 23 30 25 29 14 26 8 19 5 17 3 11 3 10 9 8 0 5 1 4 2 3 1 1 0 1 0 1 72 67 34 24 25 30 24 18 20 16 12 6 5 0 0 0 7 4 12 11 12 8 7 -1 5 3 1 0 1 1 53 59 62 56 68 107 86 58 105 80 60 67 71 0 0 0 30 16 86 138 240 267 233 -11 ** 300 50 0 ** ** * The pathways and processes were identified using Kyoto Encyclopedia of Genes and Genomes (KEGG). For full list of S. cerevisiae pathways, see Additional File 3. ** biological process not identified by oligo(dT) primers as including any genes significantly differentially expressed by N. crassa protoperithecia. complex pool of mRNAs than do oligo-dTs. The coeffi- cients of variation in number of tags across genes for the oligo-dT runs were 4.3 and 3.0, and the coefficients of var- iation for number of tags across genes for the MTP runs were 3.3 and 3.9, so that the pool of transcriptomic tag sequences returned when priming with MTPs were no more rarified than the pool of transcriptomic tag sequences returned when priming with oligo-dT. We identified a higher number of well-measured genes for the MTP-based dataset than for the oligo-dT data (Table 4, see Additional File 4). In comparison to the sig- nificantly differentially expressed gene list from microarray profiling of yeast using oligo-dT primers, tag sequencing confirmed 35% of the genes with gene expression levels consistent between the two methods of measuring tran- script abundance, but left 57% of the genes without statis- tically significant confirmation (cf. Figures 2, 3, see Additional File 5). In comparison to the MTP-primed microarray experiment, MTP-based tag sequencing con- firmed 41% of the results, leaving 48% without statistically significant confirmation (Figures 2, 3, 4, see Additional File 5). Differences in the functional category of metabo- lism were validated. In particular, MTP identified 13 out of 24 mitochondrially encoded genes as statistically signifi- cantly differentially expressed. Oligo-dT identified none. Oligo-dT priming led to fewer than six tags in both condi- tions for 22 out of 24 mitochondrial ORFs. In contrast, with MTP, only nine ORFs show fewer than six tags.