Table 4 Seventy-three genes significantly (FDR <0.05) and differentially expressed (± 1, log 2 scale) that were in common between RNA-seq normalized by the KDMM strategy and microarray data
Gene | Product | (Populus12Â hours) - (Populus37Â hours) | (Populus12Â hours) - (Switchgrass 12Â hours) | (Populus37Â hours) - (Switchgrass 37Â hours) | (Switchgrass 12Â hours) - (Switchgrass 37Â hours) | ||||
|---|---|---|---|---|---|---|---|---|---|
| Â | Â | RNA-seq (KDMM) | Array | RNA-seq (KDMM) | Array | RNA-seq (KDMM) | Array | RNA-seq (KDMM) | Array |
Cthe_0057 | Hypothetical protein | -0.18 | -0.44 | 0.56 | 0.26 | -2.27 | -1.53 | -3.01 | -2.23 |
Cthe_0264 | Hypothetical protein | -2.96 | -1.63 | -1.05 | -0.45 | -3.16 | -1.70 | -5.07 | -2.88 |
Cthe_0272 | Peptidase S11 D-alanyl-D-alanine carboxypeptidase 1 | -1.33 | -0.69 | 0.80 | 0.47 | -0.06 | -0.35 | -2.19 | -1.51 |
Cthe_0414 | Manganese containing catalase | -0.84 | -0.59 | 0.42 | 0.23 | -3.14 | -2.45 | -4.40 | -3.27 |
Cthe_0415 | Spore coat protein CotJB | -1.99 | -0.68 | -0.51 | -0.05 | -2.97 | -1.47 | -4.46 | -2.10 |
Cthe_0420 | Dipicolinate synthase subunit A | -2.50 | -1.54 | -0.41 | -0.23 | -2.08 | -0.98 | -4.18 | -2.29 |
Cthe_0453 | Hypothetical protein | -3.32 | -1.56 | -0.67 | -0.17 | -2.96 | -1.75 | -5.61 | -3.14 |
Cthe_0470 | Hypothetical protein | 1.68 | 1.05 | 1.50 | 0.73 | -0.20 | 0.07 | -0.02 | 0.39 |
Cthe_0471 | Flagellar hook-length control protein | 3.00 | 2.01 | 2.16 | 1.29 | 0.01 | -0.05 | 0.84 | 0.67 |
Cthe_0472 | Flagellar hook-capping protein | 3.16 | 1.81 | 2.39 | 1.13 | -0.07 | 0.16 | 0.71 | 0.85 |
Cthe_0473 | Flagellar operon protein | 3.08 | 1.53 | 1.91 | 1.36 | -0.26 | 0.70 | 0.91 | 0.86 |
Cthe_0516 | IS66 Orf2 family protein | -1.35 | -1.03 | -0.27 | -0.48 | -0.43 | 0.13 | -1.51 | -0.41 |
Cthe_0624 | Glycoside hydrolase (CelJ) | 0.13 | 0.13 | -1.05 | -0.44 | 0.99 | 0.52 | 2.17 | 1.09 |
Cthe_0964 | Amino acid-binding ACT domain protein | -2.52 | -1.05 | -0.44 | -0.33 | -0.48 | -0.27 | -2.55 | -0.99 |
Cthe_1081 | Hypothetical protein | -3.21 | -0.70 | 0.89 | 0.23 | -3.16 | -1.92 | -7.26 | -2.84 |
Cthe_1083 | Spore coat protein, CotS family | -2.56 | -1.11 | -0.75 | -0.46 | -2.68 | -1.99 | -4.49 | -2.63 |
Cthe_1084 | Spore coat protein, CotS family | -2.28 | -1.58 | -0.87 | -0.30 | -2.89 | -1.15 | -4.31 | -2.43 |
Cthe_1085 | Glycosyltransferase group 1 | -2.45 | -1.35 | -0.69 | -0.33 | -2.70 | -1.36 | -4.45 | -2.38 |
Cthe_1086 | NAD-dependent epimerase/dehydratase | -2.27 | -0.92 | -1.05 | -0.46 | -2.67 | -1.88 | -3.89 | -2.34 |
Cthe_1255 | Hypothetical protein | 1.18 | 1.19 | 2.11 | 1.57 | -0.98 | 0.04 | -1.92 | -0.34 |
Cthe_1256 | Glycoside hydrolase family 3 domain protein | 0.70 | 0.35 | 3.00 | 1.50 | 0.84 | 0.45 | -1.47 | -0.71 |
Cthe_1257 | Carbohydrate-binding CenC domain protein | 1.03 | 0.40 | 3.04 | 1.35 | 0.43 | -0.02 | -1.57 | -0.97 |
Cthe_1309 | Radical SAM domain protein | -0.24 | 0.07 | 4.25 | 1.95 | 1.12 | 0.09 | -3.37 | -1.79 |
Cthe_1310 | Accessory gene regulator B | 0.35 | -0.06 | 4.16 | 2.46 | -0.23 | 0.60 | -4.04 | -1.91 |
Cthe_1340 | Hypothetical protein | -0.84 | -0.44 | 1.44 | 1.00 | 0.00 | 0.09 | -2.28 | -1.36 |
Cthe_1404 | GTP-binding protein HSR1-related | -1.26 | -1.33 | 0.02 | -0.02 | -2.55 | -1.46 | -3.82 | -2.78 |
Cthe_1437 | Hypothetical protein | -2.50 | -1.23 | -0.16 | -0.04 | -0.16 | -0.07 | -2.50 | -1.26 |
Cthe_1438 | RNA polymerase sigma factor, sigma-70 family | -1.90 | -1.40 | -0.10 | -0.09 | -1.03 | -0.16 | -2.83 | -1.46 |
Cthe_1480 | Hypothetical protein | -0.38 | -0.32 | -6.34 | -3.86 | -6.28 | -3.64 | -0.31 | -0.10 |
Cthe_1481 | Hypothetical protein | -0.44 | -0.39 | -6.35 | -3.75 | -6.31 | -3.48 | -0.39 | -0.11 |
Cthe_1539 | Glutamine synthetase catalytic region | -4.71 | -3.12 | -1.25 | -0.84 | -0.27 | 0.00 | -3.74 | -2.28 |
Cthe_1540 | Glutamyl-tRNA(Gln) amidotransferase, B subunit | -2.05 | -1.63 | -0.27 | -0.43 | 0.17 | -0.05 | -1.61 | -1.25 |
Cthe_1603 | Phosphate ABC transporter, inner membrane subunit PstA | -0.06 | -0.32 | -3.03 | -2.12 | -1.45 | -0.89 | 1.51 | 0.91 |
Cthe_1604 | Phosphate ABC transporter, inner membrane subunit PstC | 0.53 | 0.26 | -3.76 | -2.85 | -2.83 | -1.46 | 1.46 | 1.65 |
Cthe_1605 | ABC-type phosphate transport system periplasmic component-like protein | 0.35 | 0.11 | -4.05 | -2.69 | -2.60 | -1.36 | 1.80 | 1.45 |
Cthe_1759 | Sporulation protein YunB | -1.91 | -1.43 | 0.22 | 0.02 | -2.03 | -1.03 | -4.16 | -2.47 |
Cthe_1807 | Hypothetical protein | -2.28 | -1.14 | -2.03 | -0.98 | 0.20 | 0.21 | -0.05 | 0.05 |
Cthe_1809 | RNA polymerase sigma factor, sigma-70 family | -1.61 | -0.80 | -2.71 | -1.07 | -0.54 | -0.18 | 0.55 | 0.09 |
Cthe_1812 | Urease accessory protein UreD | -1.67 | -1.04 | -0.41 | -0.48 | -0.39 | 0.46 | -1.64 | -0.10 |
Cthe_1813 | Urease accessory protein UreG | -1.57 | -1.22 | -0.46 | -0.48 | 0.01 | 0.89 | -1.10 | 0.15 |
Cthe_1821 | Urea ABC transporter, permease protein UrtC | -2.88 | -1.86 | -0.61 | -0.21 | 0.23 | 0.22 | -2.03 | -1.43 |
Cthe_1879 | Hypothetical protein | -1.74 | -1.17 | -0.13 | 0.04 | 1.79 | 1.32 | 0.17 | 0.11 |
Cthe_1890 | Dockerin type 1 protein | -1.07 | -0.63 | 2.05 | 1.38 | -0.59 | -0.24 | -3.71 | -2.26 |
Cthe_2299 | CRISPR-associated helicase Cas3 | 2.68 | 1.80 | 1.65 | 0.93 | -1.38 | -0.50 | -0.35 | 0.37 |
Cthe_2400 | Sporulation peptidase YabG | -3.09 | -0.44 | -0.66 | 0.06 | -1.62 | -0.60 | -4.05 | -1.10 |
Cthe_2503 | Cupin 2 conserved barrel domain protein | -2.11 | -1.11 | 0.40 | 0.16 | -2.73 | -1.96 | -5.24 | -3.23 |
Cthe_2506 | S-layer domain-containing protein | 0.79 | 0.26 | 2.99 | 1.30 | 0.15 | -0.08 | -2.05 | -1.13 |
Cthe_2531 | Sulfate ABC transporter, periplasmic sulfate-binding protein | -1.62 | -0.20 | 5.37 | 3.22 | 1.72 | 0.37 | -5.26 | -3.05 |
Cthe_2532 | Sulfate ABC transporter, inner membrane subunit CysT | -1.15 | -0.19 | 5.66 | 3.39 | 0.92 | 0.01 | -5.88 | -3.58 |
Cthe_2536 | Phosphoadenosine-phosphosulfate reductase | -1.27 | -0.41 | 4.11 | 2.60 | 1.47 | 0.50 | -3.91 | -2.51 |
Cthe_2539 | UBA/THIF-type NAD/FAD binding protein | -1.39 | -0.24 | 4.04 | 1.85 | 1.94 | 0.18 | -3.49 | -1.91 |
Cthe_2573 | ABC transporter-related | -2.80 | -1.99 | -0.31 | 0.19 | -1.81 | -1.03 | -4.29 | -3.21 |
Cthe_2575 | Hypothetical protein | -1.93 | -1.34 | -0.03 | 0.15 | -1.97 | -0.87 | -3.87 | -2.37 |
Cthe_2582 | Dihydroneopterin aldolase | 1.08 | 0.65 | 0.14 | 0.36 | -0.68 | 1.05 | 0.26 | 1.34 |
Cthe_2640 | UDP-N-acetyl-D-glucosamine 2-epimerase, UDP-hydrolyzing | -1.87 | -0.44 | 0.07 | 0.00 | -1.69 | -0.94 | -3.63 | -1.38 |
Cthe_2642 | Sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family | -2.57 | -1.75 | -0.35 | 0.36 | -1.73 | -0.13 | -3.95 | -2.24 |
Cthe_2643 | Nucleotidyltransferase | -2.48 | -0.73 | -0.89 | 0.10 | -1.97 | -0.30 | -3.55 | -1.13 |
Cthe_2644 | DegT/DnrJ/EryC1/StrS aminotransferase | -2.38 | -1.27 | 0.28 | 0.20 | -1.36 | -0.64 | -4.02 | -2.11 |
Cthe_2645 | NAD-dependent epimerase/dehydratase | -2.71 | -1.20 | -0.63 | -0.03 | -1.63 | -0.25 | -3.71 | -1.42 |
Cthe_2647 | ATP-dependent carboxylate-amine ligase domain protein ATP-grasp | -1.55 | -0.91 | -0.08 | 0.12 | -2.13 | -0.35 | -3.60 | -1.38 |
Cthe_2649 | HpcH/HpaI aldolase | -2.44 | -1.56 | 0.99 | 0.22 | -2.88 | -1.45 | -6.32 | -3.23 |
Cthe_2650 | Polysaccharide biosynthesis protein CapD | -1.83 | -0.59 | -0.59 | -0.21 | -1.93 | -0.86 | -3.17 | -1.24 |
Cthe_2651 | Hypothetical protein | -3.52 | -1.24 | 0.37 | -0.23 | -4.29 | -2.73 | -8.18 | -3.75 |
Cthe_2652 | Lipopolysaccharide biosynthesis protein | -1.41 | -0.86 | -0.19 | 0.26 | -2.34 | -1.57 | -3.56 | -2.69 |
Cthe_2653 | Capsular exopolysaccharide family | -0.14 | -1.19 | 0.39 | 0.08 | -1.87 | -0.92 | -2.40 | -2.20 |
Cthe_2654 | PHP domain protein | -1.08 | -0.54 | 0.03 | -0.16 | -1.92 | -0.76 | -3.02 | -1.14 |
Cthe_2763 | Hypothetical protein | -0.44 | -0.23 | 0.75 | 0.51 | 0.04 | -0.29 | -1.15 | -1.03 |
Cthe_3006 | ErfK/YbiS/YcfS/YnhG family protein | -1.61 | -1.30 | -1.35 | -0.24 | -2.74 | -1.16 | -3.00 | -2.22 |
Cthe_3007 | Peptidoglycan-binding lysin domain | -0.82 | -0.89 | -0.20 | -0.30 | -2.02 | -1.26 | -2.64 | -1.85 |
Cthe_3008 | Manganese/iron superoxide dismutase | -1.44 | -0.72 | 0.04 | 0.45 | -1.77 | -0.03 | -3.25 | -1.20 |
Cthe_3102 | Cell envelope-related function transcriptional attenuator, LytR/CpsA family | -3.30 | -1.06 | -0.87 | -0.62 | 0.78 | -0.13 | -1.65 | -0.58 |
Cthe_3307 | Hypothetical protein | -1.30 | -0.36 | 0.95 | 0.38 | -2.29 | -1.22 | -4.54 | -1.95 |
Cthe_3350 | Hypothetical protein | 0.14 | 0.24 | 1.39 | 0.64 | -1.16 | -1.31 | -2.40 | -1.71 |