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Table 6 Transcriptional regulation of genes involved in methanol metabolism and peroxisome formation

From: Pichia pastoris regulates its gene-specific response to different carbon sources at the transcriptional, rather than the translational, level

Short name Pp Description G-D logFC G-D adjPV M-D logFC M-D adjPV X-D logFC X-D adjPV
AOX1 Alcohol oxidase (Pichia pastoris) 0.28   7.00 *** 6.64 ***
AOX2 Alcohol oxidase (Pichia pastoris) 0.39   7.44 *** 7.48 ***
CTA1 Catalase A, breaks downhydrogen peroxide in the peroxisomal matrix 1.48 * 5.45 *** 6.11 ***
DAK2 Dihydroxyacetone kinase, required for detoxification of dihydroxyacetone (DHA) −0.18   4.13 *** 2.97 ***
DAS1 Dihydroxyacetone synthase variant 1 0.21   8.91 *** 4.72 ***
DAS2 Dihydroxyacetone synthase variant 2 0.10   8.78 *** 4.89 ***
FDH1 NAD(+)-dependent formate dehydrogenase, protect cells from formate 0.44   8.74 *** 8.75 ***
FGH1 S-formylglutathione hydrolase; involved in the detoxification of formaldehyde 0.65   5.25 *** 4.86 ***
FLD glutathione-dependent formaldehyde dehydrogenase 0.34   4.56 *** 3.89 ***
PEX1 AAA-peroxin 0.50 *** 2.56 *** 2.75 ***
PEX10 Peroxisomal membrane E3 ubiquitin ligase 0.33   3.64 *** 4.19 ***
PEX11 Peroxisomal membrane protein 1.01 *** 5.40 *** 5.57 ***
PEX12 C3HC4-type RING-finger peroxin and E3 ubiquitin ligase 0.36 ** 2.50 *** 3.75 ***
PEX13 Integral peroxisomal membrane protein 0.55 * 4.39 *** 3.90 ***
PEX14 Peroxisomal membrane peroxin 0.23   3.14 *** 3.90 ***
PEX17 Peroxisomal membrane peroxin −0.26   2.26 *** 2.96 ***
PEX19 Chaperone and import receptor for newly-synthesized class I PMPs −0.07   0.75 *** 2.10 ***
PEX2 RING-finger peroxin and E3 ubiquitin ligase 0.75 *** 3.48 *** 3.63 ***
PEX20 Peroxin 20 0.74 *** 1.03 *** 3.97 ***
PEX22 Putative peroxisomal membrane protein 0.11   0.55 * 0.85 ***
PEX25 Peripheral peroxisomal membrane peroxin −0.19   1.09 *** 3.29 ***
PEX28 Peroxisomal integral membrane peroxin 0.04   0.23   1.55 ***
PEX29 Peroxisomal integral membrane peroxin −0.24   −0.16   0.48 ***
PEX3 Peroxisomal membrane protein (PMP) 0.37 ** 2.27 *** 1.30 ***
PEX30 Peroxisomal integral membrane protein 0.10   0.09   0.47 ***
PEX31 Peroxisomal integral membrane protein 0.36   0.93 * 2.29 ***
PEX4 Peroxisomal ubiquitin conjugating enzyme 0.76 *** 2.03 *** 4.45 ***
PEX5 Peroxisomal membrane signal receptor 0.29   4.63 *** 4.87 ***
PEX6 AAA-peroxin 0.82 *** 3.53 *** 2.62 ***
PEX7 Peroxisomal signal receptor −0.22   0.30   1.98 ***
PEX8 Intraperoxisomal organizer of the peroxisomal import machinery 0.42 ** 2.93 *** 3.52 ***
PEX26 Peroxisomal membrane protein 0.94 *** 3.16 *** 4.63 ***
PEX11C Ortholog of PEX11 0.36   3.45 *** 1.53 ***
  1. Log2 fold changes and adjusted P-values (* adjPV < 0.1; ** adjPV < 0.05; *** adjPV < 0.01) are shown (see Additional file 1: Table S1 for detailed data). Up-regulated genes are in bold letters, down-regulated genes in bold and italics.