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Table 3 P. pastoris gene statistics of long, medium and short genes

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

  Long Medium Short All
Number of genes 1262 2538 1265 5065
ORF length [bp] >1807 770-1807 <770 141-14853
Mean ORF length [bp] 2786 1235 524 1444
Median ORF length [bp] 2412 1206 540 1203
Mean expression intensity 5081 7141 12092 7864
Median expression intensity 2600 2591 3416 2736
Mean SCUO 0.078 0.105 0.198 0.123
Median SCUO 0.069 0.093 0.165 0.096
Genes with 5′UTR 628 257 29 914
Genes with 5′UTR [%] 50% 10% 2% 18%
5′UTR length mean 238 253 320 245
Mean translational state −0.22 −0.01 0.18 −0.02
  1. Based on the information published by Liang et al. [2], all P. pastoris genes were split into 3 groups comprising the 25% longest (>1807 bp), the 25% shortest (<770 bp) and the remaining (50%, <1807 and >770 bp) medium length genes. Gene groups are not exactly the same size because they were split by length cut-off (some genes possess equal ORF lengths). 5′UTR information was also taken from Liang et al. [2]. Expression intensities were obtained from our total RNA microarray data which were normalized as described in the Methods section. Synonymous codon usage order (SCUO) was obtained from the CodonO platform [35].