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Table 1 Analysis of Nef residues associated with EC Nef functions (all N>5 and q<0.4)

From: Attenuation of multiple Nef functions in HIV-1 elite controllers

Nef activity Position on HXB2 AAa No. of subjectsb Relative Nef activity (%) p-value q-value
With AA Without AA With AA Without AA
HLA-I down-regulation 8 S 17 27 83.6 97.2 0.01 0.3
  8 R 14 30 106.1 91.1 0.02 0.3
  11 V 20 21 87.2 98.9 0.01 0.3
  14 P 34 11 91.1 108 0.004 0.3
  46 S 36 8 96.7 77.1 0.01 0.3
  108 D 34 11 91.1 105.8 0.02 0.3
  108 E 11 34 105.8 91.1 0.02 0.3
  138 C 5 40 79.8 96.5 0.02 0.3
  138 T 40 5 96.5 79.8 0.02 0.3
  192 H 36 9 97 78.1 0.01 0.3
  192 R 6 39 84 96.8 0.04 0.4
  205 N 22 23 101 83.6 0.02 0.3
  205 D 22 23 85.9 98.9 0.03 0.3
CD74 up-regulation 8 S 17 27 37.7 60 0.004 0.3
  28 E 14 31 73.7 42.4 0.008 0.3
  28 D 29 16 40.4 65.3 0.009 0.3
  135 F 10 35 35 57.5 0.003 0.3
  135 Y 34 11 57.1 35.1 0.01 0.3
CD4 down-regulation 8 S 17 27 84.8 92.6 0.007 0.3
  14 P 34 11 86.1 97.9 0.003 0.1
  14 S 5 40 102.9 87.2 0.02 0.4
  15 A 11 34 76.9 91.3 0.02 0.4
  21 K 11 34 70.7 91.6 0.002 0.1
  21 R 28 17 91.6 76.9 0.02 0.4
  105 R 12 33 76.6 91.9 0.003 0.1
  163 C 9 36 98.1 86.6 0.02 0.4
  1. a AA, amino acid.
  2. b Row totals vary depending on the codon position because sequences with gaps in the alignment are considered missing data.