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Table 1 Plasmodium variant gene families and classification performance

From: Variant surface antigens of malaria parasites: functional and evolutionary insights from comparative gene family classification and analysis

Gene family Sn Sp Jacc pfal pviv pkno pyoe pber pcha pgal
VSA           
  var 1.00 0.99 0.99 67 (66) 0 0 0 0 0 0
  vir-kir 0.94 0.82 0.78 1 310 (262) 66 (65) 3 2 2 1
  yir-bir-cir 0.99 0.98 0.97 0 0 0 897 100 (99) 195 (191) 0
  rif/stevor 0.99 0.98 0.98 192 (190) 0 0 0 0 0 0
  SICAvar 1.00 0.90 0.90 0 0 31 (28) 0 0 0 0
  Pfmc-2TM 1.00 1.00 1.00 12 (12) 0 0 0 0 0 0
  TryThrA-PvTRAG 1.00 1.00 1.00 4 (4) 36 (36) 26 5 7 6 1
  surfin/Pvstp1 1.00 1.00 1.00 9 (9) 2 (2) 0 0 0 0 2
  cys6 1.00 1.00 1.00 10 (10) 11 12 14 10 10 6
  P25_28 1.00 1.00 1.00 2 (2) 2 (2) 2 (2) 2 (2) 2 (2) 2 (2) 1
  PcEMA1 0.71 0.92 0.67 0 0 0 2 1 13 (17) 0
  pyst-a 1.00 0.90 0.90 1 1 1 169 (138) 23 (22) 132 (131) 1
VSA (invasion-linked)
  dbl 1.00 1.00 1.00 5 (5) 2 (2) 4 2 2 2 1
  rbp/235 kDa 1.00 1.00 1.00 5 (5) 8 (8) 1 19 6 8 0
  msp-3 0.89 0.89 0.80 4 (6) 14 (12) 4 2 2 2 0
  msp-7 1.00 1.00 1.00 6 (6) 11 (11) 4 3 3 3 1
  rhoph1/clag 1.00 1.00 1.00 5 (5) 3 (3) 1 (1) 2 2 3 1
  TRAP 0.60 0.75 0.50 4 (5) 4 3 4 4 4 3
  TSP_1 1.00 0.73 0.73 8 (6) 8 (7) 7 (5) 9 (5) 8 (5) 8 (7) 5
  PPLP 1.00 1.00 1.00 5 (5) 5 5 5 5 5 3
Exported
  phist/rad 0.97 0.89 0.86 72 (66) 74 43 2 2 2 4
  gbp130 1.00 1.00 1.00 3 (3) 0 0 0 0 0 0
  pst-a 0.97 1.00 0.97 10 (10) 9 (10) 6 12 (12) 4 28 1
  emp3 0.50 1.00 0.50 1 (2) 1 1 0 0 0 0
  ab_hyda 1.00 1.00 1.00 4 (4) 2 2 2 2 2 1
  ab_hydb 1.00 1.00 1.00 4 (4) 1 1 0 0 0 1
  HRP 1.00 1.00 1.00 2 (2) 0 0 0 0 0 0
  hyp1 0.50 1.00 0.50 1 (2) 0 0 0 0 0 0
  hyp2 0.50 0.50 0.33 2 (2) 0 0 0 0 0 0
  hyp4 1.00 1.00 1.00 9 (9) 0 0 0 0 0 0
  hyp5 1.00 0.89 0.89 9 (8) 0 0 0 0 0 0
  hyp6 1.00 0.40 0.40 5 (2) 0 0 0 0 0 0
  hyp7 1.00 1.00 1.00 3 (3) 0 0 0 0 0 0
  hyp8 1.00 1.00 1.00 2 (2) 0 0 0 0 0 0
  hyp9 1.00 1.00 1.00 5 (5) 0 0 0 0 0 0
  hyp10 1.00 1.00 1.00 2 (2) 0 0 0 0 0 0
  hyp11 1.00 1.00 1.00 5 (5) 6 5 1 1 1 0
  hyp12 1.00 0.75 0.75 4 (3) 0 0 0 0 0 0
  hyp13 1.00 1.00 1.00 2 (2) 0 0 0 0 0 0
  hyp15 0.75 0.75 0.60 4 (4) 0 0 0 0 0 0
  hyp16 1.00 1.00 1.00 2 (2) 0 0 0 0 0 0
  hyp17 1.00 0.67 0.67 3 (2) 0 0 0 0 0 0
  pk-fam-b 1.00 0.83 0.83 0 1 12 (10) 0 0 0 0
  pk-fam-c 1.00 1.00 1.00 0 0 5 (5) 0 0 0 0
  pk-fam-e 1.00 1.00 1.00 0 0 3 (3) 0 0 0 0
Other (species-specific or sub-telomeric)
  etramp 0.97 0.94 0.91 15 (14) 10 (9) 9 15 6 (7) 12 4
  acs 1.00 0.93 0.93 14 (13) 5 5 5 5 7 5
  ACBP 1.00 1.00 1.00 4 (4) 0 0 0 0 0 0
  pv-fam-g 1.00 1.00 1.00 3 3 (3) 3 3 3 3 3
  pk-fam-a 1.00 0.89 0.89 0 0 9 (8) 0 0 0 0
  pc-fam 0.85 1.00 0.85 0 0 0 5 1 17 (20) 0
  pk-fam-d 0.50 1.00 0.50 0 0 1 (2) 0 0 0 0
  pv-fam-d 1.00 0.57 0.57 1 28 (16) 9 0 0 0 0
  pyst-c 1.00 0.82 0.82 0 0 0 22 (18) 3 11 0
  pv-fam-b 1.00 1.00 1.00 0 6 (6) 1 0 0 0 0
  pv-fam-c 1.00 1.00 1.00 0 7 (7) 0 0 0 0 0
  pyst-d 0.77 1.00 0.77 0 0 0 10 (13) 0 0 0
  pyst-b 1.00 0.96 0.96 0 0 0 56 (54) 28 21 0
  pv-fam-h 1.00 0.80 0.80 4 5 (4) 3 0 0 0 0
Average 0.94 0.92 0.87        
  1. Fifty-nine Plasmodium variant gene families were curated from the literature and public databases and categorized as follows: (a) VSAs (11 families); (b) VSAs linked to erythrocyte invasion (8 families); (c) predicted to be exported to the host erythrocyte (25 families); (d) other subtelomeric or species-specific gene families (15 families). Better studied gene families are shown at the top of each category. Classification performance of each gene family is measured in terms of sensitivity (Sn), specificity (Sp), and Jaccard index (Jacc). The remaining columns show how many genes of each species have been classified to belong to this gene family (excluding annotated pseudogenes and gene fragments). Numbers in parentheses indicate how many genes of each species served as reference gene family members. A more comprehensive version of this table including numbers of identified genes in non-Plasmodium species is available in Additional file 2. Abbreviations: VSA… variant surface antigen; pfal… P. falciparum; pviv… P. vivax; pkno… P. knowlesi; pyoe… P. yoelii; pber… P. berghei; pcha… P. chabaudi; pgal… P. gallinaceum.
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