Jensen MA, Coetzer M, van 't Wout AB, Morris L, Mullins JI 2006 A reliable phenotype predictor for human immunodeficiency virus type 1 subtype C based on envelope V3 sequences. Journal of virology80104698-704 pubmed

Supplemental Data for Jensen et al.:

 All supplemental data as a Microsoft Excel workbook


  1. Training Set Data

  2. Validation Analysis

  3. NSI training set in FASTA format
    u[nn] in name line indicates sample from [nn]th infected individual GenBank acc. (indicated where available)

  4. SI training set in FASTA format
    u[nn] in name line indicates sample from [nn]th infected individual GenBank acc. (indicated where available)

  5. Validation set in FASTA format
    "multiple names after '>' are isolates with identical V3 loops; for Genbank accessions, see ""validation analysis"" sheet"


C-PSSM training set source information

ref/source clone/bulk   phenotyping no. nsi/r5 no. si/x4

ABEBE (1999)
BC + PB SI/NSI and R5/X4 46 27

TSCHERNING (1998), ALAEUS (1997)
PB SI/NSI and R5/X4 18 0

BALL (2003)
PB SI/NSI and R5/X4 1 0

BATRA (2000)
PB SI/NSI 22 3

BJORNDAL (1999)
PB SI/NSI and R5/X4 10 0

BONGERTZ (2000)
PB SI/NSI 1 0

CHEN (2000)
MC R5/X4 1 0

GAO (1996)
PB SI/NSI 4 0

LOLE (1999)
PB SI/NSI 3 0

MOCHIZUKI (1999)
MC R5/X4 1 0

MORRIS (2001)
PB SI/NSI and R5/X4 10 0

NDUNGU (2001)
MC R5/X4 1 0

PAPATHANASOPOULOS (2002)
PB R5/X4 0 2

PING (1999)
PB SI/NSI and R5/X4 16 0

RODENBURG (2001)
PB R5/X4 9 0

TORRE (2000)
PB R5/X4 1 0

TREURNICHT (2002)
PB R5/X4 14 1

TRKOLA (2001)
PB R5/X4 1 0

WILLIAMSON (2003), VAN HARMELEN (2001)
PB + MC SI/NSI and R5/X4 4 1

CHOGE (IN PRESS)
PB SI/NSI and R5/X4 23 0

COETZER (SUBM)
PB SI/NSI and R5/X4 17 8

CILLIERS (2003)
PB SI/NSI and R5/X4 8 3

COETZER (IN PREP)
PB SI/NSI and R5/X4 1 3

NICD (UNPUB)
PB SI/NSI and R5/X4 16 3

Total
228 51 279


clone/bulk legend:

BC = biological clone
MC = molecular clone
PB = population bulk





C-PSSM VALIDATION TABLE

perl pssimple.pl -MsubC.matrix -o -xSI -rNSI valid.fas (PERL scripts available on request)

C-PSSM training set source information

C-PSSM cutoff
-21.64
B-PSSM cutoff
-7
id GenBank type score predictiona sens/spec score predictiona sens/spec
C.ZM.89.ZM20 L22956 SI -24.89492048 0 0.833333333 -9.601037284 0 0.541666667
C.ZW.01.TC28_2 AY265949 SI 1.320003451 1 4.038437733 1
C.ZW.01.TC03_1 AY265930 SI 2.690203197 1 5.737247761 1
C.ET.97.PHD79C1 AY452646 SI -26.49287118 0 -11.35949029 0
C.ZW.01.TC28_1 AY265948 SI -24.4755872 0 -7.95063423 0
AC.RW.92.92RW009_di1sCD U08763 SI -21.34618437 1 -11.71045286 0
AC.RW.92.92RW009_1gCR U08631 SI -20.55772701 1 -12.11591797 0
C.ZW.01.TC22 AY265942 SI -13.55120018 1 -1.304152441 1
C.ZW.01.TC30 AY265951 SI -15.87249476 1 -2.564425855 1
C.ZW.01.TC29 AY265951 SI -5.305447284 1 1.815938961 1
C.ZA.99.DU179 AY043174 SI -17.13178663 1 -7.260950155 0
A1C.SE.96.SE9488 AF071474 SI -19.99320067 1 -9.761484486 0
C.ZW.01.TC25 AY265945 SI -17.85974004 1 -4.752852426 1
C.ZW.01.TC03_2 AY265931 SI -15.24411671 1 -2.829477476 1
C.ZA.99.ZASW7 AF397573 SI 3.028793513 1 8.06879484 1
C.ZW.01.TC13 AY265937 SI -15.74922188 1 -10.18249542 0
C.ZA.99.99ZASW20 AY230879 SI -14.62450947 1 -4.879539445 1
C.ZW.x.Z2288 AF056123 SI -23.12488326 0 -7.264575913 0
C.ZW.01.TC08 AY265934 SI -12.46854105 1 -4.019621784 1
C.ZW.01.TC23 AY265943 SI -19.84932954 1 -7.903309828 0
C.ZW.x.Z748 AF056139 SI -5.835941628 1 -0.350135886 1
C.ET.97.PHD74E7 AY452644 SI 1.922534709 1 -1.393096407 1
C.ZW.01.TC04 AY265932 SI -14.28874401 1 -1.174386841 1
C.ET.97.074D3 AF158907 SI -15.75702467 1 -10.3254563 0
C.SN.90.90SE_364 AY713416 NSI -28.16640588 0 0.829787234 -9.764070628 0 0.787234043
C.ZA.99.99ZASW35 AY170666 NSI -23.38240629 0 -6.430048616 1
C.ZW.01.TC26 AY265946 NSI -24.42293326 0 -10.95977714 0
C.ZA.90.90ZA514 U33781 NSI -24.0811052 0 -8.643025076 0
C.FR.93.FRMP169 U58797 NSI -26.2422023 0 -8.696116534 0
C.ZA.98.98ZA528 AY158535 NSI -23.72370837 0 -10.33328755 0
C.ZW.01.TC19 AY265941 NSI -26.92753971 0 -9.941985558 0
A1CDGKU.ZA.99.CM4 AF411964 NSI -13.0278942 1 0.690894749 1
C.ZA.98.TV007A AF391238 NSI -23.11130008 0 -9.222133301 0
C.ZW.01.TC17 AY265940 NSI -26.53742769 0 -7.762975422 0
C.ZA.99.99ZASW38 AY170667 NSI -23.96874952 0 -9.055862905 0
C.FR.90.FRMP19 U58790 NSI -29.24834668 0 -10.59627373 0
C.ZW.01.TC35 AY265954 NSI -26.78467946 0 -10.90537816 0
C.ZW.01.TC31 AY265957 NSI -25.79395613 0 -9.860010389 0
C.FR.93.FRMP129 U58794 NSI -29.06665664 0 -11.8999815 0
C.FR.92.FRMP148 U58796 NSI -27.65310784 0 -8.972522783 0
C.ZA.99.99ZASW38 AY170667 NSI -26.32538628 0 -8.579582718 0
C.ZA.92.92ZA517 AY170667 NSI -23.65025538 0 -9.875882439 0
C.FR.92.FRMP41 U58788 NSI -27.98866364 0 -13.23975584 0
C.ZA.98.98ZA502 AY158534 NSI -25.59336219 0 -12.03094556 0
C.MW.93.960 U08454 NSI -27.05652783 0 -8.976957851 0
C.ZW.01.TC39 AY265956 NSI -22.67287344 0 -2.122169778 1
C.ZW.01.TC24 AY265944 NSI -16.79314469 1 -2.970204875 1
C.ZW.01.TC12 AY265936 NSI -26.80438599 0 -6.355603508 1
BC.BR.92.92BR023 U86559 NSI -20.64864234 1 -12.53079562 0
C.ZA.98.TV014 AF254778 NSI -11.91565779 1 -9.768543874 0
C.ET.97.085 AF158875 NSI -27.61879533 0 -11.59626132 0
C.ZA.98.TV008A AF391240 NSI -28.36963726 0 -10.32020694 0
C.ZW.01.TC07 AY265933 NSI -29.47515187 0 -12.17113427 0
C.ZW.01.TC27 AY265947 NSI -24.00779779 0 -8.366741927 0
C.ZW.01.TC34 AY265953 NSI -26.73602021 0 -7.873518229 0
C.ZW.01.TC11 AY265935 NSI -18.27470013 1 -7.688354199 0
C.ZA.98.98ZA445 AY158533 NSI -28.83384162 0 -10.67803307 0
C.ZW.01.TC36 AY265955 NSI -20.68133822 1 -9.919600659 0
C.ZA.98.TV001 AF254766 NSI -25.04611075 0 -9.328193457 0
C.ZW.01.TC02 AY265929 NSI -27.02907165 0 -7.472169183 0
C.ET.02.02ET_288 AY713417 NSI -28.53687256 0 -10.36405043 0
C.ZW.01.TC16 AY265939 NSI -19.08554717 1 -4.511912189 1
C.ZA.98.TV018 AF254782 NSI -26.51833399 0 -6.832250677 1
A2C.ZA.98.DU178 AF411965 NSI -23.68563117 0 -9.182258694 0
C.FR.92.FRMP130 U58795 NSI -26.78421178 0 -8.531290103 0
C.ZW.01.TC15 AY265938 NSI -23.08477717 0 -6.87908799 1
C.ZW.01.TC33 AY265952 NSI -27.46929978 0 -9.832638966 0
C.FR.93.FRMP37 U58786 NSI -25.57077753 0 -7.763081618 0
C.ZW.01.TC32 AY265958 NSI -6.952498098 1 0.820711368 1
C.FR.91.FRMP197 U58798 NSI -25.93800559 0 -8.874777779 0
C.SO.89.89SM_145 AY713415 NSI -23.05344271 0 -6.746030536 1


Footnotes
C-PSSM cutoff -21.64 score
area under ROCb: 0.8812057

B-PSSM cutoff -7 score
area under ROCb:0.7087766

a: 0 = NSI, 1 = SI
b: ROC values calculated using R; scripts available on request

Department of Microbiology
School of Medicine
University of Washington
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