shows the signature site decapeptide AA patterns for each of the 109 infected subjects, aligned to the vaccine efficacy curve for reference. 92TH023 or CM244 vaccine sequences, with 95% confidence intervals, using Env amino acid sequences and computed with the HIVb PAM substitution Rabbit Polyclonal to ARFGAP3 matrix[11]. For each panel, the first p-value is for screening whether there is any VE against any computer virus genotype, and the second p-value is for screening whether VE varies with the distance distances based on the sequences and the HIVb PAM substitution matrix[16]. Box plots show the 25th percentile (lower edge of the box), 50th percentile (horizontal collection in the box), and 75th percentile (upper edge of the box). Panels (C) and (D) show SmoothMarks estimates of vaccine efficacy (VE) against acquisition with an HIV-1 CRF01_AE computer virus with distance from your 92TH023 or CM244 vaccine sequences with 95% confidence intervals. With 10 residues in AA tree divergences. Box plots show the 25th percentile (lower edge of the box), 50th percentile (horizontal collection in the box), and 75th percentile (upper edge of the box).(EPS) pcbi.1003973.s007.eps (30K) GUID:?B61BE70B-DEFC-405D-8CF5-98870FD904A3 S8 Fig: Frequencies of potential N-linked glycosylation sites (PNG sites) in gp120 for vaccine versus placebo sequences. Frequencies of PNG sites at all gp120 sites (excluding sites at which the multiple alignment was poorly resolved) for amino acid sequences. Blue bars above the horizontal collection are for placebo sequences and reddish bars below the collection are for vaccine sequences. There was no evidence of differences in PNG frequencies at any sites between vaccine and placebo sequences.(TIF) pcbi.1003973.s008.tif (1.2M) GUID:?2A83336C-8ED7-4611-8855-F2B0EE2D71E6 S9 Fig: Frequency of sites in potential antibody contact patches. The EPIMAP method used by[7] was applied to estimate potential antibody contact patches of Env sites. Sites were sorted by frequency of inclusion in these (R,R)-Formoterol patches, showing that some sites are more likely to be on the surface of the Env protein and other sites are more likely to be buried and inaccessible to antibodies.(TIFF) pcbi.1003973.s009.tiff (1007K) GUID:?02C8FEF0-FEC8-4F89-AB30-4A9F55F26575 S1 Table: Numbers of HIV-1 protein sequences measured from your n = 109 HIV-1 CRF01_AE infected subjects in the RV144 trial: Vaccine immunogen proteins.(DOC) pcbi.1003973.s010.doc (29K) GUID:?C7E628FE-135D-4472-9C1B-29A0F02749A6 S2 Table: Numbers of HIV-1 protein sequences measured from your n = 109 HIV-1 CRF01_AE infected subjects in the RV144 trial: Non-vaccine immunogen proteins.(DOC) pcbi.1003973.s011.doc (31K) GUID:?C712E220-B563-4127-A811-719DA834AB1B S3 Table: Biological annotation of the identified signature sites in vaccine proteins.(DOC) pcbi.1003973.s012.doc (71K) GUID:?DA0C7238-5F83-4DE4-AE71-DB1402D2E682 S4 Table: Biological annotation of the identified signature sites in non-vaccine proteins.(DOC) pcbi.1003973.s013.doc (89K) GUID:?2A3004B4-14CB-4F20-B8C3-6590D21B55D9 S5 Table: Significant 9-mer sieve effects in vaccine proteins (by KmerScan).(DOC) pcbi.1003973.s014.doc (51K) GUID:?D8B20AFA-35C5-4FEF-8164-2188FFDA8A69 S6 Table: Significant 9-mer sieve effects in non-vaccine proteins (by KmerScan).(DOC) pcbi.1003973.s015.doc (82K) GUID:?D8AEE5BB-A975-43D0-9173-F32AD3704889 S7 Table: Physico-chemical Properties (PCP) site-scanning results in vaccine proteins.(DOC) pcbi.1003973.s016.doc (43K) GUID:?5C64D260-851A-4228-BEED-C483D08CFF20 S8 Table: Physico-chemical Properties (PCP) site-scanning results in non-vaccine proteins.(DOC) pcbi.1003973.s017.doc (51K) GUID:?E0059148-8EAD-4DE6-80E0-43F1124BB7AC S9 Table: Physico-chemical Properties (PCP) 3-mer results in vaccine proteins.(DOC) pcbi.1003973.s018.doc (53K) GUID:?07472241-7AFD-467C-862D-63E449C6945B S10 Table: Physico-chemical Properties (PCP) 3-mer results in non-vaccine proteins.(DOC) pcbi.1003973.s019.doc (93K) GUID:?15D6386C-AC3A-4089-A8ED-4E7A033DCBD3 (R,R)-Formoterol S11 Table: Physico-chemical Properties (PCP) 9-mer results in vaccine proteins.(DOC) pcbi.1003973.s020.doc (49K) GUID:?849B0CD4-36BB-4B52-A5A8-D55F3E105ED1 S12 Table: (R,R)-Formoterol Physico-chemical Properties (PCP) 9-mer results in non-vaccine proteins.(DOC) pcbi.1003973.s021.doc (110K) GUID:?7C8BA698-A3FD-4166-A28D-87C72BA17794 S13 Table: dN/dS by Physico-chemical House (PCP) site scanning results.(DOC) pcbi.1003973.s022.doc (114K) GUID:?19A0322F-5234-4AA0-B98D-E4794FFD1D78 S14 Table: Summary of analyses of predicted T (R,R)-Formoterol cell epitope sieve effects in vaccine proteins.(DOC) pcbi.1003973.s023.doc (74K) GUID:?19549392-0E45-4391-BE93-936F6435B772 S15 Table: Summary of analyses of predicted T cell epitope sieve effects in non-vaccine proteins.(DOC) pcbi.1003973.s024.doc (66K) GUID:?86D9F9C0-B971-4FDA-B7D4-18A9FD49938C S16 Table: Significant EscapeCount 9-mer and 15-mer results.(DOC) pcbi.1003973.s025.doc (42K) GUID:?0873DD07-1F75-423F-B058-7B0F543889BE S17 Table: Comparison of phylogenetic diversity (PD) between vaccine and placebo sequences.(DOC) pcbi.1003973.s026.doc (32K) GUID:?E5DF0D5D-5A2A-43B7-954B-1548F231B0E2 S18 Table: Comparison of phylogenetic divergence between vaccine and placebo sequences.(DOC) pcbi.1003973.s027.doc (34K) GUID:?1A712663-115E-4EEB-9FBA-A2F945E39781 (R,R)-Formoterol S1 Text: Sequence data construction and processing.(DOCX) pcbi.1003973.s028.docx (121K) GUID:?9AD67FFD-2B03-4BC4-9BC1-8B05D18E4BF8 S2 Text: The SmoothMarks method.(DOCX) pcbi.1003973.s029.docx (108K) GUID:?5E822CAE-4F28-4975-9379-2BF01C54C68F S3 Text: HLA-dependent covariation analysis.(DOCX) pcbi.1003973.s030.docx (125K) GUID:?5EA641C7-AABA-408A-AB81-753EA52B4A2F S4 Text: The EscapeCount method.(DOCX) pcbi.1003973.s031.docx (118K) GUID:?ABCF2718-B13F-4751-85E3-3AE80B944C7F S5 Text: The PercentEpitopeMismatch method.(DOCX) pcbi.1003973.s032.docx (95K) GUID:?0F8EA014-BE87-4C1B-9685-305BEB326513 S6 Text: The EpitopeDistance method.(DOCX) pcbi.1003973.s033.docx (110K) GUID:?EE6A0451-C665-47C2-A6C4-9EE8C85F172C S7 Text: Supplementary references.(DOCX) pcbi.1003973.s034.docx (48K) GUID:?71A8BD41-E970-45B1-886F-CD7A1000F473 S1 Dataset: Exhaustive site-scanning and kmer-scanning results table, in a .zip file.(ZIP) pcbi.1003973.s035.zip (1.4M) GUID:?5BEEBB5A-EA92-4734-BF11-2EA4FD343B38 S2 Dataset: HLA-dependent site covariation table, in a .zip file.(ZIP) pcbi.1003973.s036.zip (7.6K) GUID:?235530CA-F6C6-4067-BC8E-698AC3461609 S3 Dataset: Site masks and.