Additional file 3: Figure S2. of A biologically informed method for detecting rare variant associations

Wilcoxon type I error per biological feature. QQ plots for the type I error Wilcoxon Rank Sum analysis showing the p-value distribution from the average gene (a), XL gene (b), and pathway (c) simulations. The different colors represent various BioBin weighting schemes analyzed. (PNG 147 kb

Additional file 1: of A biologically informed method for detecting rare variant associations

Script for generating reference sequence. Python script used to generate a reference sequence file for input into SeqSIMLA2 simulation software. The allele frequency file used in the script was obtained by parsing the protein coding regions of the autosomes in the 1000 Genomes Project VCF file. Additional specifications include the number of reference samples to generate and the number of markers to include in the reference file. (DOCX 14 kb

Additional file 2: Figure S1. of A biologically informed method for detecting rare variant associations

Logistic regression type I error per biological feature. QQ plots for the type I error logistic regression analysis showing the p-value distribution from the average gene (a), XL gene (b), and pathway (c) simulations. The different colors represent various BioBin weighting schemes analyzed. (PNG 170 kb

Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries-3

<p><b>Copyright information:</b></p><p>Taken from "Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries"</p><p>http://www.immunome-research.com/content/4/1/2</p><p>Immunome Research 2008;4():2-2.</p><p>Published online 25 Jan 2008</p><p>PMCID:PMC2248166.</p><p></p>tides. Binding assays were performed as described in the materials and methods for peptides previously [47] utilized to compare various publicly available prediction tools. Peptides were scored using the matrix as described in the text

Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries-0

<p><b>Copyright information:</b></p><p>Taken from "Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries"</p><p>http://www.immunome-research.com/content/4/1/2</p><p>Immunome Research 2008;4():2-2.</p><p>Published online 25 Jan 2008</p><p>PMCID:PMC2248166.</p><p></p>tides. Binding assays were performed as described in the materials and methods for peptides previously [47] utilized to compare various publicly available prediction tools. Peptides were scored using the matrix as described in the text

Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries-1

<p><b>Copyright information:</b></p><p>Taken from "Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries"</p><p>http://www.immunome-research.com/content/4/1/2</p><p>Immunome Research 2008;4():2-2.</p><p>Published online 25 Jan 2008</p><p>PMCID:PMC2248166.</p><p></p>g specificity factors (SF), as secondary anchor positions (green shading) were determined on the basis of standard deviation (SD), as described in the text

Additional file 1: Table S1. of Identifying gene-gene interactions that are highly associated with Body Mass Index using Quantitative Multifactor Dimensionality Reduction (QMDR)

Information for cohorts providing individual level data. Information regarding the geographic location, and numbers of individuals included from each cohort. (PDF 40 kb

Additional file 6:Â Additional Acknowledgements. of Identifying gene-gene interactions that are highly associated with Body Mass Index using Quantitative Multifactor Dimensionality Reduction (QMDR)

Acknowledgements and detailed descriptions of the five studies that provided the data for the analyses in this paper. (PDF 68 kb

Additional file 4: Table S3. of Identifying gene-gene interactions that are highly associated with Body Mass Index using Quantitative Multifactor Dimensionality Reduction (QMDR)

Details of LD expanded models. Number of LD-expanded (proxy) SNP-SNP models generated for each original discovered SNP-SNP model. (XLSX 34 kb

Effects of abacavir and acyclovir on HLA-B*57:01 binding specificity.

<p>Specific peptides with a terminal isoleucine that showed an increased affinity for HLA-B*57:01 in the presence of abacavir were tested. Values are represented as geometric mean with 95% CI of two independent runs in triplicates, analyzed for statistical significance by Mann-Whitney U test comparing log IC₅₀ values vs. vehicle; p < 0.05 was considered significant (*p < 0.05; **p < 0.01; ***p < 0.001).</p