Additional file 2 of VB-MK-LMF: fusion of drugs, targets and interactions using variational Bayesian multiple kernel logistic matrix factorization

Derivation of the lower bound using Jaakkola’s bound on the logistic sigmoid. (PDF 107 kb

Additional file 2 of VariantMetaCaller: automated fusion of variant calling pipelines for quantitative, precision-based filtering

Variant annotations used as features for SVMs. The full listing and short description of the variant annotations used as features for Support Vector Machines

Additional file 1 of VariantMetaCaller: automated fusion of variant calling pipelines for quantitative, precision-based filtering

Supplementary results, figures and tables. Supplementary results, Figures S1–S11 and Tables S1–S6

List of polymorphisms investigated in this study.

1<p>Position according to NCBI Genome Build 36.0;</p>2<p>Function according to the UCSC Genome Browser <a href="http://genome.ucsc.edu/(Accessed" target="_blank">http://genome.ucsc.edu/(Accessed</a>: 2013 Jun 20.);</p>3<p>RFC = SLC19A1;</p>4<p>SLCO1B1 = SLC21A6.</p

Probability of strong relevance of the most relevant variables in different sample groups according to the BN-BMLA.

<p>Probability of strong relevance of the most relevant variables in different sample groups according to the BN-BMLA.</p

Credible intervals (95%) corresponding to the Bayesian odds ratios of MTHFD1 rs1076991 and MTRR rs3776455.

<p>CR: credible interval, a Bayesian analogue of the confidence interval, 95% CR-U and CR-L: upper and lower thresholds of the 95% credible interval.</p

Redundancies and interactions according to the BN-BMLA method.

<p>The figure shows the magnitude of redundancies (blue curved lines) and interactions (red curved lines) between the variables in the overall (i.e. ALL susceptibility, A panel), in the B-cell lineage (B panel), in the T-cell lineage (C panel) and in the hyperdiploid patient group (D panel) according to the BN-BMLA method. The width of the curved lines is proportional to the strength of the effect. The a posteriori probability of the strong relevance of the variables is proportional to the length of the dark red columns next to the variable in the inner gray colored ring. The corresponding genes and chromosomes of the SNPs are shown on the outer ring.</p

Characteristics of cases and controls.

<p>Characteristics of cases and controls.</p

Summary of the significant results of the frequentist-based statistical analyses.

a<p>HD: Hyperdiploid ALL;</p>b<p>p-values in bold reached the p≤1.21E-03;</p><p>FDR(α) = 5.0% significant threshold.</p

Illustration of different dependency relations between relevant SNPs and hyperdiploid ALL susceptibility.

<p>Top panel: An interactional map including hyperdiploid ALL susceptibility (red node) and strongly relevant SNPs with respect to it (other nodes). The width of the edges is proportional to their a posteriori probability. The directed edges represent only probabilistic relationships between the variables which are not necessary causal. Bottom panel: The posterior probability of strong relevance (blue columns), edge (direct strong relevance, red columns), pure interaction (green columns) and association (purple columns) of the variables to hyperdiploid ALL susceptibility according to the BN-BMLA method.</p