QQ-plot (panel A) and GSEA plots (panel B) of the KEGG ABC transporter pathway.

<p>The QQ-plot is constructed using the genotyped SNPs whose snp-map contains at least one ABC transporter pathway gene. The GSEA plot shows the enrichment score of the ABC transporter pathway. The top portion of the plot shows the running enrichment score for the pathway genes as the analysis moves down the ranked list. The peak score is the enrichment score for the gene set. The bottom portion of the plot shows the value of the ranking metric as it moves down the list of ranked genes. The plots for the other two enriched pathways (Proteasome and Propanoate metabolism) look similar (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0131038#pone.0131038.s002" target="_blank">S2 Fig</a>).</p

The top REACTOME pathways enriched in differentially expressed genes from SJS/TEN active lesions and ranked by FDR (FDR<0.25).

<p>The enrichment score is computed by DAVID on the 200 DEGs from Chung et al. Abbreviations: #GENES (number of DEGs in the pathway), PV (p-value, Fisher Exact test), FE (Fold Enrichment), FDR (false discovery rate). A (*) next to a pathway name indicates that the pathway was found to be enriched by both Pointer and DAVID.</p><p>The top REACTOME pathways enriched in differentially expressed genes from SJS/TEN active lesions and ranked by FDR (FDR<0.25).</p

Enriched Reactome pathways ranked by FDR.

<p>In capital letters, pathways that contain KEGG proteasome genes.</p><p>Abbreviations: GSS (pathway gene set size); GLE (number of genes in leading edge); ES (Enrichment score), NES (Normalized Enrichment score), PV (p-value), FDR (false discovery rate), SD (p-value of shadow analysis against KEGG proteasome pathway)</p><p>Enriched Reactome pathways ranked by FDR.</p

Comparison of False Discovery Rates from the pathway analysis performed with three SNP-to-gene mapping strategies.

<p>Abbreviations: FDR1 (FDR from the pathway analysis performed using physical distance only), FDR2 (FDR from the pathway analysis performed using LD-reconstruction), FDR3 (FDR from the pathway analysis performed with Pointer).</p><p>Comparison of False Discovery Rates from the pathway analysis performed with three SNP-to-gene mapping strategies.</p

The top KEGG pathways enriched in differentially expressed genes from SJS/TEN active lesions and ranked by FDR (FDR<0.25).

<p>The enrichment score is computed by DAVID on the 200 DEGs from Chung et al. Abbreviations: #GENES (number of DEGs in the pathway), PV (p-value, Fisher Exact test), FE (Fold Enrichment), FDR (false discovery rate). A (*) next to a pathway name indicates that the pathway was found to be enriched by both Pointer and DAVID.</p><p>The top KEGG pathways enriched in differentially expressed genes from SJS/TEN active lesions and ranked by FDR (FDR<0.25).</p

The top enriched KEGG pathways for low risk genetic variants ranked by normalized enrichment score (NES).

<p>Abbreviations: #GSS (gene set size for the pathway); #GLE (number of pathway genes in GSEA leading edge); ES (enrichment score), NES (normalized enrichment score), PV (p-value of ES), FDR (false discovery rate).</p><p>The top enriched KEGG pathways for low risk genetic variants ranked by normalized enrichment score (NES).</p

Hierarchical clustering of expression profiles for genes in the KEGG proteasome pathway.

<p>The Hierarchical clustering analysis was performed on gene expression data from Chung et al., 2008. Individual gene-related signals are increased (red), unchanged (white), or decreased (blue). The analysis clearly separates cases (brown group) from controls (light blue group) and reveals the up-regulation of proteasome genes in the SJS/TEN lesions.</p

Key steps of the Pointer algorithm.

<p>Key steps of the Pointer algorithm.</p

Plot of power versus odds ratios, using 700 controls (initial analysis) and then >4000 controls.

<p>Plot of power versus odds ratios, using 700 controls (initial analysis) and then >4000 controls.</p

Manhattan Plot of logistic regression on Northwestern European cohort.

<p>Each dot represents a SNP. The x axis represents the position of the SNP on chromosome. The y axis represents the -log₁₀ of logistic regression P-value of the SNP in the case-control association study. rs2276314 and rs4799838 are marked in green with the P-value just below the genome-wide threshold (dashed line).</p