Estimated effect (odds ratio and 95% CI) from individual SNPs of 23 steroid hormone metabolisms and signalling-related genes on the occurrence of breast cancer in patients.

a<p>Data collected from literature <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037018#pone.0037018-Pharoah1" target="_blank">[14]</a>.</p>b<p>Data highlighted in bold text are statistically significant results.</p>c<p>All the [Ch/position], i.e., [Chromosome no./Chromosome position], information is based on “Assembly GRCh37”.</p>d<p>The contig information is shown in SNP no. (contig accession no.) as follows: SNP 1–2 (NT_011519.10); SNPs 3 (NT_010194.17); SNPs 4–15 (NT_025741.15); SNPs 16–19 (NT_033899.8); SNPs 20–22 (NT_010718.16); SNPs 23 (NT_167197.1).</p>e<p>Values with <i>p</i> value<0.05 are highlighted in bold fonts.</p

Results of the position of the true CpG island and the positions of the detected CpG islands using the PSO-based methods and ClusterPSO.

<p>The search regions for PSO-based methods are also shown to illustrate the difficulty in finding the optimal CpG island. True positive, false positive, false negative and true negative outcomes are clearly shown for comparison between the six methods.</p

Boxplots displaying the extremes, the upper and lower quartiles, and the median of the maximum difference between cases and controls for (A) the IPSO algorithm and (B) the PSO algorithm on three to ten combined SNPs over 20 runs.

<p>The boundary of the box closest to zero indicates the 25th percentile, a line within the box marks the median, and the boundary of the box farthest from zero indicates the 75th percentile. Error bars above and below the boxes indicate the 90th and 10th percentiles, respectively. The triangle symbols indicate the 95th and 5th percentiles.</p

Pseudo-code for randomly generated data.

<p>Pseudo-code for randomly generated data.</p

Population initialization using conservation of the best 5 results.

<p>Population initialization using conservation of the best 5 results.</p

The best estimated protective SNP combinations on the occurrence of breast cancer as determined by IPSO.

*<p>The SNP combinations on the occurrence of breast cancer are significantly different (<i>p value</i><0.05). Sen.; Sensitivity; Spe., specificity; PPV, positive predictive value; NPV, negative predictive value. The meanings of the SNP and genotype numbers are provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037018#pone-0037018-t003" target="_blank">Table 3</a>. For example, barcode SNPs (4-19)-genotype (1-1) is [rs3020314-CC]-[rs500760-AA]; SNPs (4, 19, 23) with genotype 1-1-2; [rs3020314-CC]-[rs500760-AA]-[rs2017591-TC].</p

IPSO pseudo-code.

<p>IPSO pseudo-code.</p

The maximum difference between cases and controls for PSO and IPSO on the best barcodes containing two to ten SNPs.

<p>The maximum difference between cases and controls for PSO and IPSO on the best barcodes containing two to ten SNPs.</p

ClusterPSO Flowchart.

<p>ClusterPSO Flowchart.</p

Comparison of CPU time and search efficiency amongst six methods for the six contig sequences.

<p>The CPU times for PSO, CPSO, PSORL, CPSORL and ClusterPSO are shown to assess relative search efficiency in the six contig sequences. The horizontal axis represents the implementation time, and the vertical axis represents the log₁₀ value for the presently-detected position in the sequence. Arrows a and c show that the CpGcluster step handles long sequences, hence sequence scanning may proceed more slowly at first than in other methods. Arrows a, b and c show that the CpGcluster step detects very few CpG island candidates in the region.</p