Additional file 1 of XCAVATOR: accurate detection and genotyping of copy number variants from second and third generation whole-genome sequencing experiments

Supplemental PDF file containing Figures S1-S15. (PDF 1540 kb

Xome-Blender work flow.

<p>Panel A shows how InXalizer works. Firstly, it calculates the input coverage, next it checks the parameters defined by the user (number of subclones, number of somatic variants and the presence or absence of target file.) and generates the subclones according to the selected subclonal architecture. Finally, if desired, it produces a CNA file. Panel B shows the Xome-Blender work flow. Firstly, it checks the parameters compatibility, next, according to the percentages defined by the user it generates subsamples of the BAM files produced by InXalizer, finally, it adds the CNA (if CNA file is provided) and merges the BAM files in the final product.</p

Harmonic mean of precision and recall (<i>F</i>-measure) as a function of coverage, contamination and CNA size.

<p>Panels A-C contains the insertions data and B-D deletions data. The circular barplots in panels A-B represent the <i>F</i>-score for detecting CNA of different size (1Mb, 5Mb and 10Mb) at different coverage values. The background color represent the method.</p

Cancer simulation tools.

<p>Cancer simulation tools.</p

Xome-Blender evaluation.

<p>The box plot a reports the variance of the ratio between the subsample and the full-sample coverage for each different percentage. Panel B, displays the distribution of mean coverage value in the full-sample and in four different subsamples. Each data point is averaged across ten synthetic replicates. Panels C,D and E represent the Expected vs. Synthetic AF for SNVs, insertions and deletions respectively. The violin plots report the distribution of synthetic AF for bins of expected AF averaged across four coverage values (50×, 100×, 150× and 200×). The outer graphs show the distribution of the AF deviation (difference between synthetic and expected AF) averaged across the three pairs. R represent the Pearson correlation coefficient. Legend colors are referred to the average coverage of the analyzed data. Panel F represnts Expected vs. Synthtetic <i>log</i>₂-ratio.</p

Additional file 1 of SLMSuite: a suite of algorithms for segmenting genomic profiles

Supplementary figures. The pdf file contains Figures S1-S3. (PDF 86.9 kb

Prediction results for Saccharomyces cerevisiae and Arabidopsis thaliana.

<p>Pie charts report the distributions of the cellular component (a, d), biological process (b, e) and molecular function (c, f) terms predicted by the WNP algorithm. The results for Saccharomyces cerevisiae are shown in panels a, b and c. The results for Arabidopsis thaliana are reported in panels d, e and f.</p

Summary of the prediction results obtained by WNP on the PFNs of Saccharomyces cerevisiae and Arabidopsis thaliana.

<p><i>Predicted</i> indicates the total number of GPs predicted by WPN. <i>Annotated</i> indicates the total number of GPs annotated by YGD and TAIR in the last N months for Saccharomyces cerevisiae (SC) and Arabidopsis thaliana (AT) respectively (N = 18 for Saccharomyces and N = 8 for Arabidopsis). <i>Matched</i> is the number of GPs annotated in the last N months that WNP correctly predicts.</p

Comparison between function prediction algorithms for Arabidopsis thaliana.

<p>Six algorithms (WPN, SA, FF, WA, PC and CHI-Square) are compared with leave-a-percent-out criterion (see Section “Algorithm Comparison” in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038767#pone.0038767.s012" target="_blank">Text S1</a> for more details). For each algorithm the area under the ROC curve (AUC) and the SR vs. FD curves are averaged across all the leave-a-percent-out simulations we performed (5%, 10%, 15% and 20% of the annotated proteins cleared). The results are reported for the three categories of the GO database: cellular component (a, d), biological process (b, e) and molecular function (c, f).</p

Genotype distribution and minor allele frequency of the 4 <i>LPA</i> single nucleotide polymorphisms (SNPs) investigated.

<p>Genotype distribution and minor allele frequency of the 4 <i>LPA</i> single nucleotide polymorphisms (SNPs) investigated.</p