Additional file 2: of The impact of pharmacokinetic gene profiles across human cancers

Table S1. This data file contains the full list of TCGA cases for which the TEM identified a potentially relevant interaction between PK gene expression levels and at least one administered therapy. (XLSX 41 kb

Additional file 1: of The impact of pharmacokinetic gene profiles across human cancers

PK gene profiles across human cancers. This file contains additional text and figures that support the analyses presented in the main text. (DOCX 1543 kb

Files for validation of beta diversity using 16S rDNA regions V6 to V9

Synthetic mock datasets (100 replicates) used for validation of beta diversity across synthetic communities using 16S rDNA region V6 to V9. File also includes scripts and resulting raw data for the validation

Files for validation of beta diversity using 16S rDNA regions V3 to V5

Synthetic mock datasets (100 replicates) used for validation of beta diversity across synthetic communities using 16S rDNA region V3 to V5. File also includes scripts and resulting raw data for the validation

Files for taxonomy comparison

Synthetic mock dataset used for taxonomy assignment comparison, across multiple read lengths. File includes scripts used and raw validation data

Files for validation with realistic synthetic reads

Synthetic mock datasets used for validation based on a realistic human stool microbiome dataset. These are NOT real bacterial reads. Those reads are available as example data from the IM-TORNADO pipeline. File includes scripts and raw validation data

Comparison of alignment tools.

<p>Plot of Gamma Log Likelihoods of 100 trees created from paired reads selected from the Greengenes 13_–5 database, and aligned using PyNAST and Infernal version 1.1. Likelihoods in the trees created using Infernal are significantly better than the trees created with PyNAST (<i>p</i><0.0001, Wilcoxon signed ranked test), strongly suggesting that Infernal produces better quality alignments than PyNAST for the same input reads.</p

Files for taxonomy comparison using reads with errors

Synthetic mock datasets (100 replicates) used for validation of taxonomy using reads with errors and different length. File also includes scripts and resulting raw data for the validation

Files for comparison of sequence aligners

Synthetic mock datasets used to compare the mulitple sequence aligners cmalign (from the infernal package) versus the NAST algorithm (from the PyNAST implementation). File includes R scripts and resulting raw validation data

Comparison of phylogenetic trees between libraries.

<p>Plot of a Mantel correlation test comparing cophenetic distance matrices calculated from phylogenetic trees created using paired, R1 and R2 (for both the V3–V5 and V6–V9 primer pairs) versus the distance matrix created from the corresponding full-length 16S trees. A higher correlation value means the trees are more closely related to the full-length trees. Here, the paired trees are significantly closer to the full-length trees than the R1 and R2 trees (<i>p</i><0.0001, Wilcoxon signed ranked test, using 100 synthetic mock communities), strongly suggesting that combining the use of paired reads leads to phylogenies closer to what is obtained from full-length reads, even when the chosen primers create non-overlapping reads.</p