Simplified and Unified Access to Cancer Proteogenomic Data.

Comprehensive cancer data sets recently generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) offer great potential for advancing our understanding of how to combat cancer. These data sets include DNA, RNA, protein, and clinical characterization for tumor and normal samples from large cohorts of many different cancer types. The raw data are publicly available at various Cancer Research Data Commons. However, widespread reuse of these data sets is also facilitated by easy access to the processed quantitative data tables. We have created a data application programming interface (API) to distribute these processed tables, implemented as a Python package called cptac. We implement it such that users who prefer to work in R can easily use our package for data access and then transfer the data into R for analysis. Our package distributes the finalized processed CPTAC data sets in a consistent, up-to-date format. This consistency makes it easy to integrate the data with common graphing, statistical, and machine-learning packages for advanced analysis. Additionally, consistent formatting across all cancer types promotes the investigation of pan-cancer trends. The data API structure of directly streaming data within a programming environment enhances the reproducibility. Finally, with the accompanying tutorials, this package provides a novel resource for cancer research education. View the software documentation at https://paynelab.github.io/cptac/. View the GitHub repository at https://github.com/PayneLab/cptac.

Genomic and Proteomic Analysis of Six Vi01-like Phages Reveals Wide Host Range and Multiple Tail Spike Proteins.

Enterobacteriaceae is a large family of Gram-negative bacteria composed of many pathogens, including Salmonella and Shigella. Here, we characterize six bacteriophages that infect Enterobacteriaceae, which were isolated from wastewater plants in the Wasatch front (Utah, United States). These phages are highly similar to the Kuttervirus vB_SenM_Vi01 (Vi01), which was isolated using wastewater from Kiel, Germany. The phages vary little in genome size and are between 157 kb and 164 kb, which is consistent with the sizes of other phages in the Vi01-like phage family. These six phages were characterized through genomic and proteomic comparison, mass spectrometry, and both laboratory and clinical host range studies. While their proteomes are largely unstudied, mass spectrometry analysis confirmed the production of five hypothetical proteins, several of which unveiled a potential operon that suggests a ferritin-mediated entry system on the Vi01-like phage family tail. However, no dependence on this pathway was observed for the single host tested herein. While unable to infect every genus of Enterobacteriaceae tested, these phages are extraordinarily broad ranged, with several demonstrating the ability to infect Salmonella enterica and Citrobacter freundii strains with generally high efficiency, as well as several clinical Salmonella enterica isolates, most likely due to their multiple tail fibers.

Complete Genome Sequences of Five SO-1-Like Siphoviridae Bacteriophages That Infect Enterobacteriales.

The Enterobacteriales order is composed of Gram-negative bacteria that range from harmless symbionts to well-studied pathogens. We announce complete genome sequences of five related SO-1-like Enterobacteriales bacteriophages (also known as the Dhillonvirus genus) isolated from wastewater that infect Escherichia coli (Opt-212, Over9000, Pubbukkers, and Teewinot) or Shigella boydii (StarDew).