title: PGTools: A Software Suite for Proteogenomic Data Analysis and Visualization.
abstract: We describe PGTools, an open source software suite for analysis and visualization of proteogenomic data. PGTools comprises applications, libraries, customized databases, and visualization tools for analysis of mass-spectrometry data using combined proteomic and genomic backgrounds. A single command is sufficient to search databases, calculate false discovery rates, group and annotate proteins, generate peptide databases from RNA-Seq transcripts, identify altered proteins associated with cancer, and visualize genome scale peptide data sets using sophisticated visualization tools. We experimentally confirm a subset of proteogenomic peptides in human PANC-1 cells and demonstrate the utility of PGTools using a colorectal cancer data set that led to the identification of 203 novel protein coding regions missed by conventional proteomic approaches. PGTools should be equally useful for individual proteogenomic investigations as well as international initiatives such as chromosome-centric Human Proteome Project (C-HPP). PGTools is available at http://qcmg.org/bioinformatics/PGTools.
authors.forename: Shivashankar H
authors.initials: SH
authors.lastname: Nagaraj
authors.forename: Nicola
authors.initials: N
authors.lastname: Waddell
authors.affiliation: ∥Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India.
authors.forename: Anil K
authors.initials: AK
authors.lastname: Madugundu
authors.forename: Scott
authors.initials: S
authors.lastname: Wood
authors.forename: Alun
authors.initials: A
authors.lastname: Jones
authors.forename: Ramya A
authors.initials: RA
authors.lastname: Mandyam
authors.forename: Katia
authors.initials: K
authors.lastname: Nones
authors.forename: John V
authors.initials: JV
authors.lastname: Pearson
authors.affiliation: §Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, Scotland G61 1BD, United Kingdom.
authors.forename: Sean M
authors.initials: SM
authors.lastname: Grimmond
mesh_terms: D045744:Cell Line, Tumor; D002877:Chromosomes, Human / Q000737:chemistry*; D015179:Colorectal Neoplasms / Q000235:genetics*; D030562:Databases, Protein; D006801:Humans; D013058:Mass Spectrometry; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames; D010190:Pancreatic Neoplasms / Q000235:genetics*; D020543:Proteome / Q000235:genetics; D040901:Proteomics / Q000379:methods / Q000706:statistics & numerical data*; D017423:Sequence Analysis, RNA; D012984:Software; D059467:Transcriptome
chemical_list: D020543:Proteome
keywords: RNA-seq; automated workflows; cancer; mass spectrometry; mutated peptides; noncoding RNA; proteogenomics; pseudogenes