PGTools: A Software Suite for Proteogenomic Data Analysis and Visualization
Shivashankar H Nagaraj, Nicola Waddell, Anil K Madugundu, Scott Wood, Alun Jones, Ramya A Mandyam, Katia Nones, John V Pearson, Sean M Grimnnond
JOURNAL OF PROTEOME RESEARCH | AMER CHEMICAL SOC | Published : 2015
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 ..View full abstract
We would like to thank Deborah Gwynne for support at the Queensland Centre for Medical Genomics. This work is supported by the University of Queensland Postdoctoral fellowship and QIMR SEED Grant. A.K.M. is a recipient of a BINC Fellowship from Department of Biotechnology (DBT), Government of India. We thank Dhirendra Kumar and Amit Kumar Yadav for their inputs during the development of the software.