PGTools: A Software Suite for Proteogenomic Data Analysis and Visualization
| Autor: | Ramya A Mandyam, Scott Wood, Katia Nones, Anil K. Madugundu, Shivashankar H. Nagaraj, Nicola Waddell, Sean M. Grimmond, Alun Jones, John V. Pearson |
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| Rok vydání: | 2015 |
| Předmět: |
Proteomics
060102 Bioinformatics Proteome pseudogenes Biology computer.software_genre Biochemistry noncoding RNA Mass Spectrometry Open Reading Frames Cell Line Tumor Human proteome project cancer Chromosomes Human Humans automated workflows Shotgun proteomics Databases Protein Proteogenomics 060408 Genomics Software suite Sequence Analysis RNA Molecular Sequence Annotation General Chemistry mutated peptides RNA -seq Visualization Pancreatic Neoplasms Data mining Colorectal Neoplasms Transcriptome computer Software |
| Zdroj: | Journal of Proteome Research |
| ISSN: | 1535-3907 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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