RESEARCH ARTICLE Differentially Expressed Genes and Signature Pathways of Human Prostate Cancer Jennifer S. Myers1, Ariana K. von Lersner1, Charles J. Robbins1, Qing-Xiang Amy Sang1,2* 1 Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida, United States of America, 2 Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, United States of America *
[email protected] Abstract Genomic technologies including microarrays and next-generation sequencing have enabled the generation of molecular signatures of prostate cancer. Lists of differentially expressed genes between malignant and non-malignant states are thought to be fertile sources of putative prostate cancer biomarkers. However such lists of differentially ex- OPEN ACCESS pressed genes can be highly variable for multiple reasons. As such, looking at differential Citation: Myers JS, von Lersner AK, Robbins CJ, expression in the context of gene sets and pathways has been more robust. Using next- Sang Q-XA (2015) Differentially Expressed Genes generation genome sequencing data from The Cancer Genome Atlas, differential gene and Signature Pathways of Human Prostate Cancer. expression between age- and stage- matched human prostate tumors and non-malignant PLoS ONE 10(12): e0145322. doi:10.1371/journal. pone.0145322 samples was assessed and used to craft a pathway signature of prostate cancer. Up- and down-regulated genes were assigned to pathways composed of curated groups of related Editor: Jian Cao, Stony Brook University, UNITED STATES genes from multiple databases. The significance of these pathways was then evaluated according to the number of differentially expressed genes found in the pathway and their Received: October 14, 2015 position within the pathway using Gene Set Enrichment Analysis and Signaling Pathway Accepted: December 2, 2015 Impact Analysis.