Table 2 Significantly overrepresented biological processes associated with sequence variants contributing stop_gained events in the PC3 and LNCaP prostate cancer cell lines
GO TermGenesFisher’s Exact P
PC3 private sequence variants
 Detection of bacteriumHLA-DRB1, HLA-A, HLA-DRB5, HLA-B5.1E−10
 Antigen processing and presentationHLA-DRB1, HLA-A, HLA-DRB5, HLA-B2.4E−07
 Interferon-γ-mediated signaling pathwayHLA-DRB1, HLA-A, HLA-DRB5, HLA-B6.7E−07
 Immune responseHLA-DRB1, HLA-A, HLA-DRB5, HLA-B, IL1A4.7E−05
 Antigen processing and presentation of endogenous peptide  antigen via MHC class I via ER pathway, TAP-independentHLA-A, HLA-B2.9E−06
 Regulation of interleukin-10 secretionHLA-DRB1, HLA-DRB52.9E−06
 Regulation of interleukin-4 productionHLA-DRB1, HLA-DRB55.8E−06
 Protection from natural killer cell mediated cytotoxicityHLA-A, HLA-B9.6E−06
 Immunoglobulin production involved in immunoglobulin  mediated immune responseHLA-DRB1, HLA-DRB59.6E−06
 Humoral immune response mediated by circulating immunoglobulinHLA-DRB1, HLA-DRB52E−05
 Antigen processing and presentation of exogenous peptide antigen via  MHC class I, TAP-independentHLA-A, HLA-B3.5E−05
 T-helper 1-type immune responseHLA-DRB1, HLA-DRB56.3E−05
 Positive regulation of T cell mediated cytotoxicityHLA-A, HLA-B7.5E−05
 Inflammatory response to antigenic stimulusHLA-DRB1, HLA-DRB50.0001
 Antigen processing and presentation of peptide or polysaccharide  antigen via MHC class IIHLA-DRB1, HLA-DRB50.00013
 Negative regulation of interferon-γ productionHLA-DRB1, HLA-DRB50.00036
 Positive regulation of insulin secretion involved in cellular  response to glucose stimulusHLA-DRB1, HLA-DRB50.00039
 Antigen processing and presentation of peptide antigen via MHC class IHLA-A, HLA-B0.00041
 Negative regulation of T cell proliferationHLA-DRB1, HLA-DRB50.00063
 Protein tetramerizationHLA-DRB1, HLA-DRB50.00074
 Antigen processing and presentation of exogenous peptide antigen via  MHC class I, TAP-dependentHLA-A, HLA-B0.0018
 Type I interferon signaling pathwayHLA-A, HLA-B0.0019
 T cell costimulationHLA-DRB1, HLA-DRB50.0028
 Antigen processing and presentation of exogenous peptide antigen via  MHC class IIHLA-DRB1, HLA-DRB50.0038
 Protein deubiquitinationUSP17L18, USP17L110.0044
LNCaP private sequence variants
 Bundle of His cell to Purkinje myocyte communicationGPR155, GNAS, CBR3, CHL10.00012
 Response to nitrosative stressPRKCQ, CD3E, NLRP30.00068
 CognitionFPGT-TNNI3K, TNNI3K0.0008
 Interleukin-1 β productionMEN1, NTRK3, PAX6, PRKDC0.0011
 Positive regulation of interleukin-4 productionLAMA2, PRKCQ, ROBO1, PAX6, SPTBN1, CHL10.0012
 Humoral immune response mediated by circulating immunoglobulinGCLC, DUSP60.0023
 Type B pancreatic cell differentiationNTRK3, AP1B1, FREM2, ROBO1, PRKDC, TBC1D320.004
 Negative regulation of protein phosphorylationLRP1, STAB1, VTN, SSC4D, AMN, DMBT10.0042
 Axon guidanceNLRP3, CASP10.0076
 Heart developmentLAMA2, FREM2, ROBO1, STAB1, ITGB4, VTN, CERCAM, COL16A1, CHL1, AOC30.014
 Receptor-mediated endocytosisEXO1, HLA-DQB10.016
 Cell adhesionMEN1, PAX60.027
Shared sequence variants (PC3 and LNCaP)
 Sensory perception of tasteTAS2R43, TAS2R310.00048
 Detection of chemical stimulus involved in sensory  perception of bitter tasteTAS2R43, TAS2R310.00092
O-glycan processingMUC3A, MUC60.0021
 DigestionPRSS2, PRSS10.0023
 Extracellular matrix disassemblyPRSS2, PRSS10.0033
  • Stop_gained events are denoted changes predicted to confer nonsense mutations and result in nonfunctional proteins or proteins with reduced function. Gene enrichment analysis was performed using DAVID (Database for Annotation, Visualization and Integrated Discovery). MHC, major histocompatibility complex; ER, endoplasmic reticulum; TAP, transporter associated with antigen processing.