1,768
Views
10
CrossRef citations to date
0
Altmetric
Applications and Case Studies

Bayesian Hierarchical Varying-Sparsity Regression Models with Application to Cancer Proteogenomics

, ORCID Icon, , &
Pages 48-60 | Received 01 May 2017, Published online: 15 Aug 2018

References

  • Akbani, R., Ng, P. K. S., Werner, H. M., Shahmoradgoli, M., Zhang, F., Ju, Z., Liu, W., Yang, J.-Y., Yoshihara, K., Li, J. et al. (2014), “A Pan-Cancer Proteomic Perspective on the Cancer Genome Atlas,” Nature Communications, 5, 1–14.
  • Alfaro, J. A., Sinha, A., Kislinger, T., and Boutros, P. C. (2014), “Onco-Proteogenomics: Cancer Proteomics Joins Forces with Genomics,” Nature methods, 11, 1107–1113.
  • Anvekar, R. A., Asciolla, J. J., Missert, D. J., and Chipuk, J. E. (2011), “Born to be Alive: A Role for the BCL-2 Family in Melanoma Tumor Cell Survival, Apoptosis, and Treatment,” Frontiers in Oncology, 1, 1–14.
  • Banumathy, G., and Cairns, P. (2010), “Signaling Pathways in Renal Cell Carcinoma,” Cancer Biology & Therapy, 10, 658–664.
  • Barbieri, M. M., and Berger, J. O. (2004), “Optimal Predictive Model Selection,” The Annals of Statistics, 32, 870–897.
  • Cantley, L. C., and Neel, B. G. (1999), “New Insights Into Tumor Suppression: PTEN Suppresses Tumor Formation by Restraining the Phosphoinositide 3-Kinase/AKT Pathway,” Proceedings of the National Academy of Sciences, 96, 4240–4245.
  • Chang, W., Cheng, J., Allaire, J., Xie, Y., and McPherson, J. (2015), Shiny: Web Application Framework for R. R package version 0.12.2.
  • Chen, M., and Manley, J. L. (2009), “Mechanisms of Alternative Splicing Regulation: Insights from Molecular and Genomics Approaches,” Nature reviews Molecular Cell Biology, 10, 741–754.
  • Chintakuntlawar, A. V., Okuno, S. H., and Price, K. A. (2016), “Systemic Therapy for Recurrent or Metastatic Salivary Gland Malignancies,” Cancers of the Head & Neck, 1, 11.
  • Church, G. M. (2004), “Proteogenomic Mapping as a Complementary Method to Perform Genome Annotation,” Proteomics, 4, 59–77.
  • Dalin, M. G., Watson, P. A., Ho, A. L., and Morris, L. G. (2017), “Androgen Receptor Signaling in Salivary Gland Cancer,” Cancers, 9, 17.
  • Davies, M., Hennessy, B., and Mills, G. B. (2006), “Point Mutations of Protein Kinases and Individualised Cancer Therapy,” Expert Opinion on Pharmacotherapy, 7, 2243–2261.
  • De Bono, J., and Ashworth, A. (2010), “Translating Cancer Research into Targeted Therapeutics,” Nature, 467, 543–549.
  • Fan, J., Ma, Y., and Dai, W. (2014), “Nonparametric Independence Screening in Sparse Ultra-High-Dimensional Varying Coefficient Models,” Journal of the American Statistical Association, 109, 1270–1284.
  • Gygi, S. P., Rochon, Y., Franza, B. R., and Aebersold, R. (1999), “Correlation Between Protein and mRNA Abundance in Yeast,” Molecular and Cellular Biology, 19, 1720–1730.
  • Hartwell, L. H., Hopfield, J. J., Leibler, S., and Murray, A. W. (1999), “From Molecular to Modular Cell Biology,” Nature, 402, C47–C52.
  • Hastie, T., and Tibshirani, R. (1993), “Varying-Coefficient Models,” Journal of the Royal Statistical Society, Series B, 55, 757–796.
  • Heppner, G. H., and Miller, B. E. (1983), “Tumor Heterogeneity: Biological Implications and Therapeutic Consequences,” Cancer and Metastasis Reviews, 2, 5–23.
  • Jacob, F., Goldstein, D. R., Fink, D., and Heinzelmann-Schwarz, V. (2009), “Proteogenomic Studies in Epithelial Ovarian Cancer: Established Knowledge and Future Needs,” Biomarkers in Medicine, 3, 743–756.
  • Kitano, H. (2002), “Computational Systems Biology,” Nature, 420, 206–210.
  • Lee, C. T., Genega, E. M., Hutchinson, B., Fearn, P. A., Kattan, M. W., Russo, P., and Reuter, V. E. (2003), “Conventional (Clear Cell) Renal Carcinoma Metastases have Greater BCL-2 Expression Than High-Risk Primary Tumors,” in Urologic Oncology: Seminars and Original Investigations, volume 21, Elsevier, pp. 179–184.
  • Lessene, G., Czabotar, P. E., and Colman, P. M. (2008), “BCL-2 Family Antagonists for Cancer Therapy,” Nature Reviews Drug Discovery, 7, 989–1000.
  • Li, B., and Dewey, C. N. (2011), “RSEM: Accurate Transcript Quantification from RNA-Seq Data with or without a Reference Genome,” BMC Bioinformatics, 12, 323.
  • Li, J., Lu, Y., Akbani, R., Ju, Z., Roebuck, P. L., Liu, W., Yang, J.-Y., Broom, B. M., Verhaak, R. G., Kane, D. W. et al (2013), “Tcpa: A Resource for Cancer Functional Proteomics Data,” Nature Methods, 10, 1046–1047.
  • Lim, Y. C., Kang, H. J., Kim, Y. S., and Choi, E. C. (2012), “All-Trans-Retinoic Acid Inhibits Growth of Head and Neck Cancer Stem Cells by Suppression of wnt/β-Catenin Pathway,” European Journal of Cancer, 48, 3310–3318.
  • Lin, F., Zhang, P. L., Yang, X. J., Prichard, J. W., Lun, M., and Brown, R. E. (2006), “Morphoproteomic and Molecular Concomitants of an Overexpressed and Activated Mtor Pathway in Renal Cell Carcinomas,” Annals of Clinical & Laboratory Science, 36, 283–293.
  • Locard-Paulet, M., Pible, O., de Peredo, A. G., Alpha-Bazin, B., Almunia, C., Burlet-Schiltz, O., and Armengaud, J. (2016), “Clinical Implications of Recent Advances in Proteogenomics,” Expert Review of Proteomics, (just-accepted).
  • Longo, D. L. (2012), “Tumor Heterogeneity and Personalized Medicine,” N Engl J Med, 366, 956–957.
  • Margulis, V., Lin, J., Yang, H., Wang, W., Wood, C. G., and Wu, X. (2008), “Genetic Susceptibility to Renal Cell Carcinoma: The Role of DNA Double-Strand Break Repair Pathway,” Cancer Epidemiology Biomarkers & Prevention, 17, 2366–2373.
  • McLendon, R., Friedman, A., Bigner, D., Van Meir, E. G., Brat, D. J., Mastrogianakis, G. M., Olson, J. J., Mikkelsen, T., Lehman, N., Aldape, K. et al (2008), “Comprehensive Genomic Characterization Defines Human Glioblastoma Genes and Core Pathways,” Nature, 455, 1061–1068.
  • Nagalakshmi, U., Waern, K., and Snyder, M. (2010), “RNA-Seq: A Method for Comprehensive Transcriptome Analysis,” Current Protocols in Molecular Biology, 89, 4–11.
  • Nesvizhskii, A. I. (2014), “Proteogenomics: Concepts, Applications and Computational Strategies,” Nature Methods, 11, 1114–1125.
  • Omberg, L., Ellrott, K., Yuan, Y., Kandoth, C., Wong, C., Kellen, M. R., Friend, S. H., Stuart, J., Liang, H., and Margolin, A. A. (2013), “Enabling Transparent and Collaborative Computational Analysis of 12 Tumor Types within the Cancer Genome Atlas,” Nature Genetics, 45, 1121–1126.
  • Paweletz, C. P., Charboneau, L., Bichsel, V. E., Simone, N. L., Chen, T., Gillespie, J. W., Emmert-Buck, M. R., Roth, M. J., Petricoin, E., and Liotta, L. A. (2001), “Reverse Phase Protein Microarrays Which Capture Disease Progression Show Activation of Pro-survival Pathways at the Cancer Invasion Front,” Oncogene, 20, 1981–1989.
  • Pinto, N., Black, M., Patel, K., Yoo, J., Mymryk, J. S., Barrett, J. W., and Nichols, A. C. (2014), “Genomically Driven Precision Medicine to Improve Outcomes in Anaplastic Thyroid Cancer,” Journal of Oncology, 2014.
  • Rades, D., Seibold, N., Schild, S., Gebhard, M., and Noack, F. (2013), “Androgen Receptor Expression,” Strahlentherapie und Onkologie, 189, 849–855.
  • Ruppert, D., Wand, M. P., and Carroll, R. J. (2003), Semiparametric Regression, Number 12, Cambridge, UK: Cambridge University Press.
  • Scheipl, F., Fahrmeir, L., and Kneib, T. (2012), “Spike-and-Slab Priors for Function Selection in Structured Additive Regression Models,” Journal of the American Statistical Association, 107, 1518–1532.
  • Scott, J. G., and Berger, J. O. (2010), “Bayes and Empirical-Bayes Multiplicity Adjustment in the Variable-Selection Problem,” The Annals of Statistics, 38, 2587–2619.
  • Soper, M. S., Iganej, S., and Thompson, L. D. (2014), “Definitive Treatment of Androgen Receptor–Positive Salivary Duct Carcinoma with Androgen Deprivation Therapy and External Beam Radiotherapy,” Head & Neck, 36, E4–E7.
  • Squarize, C. H., Castilho, R. M., Abrahao, A. C., Molinolo, A., Lingen, M. W., and Gutkind, J. S. (2013), “PTEN Deficiency Contributes to the Development and Progression of Head and Neck Cancer,” Neoplasia, 15, 461–471.
  • TCGA (2012), “Comprehensive Genomic Characterization of Squamous Cell Lung Cancers,” Nature, 489, 519–525.
  • ——— (2013), “Comprehensive Molecular Characterization of Clear Cell Renal Cell Carcinoma,” Nature, 499, 43–49.
  • Thorstenson, Y. R., Roxas, A., Kroiss, R., Jenkins, M. A., Kristine, M. Y., Bachrich, T., Muhr, D., Wayne, T. L., Chu, G., Davis, R. W. et al (2003), “Contributions of ATM Mutations to Familial Breast and Ovarian Cancer,” Cancer Research, 63, 3325–3333.
  • Tibes, R., Qiu, Y., Lu, Y., Hennessy, B., Andreeff, M., Mills, G. B., and Kornblau, S. M. (2006), “Reverse Phase Protein Array: Validation of a Novel Proteomic Technology and Utility for Analysis of Primary Leukemia Specimens and Hematopoietic Stem Cells,” Molecular Cancer Therapeutics, 5, 2512–2521.
  • Wang, H., Zhang, P., Lin, C., Yu, Q., Wu, J., Wang, L., Cui, Y., Wang, K., Gao, Z., and Li, H. (2015), “Relevance and Therapeutic Possibility of PTEN-Long in Renal Cell Carcinoma,” PloS One, 10, e114250.
  • Wang, K., Singh, D., Zeng, Z., Coleman, S. J., Huang, Y., Savich, G. L., He, X., Mieczkowski, P., Grimm, S. A., Perou, C. M. et al (2010), “Mapsplice: Accurate Mapping of RNA-Seq Reads for Splice Junction Discovery,” Nucleic Acids Research, 38, e178–e178.
  • Wang, L., Li, H., and Huang, J. Z. (2008a), “Variable Selection in Nonparametric Varying-Coefficient Models for Analysis of Repeated Measurements,” Journal of the American Statistical Association, 103, 1556–1569.
  • Wang, S., Nan, B., Zhu, J., and Beer, D. G. (2008b), “Doubly Penalized Buckley–James Method for Survival Data with High-Dimensional Covariates,” Biometrics, 64, 132–140.
  • Wang, Z., Gerstein, M., and Snyder, M. (2009), “RNA-Seq: A Revolutionary Tool for Transcriptomics,” Nature Reviews Genetics, 10, 57–63.
  • Weinstein, J. N., Collisson, E. A., Mills, G. B., Shaw, K. R. M., Ozenberger, B. A., Ellrott, K., Shmulevich, I., Sander, C., Stuart, J. M., Network, C. G. A. R. et al (2013), “The Cancer Genome Atlas Pan-Cancer Analysis Project,” Nature Genetics, 45, 1113–1120.
  • Yang, F., Zeng, Q., Yu, G., Li, S., and Wang, C.-Y. (2006), “Wnt/β-Catenin Signaling Inhibits Death Receptor-Mediated Apoptosis and Promotes Invasive Growth of hnscc,” Cellular Signalling, 18, 679–687.
  • Zhu, Y., Qiu, P., and Ji, Y. (2014), “TCGA-Assembler: Open-Source Software for Retrieving and Processing TCGA Data,” Nature Methods, 11, 599–600.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.