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A GENE SIGNATURE FOR PREDICTING RADIATION EXPOSURE

A frequency-based gene selection method to identify robust biomarkers for radiation dose prediction

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Pages 267-276 | Received 13 Jan 2011, Accepted 26 Oct 2011, Published online: 10 Jan 2012

References

  • Abeel T, Helleputte T, Van de Peer Y, Dupont P, Saeys Y. 2010. Robust biomarker identification for cancer diagnosis with ensemble feature selection methods. Bioinformatics 26:392–398.
  • Aha DW, Kibler D, Albert MK. 1991. Instance-based learning algorithms. Machine Learning 6:37–66.
  • Al-Shahrour F, Diaz-Uriarte R, Dopazo J. 2004. FatiGO: A web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics 20:578–580.
  • Amundson SA, Do KT, Shahab S, Bittner M, Meltzer P, Trent J, Fornace AJ Jr. 2000. Identification of potential mRNA biomarkers in peripheral blood lymphocytes for human exposure to ionizing radiation. Radiation Research 154:342–346.
  • Amundson SA, Grace MB, McLeland CB, Epperly MW, Yeager A, Zhan Q, Greenberger JS, Fornace AJ Jr. 2004. Human in vivo radiation-induced biomarkers: Gene expression changes in radiotherapy patients. Cancer Research 64:6368–6371.
  • Amundson SA, Do KT, Vinikoor LC, Lee RA, Koch-Paiz CA, Ahn J, Reimers M, Chen Y, Scudiero DA, Weinstein JN, . 2008. Integrating global gene expression and radiation survival parameters across the 60 cell lines of the National Cancer Institute Anticancer Drug Screen. Cancer Research 68:415–424.
  • Baek S, Tsai CA, Chen JJ. 2009. Development of biomarker classifiers from high-dimensional data. Briefings in Bioinformatics 10: 537–546.
  • Blakely WF, Miller AC, Luo L, Lukas J, Hornby ZD, Hamel CJ, Nelson JT, Escalada NE, Prasanna PG. 2002. Nucleic acid molecular biomarkers for diagnostic biodosimetry applications: Use of the fluorogenic 5′-nuclease polymerase chain reaction assay. Military Medicine 167:16–19.
  • Bornstein C, Brosh R, Molchadsky A, Madar S, Kogan-Sakin I, Goldstein I, Chakravarti D, Flores ER, Goldfinger N, Sarig R, Rotter V. 2011. SPATA18, a spermatogenesis-associated gene, is a novel transcriptional target of p53 and p63. Molecular and Cellular Biology 31:1679–1689.
  • Brengues M, Paap B, Bittner M, Amundson S, Seligmann B, Korn R, Lenigk R, Zenhausern F. 2010. Biodosimetry on small blood volume using gene expression assay. Health Physics 98:179–185.
  • Chen JJ, Tsai CA, Tzeng S, Chen CH. 2007. Gene selection with multiple ordering criteria. BMC Bioinformatics 8:74.
  • Dennis G Jr, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA. 2003. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biology 4:P3.
  • Dressman HK, Muramoto GG, Chao NJ, Meadows S, Marshall D, Ginsburg GS, Nevins JR, Chute JP. 2007. Gene expression signatures that predict radiation exposure in mice and humans. Public Library of Science Medicine 4:e106.
  • Du R, Huang C, Bi Q, Zhai Y, Xia L, Liu J, Sun S, Fan D. 2010. URG11 mediates hypoxia-induced epithelial-to-mesenchymal transition by modulation of E-cadherin and beta-catenin. Biochemical and Biophysical Research Communications 391:135–141.
  • Ein-Dor L, Zuk O, Domany E. 2006. Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proceedings of the National Academy of Sciences of the USA 103: 5923–5928.
  • Etienne W, Meyer MH, Peppers J, Meyer RA Jr. 2004. Comparison of mRNA gene expression by RT-PCR and DNA microarray. Biotechniques 36:618–620,622,624–616.
  • Fan X, Shi L, Fang H, Cheng Y, Perkins R, Tong W. 2010. DNA microarrays are predictive of cancer prognosis: A re-evaluation. Clinical Cancer Research 16:629–636.
  • Fei P, El-Deiry WS. 2003. P53 and radiation responses. Oncogene 22:5774–5783.
  • Fisher RA. 1925. Statistical Methods for Research Workers. Edinburgh, UK: Oliver & Boyd.
  • Grace MB, McLeland CB, Blakely W. 2002. Real-time quantitative RT-PCR assay of GADD45 gene expression changes as a biomarker for radiation biodosimetry. International Journal of Radiation Biology 78:1011–1021.
  • Gruel G, Lucchesi C, Pawlik A, Frouin V, Alibert O, Kortulewski T, Zarour A, Jacquelin B, Gidrol X, Tronik-Le Roux D. 2006. Novel microarray-based method for estimating exposure to ionizing radiation. Radiation Research 166:746–756.
  • Huang DW, Sherman BT, Lempicki RA. 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols 4:44–57.
  • Kanda R. 2000. Improvement of accuracy of chromosome aberration analysis for biological radiation dosimetry. Journal of Radiation Research 41:1–8.
  • Kanehisa M, Goto S. 2000. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Research 28:27–30.
  • Kang CM, Park KP, Song JE, Jeoung DI, Cho CK, Kim TH, Bae S, Lee SJ, Lee YS. 2003. Possible biomarkers for ionizing radiation exposure in human peripheral blood lymphocytes. Radiation Research 159:312–319.
  • Kawase T, Ohki R, Shibata T, Tsutsumi S, Kamimura N, Inazawa J, Ohta T, Ichikawa H, Aburatani H, Tashiro F, . 2009. PH domain-only protein PHLDA3 is a p53-regulated repressor of Akt. Cell 136: 535–550.
  • Kis E, Szatmari T, Keszei M, Farkas R, Esik O, Lumniczky K, Falus A, Safrany G. 2006. Microarray analysis of radiation response genes in primary human fibroblasts. International Journal of Radiation Oncology, Biology, Physics 66:1506–1514.
  • Kondo K, Okuma K, Tanaka R, Matsuzaki G, Ansari AA, Tanaka Y. 2008. Rapid induction of OX40 ligand on primary T cells activated under DNA-damaging conditions. Human Immunology 69: 533–542.
  • Liu G, Chen X. 2002. The ferredoxin reductase gene is regulated by the p53 family and sensitizes cells to oxidative stress-induced apoptosis. Oncogene 21:7195–7204.
  • Marshall E. 2004. Getting the noise out of gene arrays. Science 306: 630–631.
  • Michiels S, Koscielny S, Hill C. 2005. Prediction of cancer outcome with microarrays: A multiple random validation strategy. The Lancet 365:488–492.
  • Paul S, Amundson SA. 2008. Development of gene expression signatures for practical radiation biodosimetry. International Journal of Radiation Oncology, Biology, Physics 71:1236–1244.
  • Pogosova-Agadjanyan EL, Fan W, Georges GE, Schwartz JL, Kepler CM, Lee H, Suchanek AL, Cronk MR, Brumbaugh A, Engel JH, Yukawa M, Zhao LP, Heimfeld S, Stirewalt DL. 2011. Identification of radiation-induced expression changes in nonimmortalized human T cells. Radiation Research 175:172–184.
  • Rockett JC, Hellmann GM. 2004. Confirming microarray data – is it really necessary? Genomics 83:541–549.
  • Roy L, Gruel G, Vaurijoux A. 2009. Cell response to ionising radiation analysed by gene expression patterns. Ann Ist Super Sanita 45: 272–277.
  • Simon SL, Bouville A, Kleinerman R. 2010. Current use and future needs of biodosimetry in studies of long-term health risk following radiation exposure. Health Physics 98:109–117.
  • Taylor JM, Ankerst DP, Andridge RR. 2008. Validation of biomarker-based risk prediction models. Clinical Cancer Research 14: 5977–5983.
  • Vogt J, Morgan NV, Marton T, Maxwell S, Harrison BJ, Beeson D, Maher ER. 2009. Germline mutation in DOK7 associated with fetal akinesia deformation sequence. Journal of Medical Genetics 46:338–340.
  • Wang Q, Chen Y, Xie F, Ge Y, Wang X, Zhang X. 2009. A novel agonist anti-human OX40L monoclonal antibody that stimulates T cell proliferation and enhances cytokine secretion. Hybridoma (Larchmt) 28:269–276.
  • Wright GW, Simon R. 2003. A random variance model for detection of differential gene expression in small microarray experiments. Bioinformatics 19:2448–2455.

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