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BioMed Research International
Volume 2016, Article ID 8642703, 21 pages
http://dx.doi.org/10.1155/2016/8642703
Research Article

Candidate SNP Markers of Chronopathologies Are Predicted by a Significant Change in the Affinity of TATA-Binding Protein for Human Gene Promoters

1Children’s Hospital Los Angeles, University of Southern California, Los Angeles, CA 90027, USA
2Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
3Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia

Received 4 March 2016; Revised 25 June 2016; Accepted 28 June 2016

Academic Editor: Rituraj Purohit

Copyright © 2016 Petr Ponomarenko et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. R. Zhang, N. F. Lahens, H. I. Ballance, M. E. Hughes, and J. B. Hogenesch, “A circadian gene expression atlas in mammals: implications for biology and medicine,” Proceedings of the National Academy of Sciences of the United States of America, vol. 111, no. 45, pp. 16219–16224, 2014. View at Publisher · View at Google Scholar · View at Scopus
  2. S. M. Reppert and D. R. Weaver, “Molecular analysis of mammalian circadian rhythms,” Annual Review of Physiology, vol. 63, pp. 647–676, 2001. View at Publisher · View at Google Scholar · View at Scopus
  3. S. A. Brown, E. Kowalska, and R. Dallmann, “(Re)inventing the circadian feedback loop,” Developmental Cell, vol. 22, no. 3, pp. 477–487, 2012. View at Publisher · View at Google Scholar · View at Scopus
  4. J. K. Kim and D. B. Forger, “A mechanism for robust circadian timekeeping via stoichiometric balance,” Molecular Systems Biology, vol. 8, no. 1, article 630, 2012. View at Publisher · View at Google Scholar · View at Scopus
  5. L. Chen and G. Yang, “PPARs integrate the mammalian clock and energy metabolism,” PPAR Research, vol. 2014, Article ID 653017, 6 pages, 2014. View at Publisher · View at Google Scholar · View at Scopus
  6. K. Padmanabhan, M. S. Robles, T. Westerling, and C. J. Weitz, “Feedback regulation of transcriptional termination by the mammalian circadian clock PERIOD complex,” Science, vol. 337, no. 6094, pp. 599–602, 2012. View at Publisher · View at Google Scholar · View at Scopus
  7. K. Eckel-Mahan and P. Sassone-Corsi, “Epigenetic regulation of the molecular clockwork,” Progress in Molecular Biology and Translational Science, vol. 119, pp. 29–50, 2013. View at Publisher · View at Google Scholar · View at Scopus
  8. K. Bozek, A. Relógio, S. M. Kielbasa et al., “Regulation of clock-controlled genes in mammals,” PLoS ONE, vol. 4, no. 3, Article ID e4882, 2009. View at Publisher · View at Google Scholar · View at Scopus
  9. K. Bozek, A. L. Rosahl, S. Gaub, S. Lorenzen, and H. Herzel, “Circadian transcription in liver,” BioSystems, vol. 102, no. 1, pp. 61–69, 2010. View at Publisher · View at Google Scholar · View at Scopus
  10. J. S. Menet, S. Pescatore, and M. Rosbash, “CLOCK: BMAL1 is a pioneer-like transcription factor,” Genes and Development, vol. 28, no. 1, pp. 8–13, 2014. View at Publisher · View at Google Scholar · View at Scopus
  11. J. Wang, Y. Luo, K. Wang et al., “Clock-controlled StAR's expression and corticosterone production contribute to the endotoxemia immune response,” Chronobiology International, vol. 32, no. 3, pp. 358–367, 2015. View at Publisher · View at Google Scholar · View at Scopus
  12. P. Marckmann, B. Sandström, and J. Jespersen, “Dietary effects on circadian fluctuation in human blood coagulation factor VII and fibrinolysis,” Atherosclerosis, vol. 101, no. 2, pp. 225–234, 1993. View at Publisher · View at Google Scholar · View at Scopus
  13. S. Ohdo, K. Inoue, E. Yukawa, S. Higuchi, S. Nakano, and N. Ogawa, “Chronotoxicity of methotrexate in mice and its relation to circadian rhythm of DNA synthesis and pharmacokinetics,” Japanese Journal of Pharmacology, vol. 75, no. 3, pp. 283–290, 1997. View at Publisher · View at Google Scholar · View at Scopus
  14. V. Y. Gorbacheva, R. V. Kondratov, R. Zhang et al., “Circadian sensitivity to the chemotherapeutic agent cyclophosphamide depends on the functional status of the CLOCK/BMAL1 transactivation complex,” Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 9, pp. 3407–3412, 2005. View at Publisher · View at Google Scholar · View at Scopus
  15. C. H. Ko and J. S. Takahashi, “Molecular components of the mammalian circadian clock,” Human Molecular Genetics, vol. 15, no. 2, pp. R271–R277, 2006. View at Publisher · View at Google Scholar · View at Scopus
  16. S. Sahar and P. Sassone-Corsi, “Regulation of metabolism: the circadian clock dictates the time,” Trends in Endocrinology and Metabolism, vol. 23, no. 1, pp. 1–8, 2012. View at Publisher · View at Google Scholar · View at Scopus
  17. N. M. Kettner, C. A. Katchy, and L. Fu, “Circadian gene variants in cancer,” Annals of Medicine, vol. 46, no. 4, pp. 208–220, 2014. View at Publisher · View at Google Scholar · View at Scopus
  18. O. A. Podkolodnaya, “Molecular and genetic aspects of interactions of the circadian clock and the energy-producing substrate metabolism in mammals,” Russian Journal of Genetics, vol. 50, no. 2, pp. 111–122, 2014. View at Publisher · View at Google Scholar · View at Scopus
  19. G. V. Vasiliev, V. M. Merkulov, V. F. Kobzev, T. I. Merkulova, M. P. Ponomarenko, and N. A. Kolchanov, “Point mutations within 663-666 bp of intron 6 of the human TDO2 gene, associated with a number of psychiatric disorders, damage the YY-1 transcription factor binding site,” FEBS Letters, vol. 462, no. 1-2, pp. 85–88, 1999. View at Publisher · View at Google Scholar · View at Scopus
  20. J. V. Ponomarenko, T. I. Merkulova, G. V. Vasiliev et al., “rSNP_Guide, a database system for analysis of transcription factor binding to target sequences: application to SNPs and site-directed mutations,” Nucleic Acids Research, vol. 29, no. 1, pp. 312–316, 2001. View at Publisher · View at Google Scholar
  21. J. V. Ponomarenko, G. V. Orlova, T. I. Merkulova et al., “rSNP_Guide: an integrated database-tools system for studying SNPs and site-directed mutations in transcription factor binding sites,” Human Mutation, vol. 20, no. 4, pp. 239–248, 2002. View at Publisher · View at Google Scholar · View at Scopus
  22. J. V. Ponomarenko, T. I. Merkulova, G. V. Orlova et al., “rSNP Guide, a database system for analysis of transcription factor binding to DNA with variations: application to genome annotation,” Nucleic Acids Research, vol. 31, no. 1, pp. 118–121, 2003. View at Publisher · View at Google Scholar · View at Scopus
  23. O. Delaneau, J. Marchini, and 1000 Genomes Project Consortium, “Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel,” Nature Communications, vol. 5, article 3934, 2014. View at Google Scholar
  24. S. T. Sherry, M.-H. Ward, M. Kholodov et al., “DbSNP: the NCBI database of genetic variation,” Nucleic Acids Research, vol. 29, no. 1, pp. 308–311, 2001. View at Publisher · View at Google Scholar · View at Scopus
  25. M. Haeussler, B. J. Raney, A. S. Hinrichs et al., “Navigating protected genomics data with UCSC Genome Browser in a box,” Bioinformatics, vol. 31, no. 5, pp. 764–766, 2015. View at Publisher · View at Google Scholar · View at Scopus
  26. D. R. Zerbino, S. P. Wilder, N. Johnson, T. Juettemann, and P. R. Flicek, “The ensembl regulatory build,” Genome Biology, vol. 16, no. 1, article 56, 2015. View at Publisher · View at Google Scholar · View at Scopus
  27. A. Abbas, M. Lechevrel, and F. Sichel, “Identification of new single nucleotid polymorphisms (SNP) in alcohol dehydrogenase class IV ADH7 gene within a French population,” Archives of Toxicology, vol. 80, no. 4, pp. 201–205, 2006. View at Publisher · View at Google Scholar · View at Scopus
  28. J. S. Amberger, C. A. Bocchini, F. Schiettecatte, A. F. Scott, and A. Hamosh, “OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders,” Nucleic Acids Research, vol. 43, no. 1, pp. D789–D798, 2015. View at Publisher · View at Google Scholar · View at Scopus
  29. H. Mitsuyasu, K. Izuhara, X. Q. Mao et al., “Ile50Val variant of IL4R alpha upregulates IgE synthesis and associates with atopic asthma,” Nature Genetics, vol. 19, no. 2, pp. 119–120, 1998. View at Publisher · View at Google Scholar · View at Scopus
  30. V. Rajendran, “Structural analysis of oncogenic mutation of isocitrate dehydrogenase 1,” Molecular BioSystems, vol. 12, no. 7, pp. 2276–2287, 2016. View at Publisher · View at Google Scholar
  31. M. Lopus, D. M. Paul, and R. Rajasekaran, “Unraveling the deleterious effects of cancer-driven stk11 mutants through conformational sampling approach,” Cancer Informatics, vol. 15, pp. 35–44, 2016. View at Publisher · View at Google Scholar
  32. D. Meshach Paul and R. Rajasekaran, “Exploration of structural and functional variations owing to point mutations in α-NAGA,” Interdisciplinary Sciences: Computational Life Sciences, 2016. View at Publisher · View at Google Scholar
  33. V. Rajendran and R. Sethumadhavan, “Drug resistance mechanism of PncA in Mycobacterium tuberculosis,” Journal of Biomolecular Structure and Dynamics, vol. 32, no. 2, pp. 209–221, 2014. View at Publisher · View at Google Scholar · View at Scopus
  34. B. Senthilkumar and R. Rajasekaran, “Analysis of the structural stability among cyclotide members through cystine knot fold that underpins its potential use as a drug scaffold,” International Journal of Peptide Research and Therapeutics, pp. 1–11, 2016. View at Publisher · View at Google Scholar
  35. M. Ponomarenko, D. Rasskazov, O. Arkova et al., “How to use SNP_TATA_comparator to find a significant change in gene expression caused by the regulatory SNP of this gene's promoter via a change in affinity of the TATA-binding protein for this promoter,” BioMed Research International, vol. 2015, Article ID 359835, 17 pages, 2015. View at Publisher · View at Google Scholar · View at Scopus
  36. L. K. Savinkova, M. P. Ponomarenko, P. M. Ponomarenko et al., “TATA box polymorphisms in human gene promoters and associated hereditary pathologies,” Biochemistry, vol. 74, no. 2, pp. 117–129, 2009. View at Publisher · View at Google Scholar · View at Scopus
  37. M. Ponomarenko, V. Mironova, K. Gunbin, and L. Savinkova, “Hogness box,” in Brenner's Encyclopedia of Genetics, S. Maloy and K. Hughes, Eds., vol. 3, pp. 491–494, Academic Press, Elsevier Inc, San Diego, Calif, USA, 2nd edition, 2013. View at Google Scholar
  38. O. V. Arkova, M. P. Ponomarenko, D. A. Rasskazov et al., “Obesity-related known and candidate SNP markers can significantly change affinity of TATA-binding protein for human gene promoters,” BMC Genomics, vol. 16, supplement 13, article S5, 2015. View at Publisher · View at Google Scholar
  39. M. P. Ponomarenko, O. Arkova, D. Rasskazov, P. Ponomarenko, L. Savinkova, and N. Kolchanov, “Candidate SNP markers of gender-biased autoimmune complications of monogenic diseases are predicted by a significant change in the affinity of TATA-binding protein for human gene promoters,” Frontiers in Immunology, vol. 7, article 130, 2016. View at Publisher · View at Google Scholar
  40. I. I. Turnaev, D. A. Rasskazov, O. V. Arkova et al., “Hypothetical SNP markers that significantly affect the affinity of the TATA-binding protein to VEGFA, ERBB2, IGF1R, FLT1, KDR, and MET oncogene promoters as chemotherapy targets,” Molecular Biology, vol. 50, no. 1, pp. 141–152, 2016. View at Publisher · View at Google Scholar
  41. G. M. Trovato, “Sustainable medical research by effective and comprehensive medical skills: overcoming the frontiers by predictive, preventive and personalized medicine,” EPMA Journal, vol. 5, no. 1, article 14, 2014. View at Publisher · View at Google Scholar · View at Scopus
  42. R. M. Bannerman, L. M. Garrick, P. Rusnak-Smalley, J. E. Hoke, and J. A. Edwards, “Hemoglobin deficit: an inherited hypochromic anemia in the mouse,” Proceedings of the Society for Experimental Biology and Medicine, vol. 182, no. 1, pp. 52–57, 1986. View at Publisher · View at Google Scholar · View at Scopus
  43. E. L. Unger, C. J. Earley, and J. L. Beard, “Diurnal cycle influences peripheral and brain iron levels in mice,” Journal of Applied Physiology, vol. 106, no. 1, pp. 187–193, 2009. View at Publisher · View at Google Scholar · View at Scopus
  44. A.-H. Sun, Z.-M. Wang, S.-Z. Xiao, Z.-J. Li, J.-Y. Li, and L.-S. Kong, “Red cell basic ferritin concentration in sensorineural hearing loss,” ORL Journal for Oto-Rhino-Laryngology and Its Related Specialties, vol. 53, no. 5, pp. 270–272, 1991. View at Publisher · View at Google Scholar · View at Scopus
  45. R. P. Allen, S. Auerbach, H. Bahrain, M. Auerbach, and C. J. Earley, “The prevalence and impact of restless legs syndrome on patients with iron deficiency anemia,” American Journal of Hematology, vol. 88, no. 4, pp. 261–264, 2013. View at Publisher · View at Google Scholar · View at Scopus
  46. S. Verma, R. Gupta, M. Kudesia, A. Mathur, G. Krishan, and S. Singh, “Coexisting iron deficiency anemia and Beta thalassemia trait: effect of iron therapy on red cell parameters and hemoglobin subtypes,” ISRN Hematology, vol. 2014, Article ID 293216, 5 pages, 2014. View at Publisher · View at Google Scholar
  47. D. Thio, V. Prasad, P. Anslow, and P. Lennox, “Marrow proliferation as a cause of hearing loss in beta-thalassaemia major,” The Journal of Laryngology and Otology, vol. 122, no. 11, pp. 1253–1256, 2008. View at Publisher · View at Google Scholar · View at Scopus
  48. M. Manetti, L. Ibba-Manneschi, C. Fatini et al., “Association of a functional polymorphism in the matrix metalloproteinase-12 promoter region with systemic sclerosis in an Italian population,” Journal of Rheumatology, vol. 37, no. 9, pp. 1852–1857, 2010. View at Publisher · View at Google Scholar · View at Scopus
  49. N. L. Starodubtseva, V. V. Sobolev, A. G. Soboleva, A. A. Nikolaev, and S. A. Bruskin, “Genes expression of metalloproteinases (MMP-1, MMP-2, MMP-9, and MMP-12) associated with psoriasis,” Russian Journal of Genetics, vol. 47, no. 9, pp. 1117–1123, 2011. View at Publisher · View at Google Scholar · View at Scopus
  50. G. M. Hunninghake, M. H. Cho, Y. Tesfaigzi et al., “MMP12, lung function, and COPD in high-risk populations,” The New England Journal of Medicine, vol. 361, no. 27, pp. 2599–2608, 2009. View at Publisher · View at Google Scholar · View at Scopus
  51. H. J. Durrington, S. N. Farrow, A. S. Loudon, and D. W. Ray, “The circadian clock and asthma,” Thorax, vol. 69, no. 1, pp. 90–92, 2014. View at Publisher · View at Google Scholar · View at Scopus
  52. E. M. El-Omar, M. Carrington, W.-H. Chow et al., “Interleukin-1 polymorphisms associated with increased risk of gastric cancer,” Nature, vol. 404, no. 6776, pp. 398–402, 2000. View at Publisher · View at Google Scholar · View at Scopus
  53. Y. Wang, N. Kato, Y. Hoshida et al., “Interleukin-1β gene polymorphisms associated with hepatocellular carcinoma in hepatitis C virus infection,” Hepatology, vol. 37, no. 1, pp. 65–71, 2003. View at Publisher · View at Google Scholar · View at Scopus
  54. K.-S. Wu, X. Zhou, F. Zheng, X.-Q. Xu, Y.-H. Lin, and J. Yang, “Influence of interleukin-1 beta genetic polymorphism, smoking and alcohol drinking on the risk of non-small cell lung cancer,” Clinica Chimica Acta, vol. 411, no. 19-20, pp. 1441–1446, 2010. View at Publisher · View at Google Scholar · View at Scopus
  55. D. N. Martínez-Carrillo, E. Garza-González, R. Betancourt-Linares et al., “Association of IL1B -511C/-31T haplotype and Helicobacter pylori vacA genotypes with gastric ulcer and chronic gastritis,” BMC Gastroenterology, vol. 10, article 126, 2010. View at Publisher · View at Google Scholar · View at Scopus
  56. F. Hayashi, M. Watanabe, T. Nanba, N. Inoue, T. Akamizu, and Y. Iwatani, “Association of the -31C/T functional polymorphism in the interleukin-1β gene with the intractability of Graves' disease and the proportion of T helper type 17 cells,” Clinical and Experimental Immunology, vol. 158, no. 3, pp. 281–286, 2009. View at Publisher · View at Google Scholar · View at Scopus
  57. L. Strandberg, D. Mellström, Ö. Ljunggren et al., “IL6 and IL1B polymorphisms are associated with fat mass in older men: The MrOS Study Sweden,” Obesity, vol. 16, no. 3, pp. 710–713, 2008. View at Publisher · View at Google Scholar · View at Scopus
  58. P. Borkowska, K. Kucia, S. Rzezniczek et al., “Interleukin-1beta promoter (-31T/C and -511C/T) polymorphisms in major recurrent depression,” Journal of Molecular Neuroscience, vol. 44, no. 1, pp. 12–16, 2011. View at Publisher · View at Google Scholar · View at Scopus
  59. C. Ávila Moraes, T. Cambras, A. Diez-Noguera et al., “A new chronobiological approach to discriminate between acute and chronic depression using peripheral temperature, rest-activity, and light exposure parameters,” BMC Psychiatry, vol. 13, article 77, 2013. View at Publisher · View at Google Scholar · View at Scopus
  60. O. Pivovarova, K. Jürchott, N. Rudovich et al., “Changes of dietary fat and carbohydrate content alter central and peripheral clock in humans,” Journal of Clinical Endocrinology and Metabolism, vol. 100, no. 6, pp. 2291–2302, 2015. View at Publisher · View at Google Scholar · View at Scopus
  61. C. J. Carter, “Multiple genes and factors associated with bipolar disorder converge on growth factor and stress activated kinase pathways controlling translation initiation: implications for oligodendrocyte viability,” Neurochemistry International, vol. 50, no. 3, pp. 461–490, 2007. View at Publisher · View at Google Scholar · View at Scopus
  62. H. Yamazaki, M. Takeoka, M. Kitazawa et al., “ASC plays a role in the priming phase of the immune response to type II collagen in collagen-induced arthritis,” Rheumatology International, vol. 32, no. 6, pp. 1625–1632, 2012. View at Publisher · View at Google Scholar · View at Scopus
  63. I. C. Chikanza, P. Petrou, G. Kingsley, G. Chrousos, and G. S. Panayi, “Defective hypothalamic response to immune and inflammatory stimuli in patients with rheumatoid arthritis,” Arthritis and Rheumatism, vol. 35, no. 11, pp. 1281–1288, 1992. View at Publisher · View at Google Scholar · View at Scopus
  64. E. Arnaud, V. Barbalat, V. Nicaud et al., “Polymorphisms in the 5′ regulatory region of the tissue factor gene and the risk of myocardial infarction and venous thromboembolism: the ECTIM and PATHROS studies,” Arteriosclerosis, Thrombosis, and Vascular Biology, vol. 20, no. 3, pp. 892–898, 2000. View at Publisher · View at Google Scholar
  65. E. Haus, “Chronobiology of hemostasis and inferences for the chronotherapy of coagulation disorders and thrombosis prevention,” Advanced Drug Delivery Reviews, vol. 59, no. 9-10, pp. 966–984, 2007. View at Publisher · View at Google Scholar · View at Scopus
  66. K. Oishi, S. Koyanagi, and N. Ohkura, “Circadian mRNA expression of coagulation and fibrinolytic factors is organ-dependently disrupted in aged mice,” Experimental Gerontology, vol. 46, no. 12, pp. 994–999, 2011. View at Publisher · View at Google Scholar · View at Scopus
  67. A. Kavlie, L. Hiltunen, V. Rasi, and H. P. B. Prydz, “Two novel mutations in the human coagulation factor VII promoter,” Thrombosis and Haemostasis, vol. 90, no. 2, pp. 194–205, 2003. View at Google Scholar · View at Scopus
  68. I. Colognesi, V. Pasquali, A. Foà et al., “Temporal variations of coagulation factor VII activity in mice are influenced by lighting regime,” Chronobiology International, vol. 24, no. 2, pp. 305–313, 2007. View at Publisher · View at Google Scholar · View at Scopus
  69. J. Carvalho De Sousa, E. Bruckert, P. Giral et al., “Coagulation factor VII and plasma triglycerides. Decreased catabolism as a possible mechanism of factor VII hyperactivity,” Haemostasis, vol. 19, no. 3, pp. 125–130, 1989. View at Google Scholar · View at Scopus
  70. P. Marckmann, B. Sandström, and J. Jespersen, “Dietary effects on circadian fluctuation in human blood coagulation factor VII and fibrinolysis,” Atherosclerosis, vol. 101, no. 2, pp. 225–234, 1993. View at Publisher · View at Google Scholar · View at Scopus
  71. I. A. Clark, K. A. Rockett, and D. Burgner, “Genes, nitric oxide and malaria in African children,” Trends in Parasitology, vol. 19, no. 8, pp. 335–337, 2003. View at Publisher · View at Google Scholar · View at Scopus
  72. J. A. González-Martínez, G. Möddel, Z. Ying, R. A. Prayson, W. E. Bingaman, and I. M. Najm, “Neuronal nitric oxide synthase expression in resected epileptic dysplastic neocortex,” Journal of Neurosurgery, vol. 110, no. 2, pp. 343–349, 2009. View at Publisher · View at Google Scholar · View at Scopus
  73. W. A. Hofstra and A. W. de Weerd, “The circadian rhythm and its interaction with human epilepsy: a review of literature,” Sleep Medicine Reviews, vol. 13, no. 6, pp. 413–420, 2009. View at Publisher · View at Google Scholar · View at Scopus
  74. B. Kaya, S. Ünal, A. B. Karabulut, and Y. Türköz, “Altered diurnal variation of nitric oxide production in patients with panic disorder,” Tohoku Journal of Experimental Medicine, vol. 204, no. 2, pp. 147–154, 2004. View at Publisher · View at Google Scholar · View at Scopus
  75. F. Al-Shakfa, S. Dulucq, I. Brukner et al., “DNA variants in region for noncoding interfering transcript of Dihydrofolate reductase gene and outcome in childhood acute lymphoblastic leukemia,” Clinical Cancer Research, vol. 15, no. 22, pp. 6931–6938, 2009. View at Publisher · View at Google Scholar · View at Scopus
  76. A. J. Casal, V. J. P. Sinclair, A. M. Capponi, J. Nicod, U. Huynh-Do, and P. Ferrari, “A novel mutation in the steroidogenic acute regulatory protein gene promoter leading to reduced promoter activity,” Journal of Molecular Endocrinology, vol. 37, no. 1, pp. 71–80, 2006. View at Publisher · View at Google Scholar · View at Scopus
  77. W. Plengpanich, W. Le Goff, S. Poolsuk, Z. Julia, M. Guerin, and W. Khovidhunkit, “CETP deficiency due to a novel mutation in the CETP gene promoter and its effect on cholesterol efflux and selective uptake into hepatocytes,” Atherosclerosis, vol. 216, no. 2, pp. 370–373, 2011. View at Publisher · View at Google Scholar · View at Scopus
  78. K. Oka, L. M. Belalcazar, C. Dieker et al., “Sustained phenotypic correction in a mouse model of hypoalphalipoproteinemia with a helper-dependent adenovirus vector,” Gene Therapy, vol. 14, no. 3, pp. 191–202, 2007. View at Google Scholar
  79. S. Hirayama, S. Soda, Y. Ito et al., “Circadian change of serum concentration of small dense LDL-cholesterol in type 2 diabetic patients,” Clinica Chimica Acta, vol. 411, no. 3-4, pp. 253–257, 2010. View at Publisher · View at Google Scholar · View at Scopus
  80. C. Gabás-Rivera, R. Martínez-Beamonte, J. L. Ríos et al., “Dietary oleanolic acid mediates circadian clock gene expression in liver independently of diet and animal model but requires apolipoprotein A1,” Journal of Nutritional Biochemistry, vol. 24, no. 12, pp. 2100–2109, 2013. View at Publisher · View at Google Scholar · View at Scopus
  81. A. Matsunaga, J. Sasaki, H. Han et al., “Compound heterozygosity for an apolipoprotein A1 gene promoter mutation and a structural nonsense mutation with apolipoprotein A1 deficiency,” Arteriosclerosis, Thrombosis, and Vascular Biology, vol. 19, no. 2, pp. 348–355, 1999. View at Publisher · View at Google Scholar · View at Scopus
  82. J. Zukunft, T. Lang, T. Richter et al., “A natural CYP2B6 TATA box polymorphism (-82TC) leading to enhanced transcription and relocation of the transcriptional start site,” Molecular Pharmacology, vol. 67, no. 5, pp. 1772–1782, 2005. View at Publisher · View at Google Scholar · View at Scopus
  83. A. L. Mereness, Z. C. Murphy, and M. T. Sellix, “Developmental programming by androgen affects the circadian timing system in female mice1,” Biology of Reproduction, vol. 92, no. 4, article 88, 2015. View at Publisher · View at Google Scholar · View at Scopus
  84. S. Bianchi, R. Bigazzi, R. Nenci, and V. M. Campese, “Hyperinsulinemia, circadian variation of blood pressure and end-organ damage in hypertension,” Journal of Nephrology, vol. 10, no. 6, pp. 325–333, 1997. View at Google Scholar · View at Scopus
  85. D. E. Blask, R. T. Dauchy, E. M. Dauchy et al., “Light exposure at night disrupts host/cancer circadian regulatory dynamics: impact on the Warburg effect, lipid signaling and tumor growth prevention,” PLoS ONE, vol. 9, no. 8, Article ID e102776, 2014. View at Publisher · View at Google Scholar · View at Scopus
  86. G. A. Laughlin, C. E. Dominguez, and S. S. C. Yen, “Nutritional and endocrine-metabolic aberrations in women with functional hypothalamic amenorrhea,” Journal of Clinical Endocrinology and Metabolism, vol. 83, no. 1, pp. 25–32, 1998. View at Publisher · View at Google Scholar · View at Scopus
  87. A. M. Sieuwerts, M. Ansems, M. P. Look et al., “Clinical significance of the nuclear receptor co-regulator DC-SCRIPT in breast cancer: an independent retrospective validation study,” Breast Cancer Research, vol. 12, no. 6, article R103, 2010. View at Publisher · View at Google Scholar · View at Scopus
  88. S. Philips, A. Richter, S. Oesterreich et al., “Functional characterization of a genetic polymorphism in the promoter of the ESR2 gene,” Hormones and Cancer, vol. 3, no. 1-2, pp. 37–43, 2012. View at Publisher · View at Google Scholar · View at Scopus
  89. L. Binkhorst, J. S. L. Kloth, A. S. de Wit et al., “Circadian variation in tamoxifen pharmacokinetics in mice and breast cancer patients,” Breast Cancer Research and Treatment, vol. 152, no. 1, pp. 119–128, 2015. View at Publisher · View at Google Scholar · View at Scopus
  90. S. E. Royston, N. Yasui, A. G. Kondilis, S. V. Lord, J. A. Katzenellenbogen, and M. M. Mahoney, “ESR1 and ESR2 differentially regulate daily and circadian activity rhythms in female mice,” Endocrinology, vol. 155, no. 7, pp. 2613–2623, 2014. View at Publisher · View at Google Scholar · View at Scopus
  91. L. K. Savinkova, I. A. Drachkova, T. V. Arshinova, P. Ponomarenko, M. Ponomarenko, and N. Kolchanov, “An experimental verification of the predicted effects of promoter TATA-box polymorphisms associated with human diseases on interactions between the TATA boxes and TATA-binding protein,” PLoS ONE, vol. 8, no. 2, Article ID e54626, 2013. View at Publisher · View at Google Scholar · View at Scopus
  92. K. Oishi, N. Ohkura, N. Amagai, and N. Ishida, “Involvement of circadian clock gene Clock in diabetes-induced circadian augmentation of plasminogen activator inhibitor-1 (PAI-1) expression in the mouse heart,” FEBS Letters, vol. 579, no. 17, pp. 3555–3559, 2005. View at Publisher · View at Google Scholar · View at Scopus
  93. M. Elshazley, M. Sato, T. Hase et al., “The circadian clock gene BMAL1 is a novel therapeutic target for malignant pleural mesothelioma,” International Journal of Cancer, vol. 131, no. 12, pp. 2820–2831, 2012. View at Publisher · View at Google Scholar · View at Scopus
  94. C.-X. He, N. Prevot, C. Boitard, P. Avner, and U. C. Rogner, “Inhibition of type 1 diabetes by upregulation of the circadian rhythm-related aryl hydrocarbon receptor nuclear translocator-like 2,” Immunogenetics, vol. 62, no. 9, pp. 585–592, 2010. View at Publisher · View at Google Scholar · View at Scopus
  95. C.-X. He, P. Avner, C. Boitard, and U. C. Rogner, “Downregulation of the circadian rhythm related gene Arntl2 suppresses diabetes protection in Idd6 NOD.C3H congenic mice,” Clinical and Experimental Pharmacology and Physiology, vol. 37, no. 12, pp. 1154–1158, 2010. View at Publisher · View at Google Scholar · View at Scopus
  96. A. Hashiramoto, T. Yamane, K. Tsumiyama et al., “Mammalian clock gene Cryptochrome regulates arthritis via proinflammatory cytokine TNF-α,” The Journal of Immunology, vol. 184, no. 3, pp. 1560–1565, 2010. View at Publisher · View at Google Scholar · View at Scopus
  97. G. Savalli, W. Diao, S. Berger, M. Ronovsky, T. Partonen, and D. D. Pollak, “Anhedonic behavior in cryptochrome 2-deficient mice is paralleled by altered diurnal patterns of amygdala gene expression,” Amino Acids, vol. 47, no. 7, pp. 1367–1377, 2015. View at Publisher · View at Google Scholar · View at Scopus
  98. L. Fang, Z. Yang, J. Zhou et al., “Circadian clock gene CRY2 degradation is involved in chemoresistance of colorectal cancer,” Molecular Cancer Therapeutics, vol. 14, no. 6, pp. 1476–1487, 2015. View at Publisher · View at Google Scholar · View at Scopus
  99. H. Zhao, Z.-L. Zeng, J. Yang et al., “Prognostic relevance of Period1 (Per1) and Period2 (Per2) expression in human gastric cancer,” International Journal of Clinical and Experimental Pathology, vol. 7, no. 2, pp. 619–630, 2014. View at Google Scholar · View at Scopus
  100. Q. Cao, S. Gery, A. Dashti et al., “A role for the clock gene Per1 in prostate cancer,” Cancer Research, vol. 69, no. 19, pp. 7619–7625, 2009. View at Publisher · View at Google Scholar · View at Scopus
  101. S. Gery, N. Komatsu, L. Baldjyan, A. Yu, D. Koo, and H. P. Koeffler, “The circadian gene per1 plays an important role in cell growth and DNA damage control in human cancer cells,” Molecular Cell, vol. 22, no. 3, pp. 375–382, 2006. View at Publisher · View at Google Scholar · View at Scopus
  102. A. Jilg, S. Lesny, N. Peruzki et al., “Temporal dynamics of mouse hippocampal clock gene expression support memory processing,” Hippocampus, vol. 20, no. 3, pp. 377–388, 2010. View at Publisher · View at Google Scholar · View at Scopus
  103. T. Wang, P. Yang, Y. Zhan, L. Xia, Z. Hua, and J. Zhang, “Deletion of circadian gene Per1 alleviates acute ethanol-induced hepatotoxicity in mice,” Toxicology, vol. 314, no. 2-3, pp. 193–201, 2013. View at Publisher · View at Google Scholar · View at Scopus
  104. V. Mehraj, J. Textoris, C. Capo, D. Raoult, M. Leone, and J.-L. Mege, “Overexpression of the per2 gene in male patients with acute Q fever,” Journal of Infectious Diseases, vol. 206, no. 11, pp. 1768–1770, 2012. View at Publisher · View at Google Scholar · View at Scopus
  105. K. Miyazaki, M. Wakabayashi, Y. Hara, and N. Ishida, “Tumor growth suppression in vivo by overexpression of the circadian component, PER2,” Genes to Cells, vol. 15, no. 4, pp. 351–358, 2010. View at Publisher · View at Google Scholar · View at Scopus
  106. Y. Shi, J. Cao, J. Gao et al., “Retinoic acid-related orphan receptor-α is induced in the setting of DNA damage and promotes pulmonary emphysema,” American Journal of Respiratory and Critical Care Medicine, vol. 186, no. 5, pp. 412–419, 2012. View at Publisher · View at Google Scholar · View at Scopus
  107. M. Doulazmi, F. Frédéric, F. Capone, M. Becker-André, N. Delhaye-Bouchaud, and J. Mariani, “A comparative study of Purkinje cells in two RORα gene mutant mice: staggerer and RORα−/−,” Developmental Brain Research, vol. 127, no. 2, pp. 165–174, 2001. View at Publisher · View at Google Scholar · View at Scopus
  108. A. Hamzaoui, H. Maalmi, A. Berraies et al., “Transcriptional characteristics of CD4 T cells in young asthmatic children: RORC and FOXP3 axis,” Journal of Inflammation Research, vol. 4, pp. 139–146, 2011. View at Google Scholar
  109. K. Hamzaoui, A. Borhani Haghighi, I. B. Ghorbel, and H. Houman, “RORC and Foxp3 axis in cerebrospinal fluid of patients with Neuro-Behçet's Disease,” Journal of Neuroimmunology, vol. 233, no. 1-2, pp. 249–253, 2011. View at Publisher · View at Google Scholar · View at Scopus
  110. M. Toyoshima, H. L. Howie, M. Imakura et al., “Functional genomics identifies therapeutic targets for MYC-driven cancer,” Proceedings of the National Academy of Sciences of the United States of America, vol. 109, no. 24, pp. 9545–9550, 2012. View at Publisher · View at Google Scholar · View at Scopus
  111. N. Rodriguez, J. Yang, K. Hasselblatt et al., “Casein kinase I epsilon interacts with mitochondrial proteins for the growth and survival of human ovarian cancer cells,” EMBO Molecular Medicine, vol. 4, no. 9, pp. 952–963, 2012. View at Publisher · View at Google Scholar · View at Scopus
  112. M. Flajolet, G. He, M. Heiman, A. Lin, A. C. Nairn, and P. Greengard, “Regulation of Alzheimer's disease amyloid-β formation by casein kinase I,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 10, pp. 4159–4164, 2007. View at Publisher · View at Google Scholar · View at Scopus
  113. C. D. Bryant, C. C. Parker, L. Zhou et al., “Csnk1e is a genetic regulator of sensitivity to psychostimulants and opioids,” Neuropsychopharmacology, vol. 37, no. 4, pp. 1026–1035, 2012. View at Publisher · View at Google Scholar · View at Scopus
  114. M. C. Abba, H. Sun, K. A. Hawkins et al., “Breast cancer molecular signatures as determined by SAGE: correlation with lymph node status,” Molecular Cancer Research, vol. 5, no. 9, pp. 881–890, 2007. View at Publisher · View at Google Scholar · View at Scopus
  115. J. E. Stajich, D. Block, K. Boulez et al., “The Bioperl toolkit: perl modules for the life sciences,” Genome Research, vol. 12, no. 10, pp. 1611–1618, 2002. View at Publisher · View at Google Scholar · View at Scopus
  116. P. M. Ponomarenko, L. K. Savinkova, I. A. Drachkova et al., “A step-by-step model of TBP/TATA box binding allows predicting human hereditary diseases by single nucleotide polymorphism,” Doklady Biochemistry and Biophysics, vol. 419, no. 1, pp. 88–92, 2008. View at Publisher · View at Google Scholar · View at Scopus
  117. V. V. Mironova, N. A. Omelyanchuk, P. M. Ponomarenko, M. P. Ponomarenko, and N. A. Kolchanov, “Specific/nonspecific binding of TBP to promoter DNA of the auxin response factor genes in plants correlated with ARFs function on gene transcription (activator/repressor),” Doklady Biochemistry and Biophysics, vol. 433, no. 1, pp. 191–196, 2010. View at Publisher · View at Google Scholar · View at Scopus
  118. S. Hahn, S. Buratowski, P. A. Sharp, and L. Guarente, “Yeast TATA-binding protein TFIID binds to TATA elements with both consensus and nonconsensus DNA sequences,” Proceedings of the National Academy of Sciences of the United States of America, vol. 86, no. 15, pp. 5718–5722, 1989. View at Publisher · View at Google Scholar · View at Scopus
  119. M. P. Ponomarenko, J. V. Ponomarenko, A. S. Frolov et al., “Identification of sequence-dependent DNA features correlating to activity of DNA sites interacting with proteins,” Bioinformatics, vol. 15, no. 7-8, pp. 687–703, 1999. View at Publisher · View at Google Scholar · View at Scopus
  120. P. Bucher, “Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences,” Journal of Molecular Biology, vol. 212, no. 4, pp. 563–578, 1990. View at Publisher · View at Google Scholar · View at Scopus
  121. D. Flatters and R. Lavery, “Sequence-dependent dynamics of TATA-box binding sites,” Biophysical Journal, vol. 75, no. 1, pp. 372–381, 1998. View at Publisher · View at Google Scholar · View at Scopus
  122. M. P. Ponomarenko, L. K. Savinkova, Y. V. Ponomarenko, A. E. Kel', I. I. Titov, and N. A. Kolchanov, “Simulation of TATA box sequences in eukaryotes,” Molecular Biology, vol. 31, no. 4, pp. 616–622, 1997. View at Google Scholar · View at Scopus
  123. IUPAC-IUB Commission on Biochemical Nomenclature (CBN), “Abbreviations and symbols for nucleic acids, polynucleotides and their constituents,” Journal of Molecular Biology, vol. 55, no. 3, pp. 299–310, 1971. View at Publisher · View at Google Scholar
  124. A. J. Waardenberg, S. D. Basset, R. Bouveret, and R. P. Harvey, “CompGO: an R package for comparing and visualizing Gene Ontology enrichment differences between DNA binding experiments,” BMC Bioinformatics, vol. 16, no. 1, article 275, 2015. View at Publisher · View at Google Scholar · View at Scopus
  125. I. Mogno, F. Vallania, R. D. Mitra, and B. A. Cohen, “TATA is a modular component of synthetic promoters,” Genome Research, vol. 20, no. 10, pp. 1391–1397, 2010. View at Publisher · View at Google Scholar · View at Scopus
  126. I. Missala, U. Kassner, and E. Steinhagen-Thiessen, “A systematic literature review of the association of lipoprotein(a) and autoimmune diseases and atherosclerosis,” International Journal of Rheumatology, vol. 2012, Article ID 480784, 10 pages, 2012. View at Publisher · View at Google Scholar · View at Scopus
  127. G. R. Abecasis, A. Auton, L. D. Brooks et al., “An integrated map of genetic variation from 1,092 human genomes,” Nature, vol. 491, no. 7422, pp. 56–65, 2012. View at Google Scholar
  128. M. Kasowski, F. Grubert, C. Heffelfinger et al., “Variation in transcription factor binding among humans,” Science, vol. 328, no. 5975, pp. 232–235, 2010. View at Publisher · View at Google Scholar · View at Scopus
  129. I. Ioshikhes, E. N. Trifonov, and M. Q. Zhang, “Periodical distribution of transcription factor sites in promoter regions and connection with chromatin structure,” Proceedings of the National Academy of Sciences of the United States of America, vol. 96, no. 6, pp. 2891–2895, 1999. View at Publisher · View at Google Scholar · View at Scopus
  130. C.-Y. Chen, I.-S. Chang, C. A. Hsiung, and W. W. Wasserman, “On the identification of potential regulatory variants within genome wide association candidate SNP sets,” BMC Medical Genomics, vol. 7, article 34, 2014. View at Publisher · View at Google Scholar · View at Scopus
  131. M. Barenboim and T. Manke, “ChroMoS: an integrated web tool for SNP classification, prioritization and functional interpretation,” Bioinformatics, vol. 29, no. 17, pp. 2197–2198, 2013. View at Publisher · View at Google Scholar · View at Scopus
  132. A. Riva, “Large-scale computational identification of regulatory SNPs with rSNP-MAPPER,” BMC genomics, vol. 13, supplement 4, article S7, 2012. View at Google Scholar · View at Scopus
  133. J. V. Ponomarenko, G. V. Orlova, A. S. Frolov, M. S. Gelfand, and M. P. Ponomarenko, “SELEX_DB: a database on in vitro selected oligomers adapted for recognizing natural sites and for analyzing both SNPs and site-directed mutagenesis data,” Nucleic Acids Research, vol. 30, no. 1, pp. 195–199, 2002. View at Publisher · View at Google Scholar · View at Scopus
  134. I. V. Deyneko, Y. M. Kalybaeva, A. E. Kel, and H. Blöcker, “Human-chimpanzee promoter comparisons: property-conserved evolution?” Genomics, vol. 96, no. 3, pp. 129–133, 2010. View at Publisher · View at Google Scholar · View at Scopus
  135. M. C. Andersen, P. G. Engstrom, S. Lithwick et al., “In silico detection of sequence variations modifying transcriptional regulation,” PLoS Computational Biology, vol. 4, no. 1, article e5, 2008. View at Publisher · View at Google Scholar · View at MathSciNet · View at Scopus
  136. C.-C. Chen, S. Xiao, D. Xie et al., “Understanding variation in transcription factor binding by modeling transcription factor genome-epigenome interactions,” PLoS Computational Biology, vol. 9, no. 12, Article ID e1003367, 2013. View at Publisher · View at Google Scholar · View at Scopus
  137. G. Macintyre, J. Bailey, I. Haviv, and A. Kowalczyk, “is-rSNP: a novel technique for in silico regulatory SNP detection,” Bioinformatics, vol. 26, no. 18, pp. i524–i530, 2010. View at Publisher · View at Google Scholar · View at Scopus
  138. A. P. Boyle, E. L. Hong, M. Hariharan et al., “Annotation of functional variation in personal genomes using RegulomeDB,” Genome Research, vol. 22, no. 9, pp. 1790–1797, 2012. View at Publisher · View at Google Scholar · View at Scopus
  139. J. V. Ponomarenko, D. P. Furman, A. S. Frolov et al., “ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another,” Nucleic Acids Research, vol. 29, no. 1, pp. 284–287, 2001. View at Publisher · View at Google Scholar · View at Scopus
  140. L. O. Bryzgalov, E. V. Antontseva, M. Y. Matveeva et al., “Detection of regulatory SNPs in human genome using ChIP-seq ENCODE data,” PLoS ONE, vol. 8, no. 10, Article ID e78833, 2013. View at Google Scholar · View at Scopus
  141. N. L. Podkolodnyy, D. A. Afonnikov, Y. Y. Vaskin et al., “Program complex SNP-MED for analysis of single-nucleotide polymorphism (SNP) effects on the function of genes associated with socially significant diseases,” Russian Journal of Genetics: Applied Research, vol. 4, no. 3, pp. 159–167, 2014. View at Publisher · View at Google Scholar · View at Scopus
  142. A. D. Johnson, R. E. Handsaker, S. L. Pulit, M. M. Nizzari, C. J. O'Donnell, and P. I. W. De Bakker, “SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap,” Bioinformatics, vol. 24, no. 24, pp. 2938–2939, 2008. View at Publisher · View at Google Scholar · View at Scopus
  143. I. V. Deyneko, B. Bredohl, D. Wesely et al., “FeatureScan: revealing property-dependent similarity of nucleotide sequences,” Nucleic Acids Research, vol. 34, pp. W591–W595, 2006. View at Publisher · View at Google Scholar · View at Scopus
  144. S. F. Saccone, R. Bolze, P. Thomas et al., “SPOT: a web-based tool for using biological databases to prioritize SNPs after a genome-wide association study,” Nucleic Acids Research, vol. 38, no. 2, pp. W201–W209, 2010. View at Publisher · View at Google Scholar · View at Scopus
  145. Y. Fu, Z. Liu, S. Lou et al., “FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer,” Genome Biology, vol. 15, no. 10, article 480, 2014. View at Publisher · View at Google Scholar
  146. S. G. Coetzee, S. K. Rhie, B. P. Berman, G. A. Coetzee, and H. Noushmehr, “FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs,” Nucleic Acids Research, vol. 40, no. 18, article e139, 2012. View at Publisher · View at Google Scholar · View at Scopus
  147. D. A. Rasskazov, E. V. Antontseva, L. O. Bryzgalov et al., “rSNP_Guide-based evaluation of SNPs in promoters of the human APC and MLH1 genes associated with colon cancer,” Russian Journal of Genetics: Applied Research, vol. 4, no. 4, pp. 245–253, 2014. View at Publisher · View at Google Scholar · View at Scopus
  148. J. Ponomarenko, T. Merkulova, G. Orlova, O. Fokin, E. Gorshkov, and M. Ponomarenko, “Mining DNA sequences to predict sites which mutations cause genetic diseases,” Knowledge-Based Systems, vol. 15, no. 4, pp. 225–233, 2002. View at Publisher · View at Google Scholar · View at Scopus
  149. J. Ponomarenko, G. Orlova, T. Merkulova, G. Vasiliev, and M. Ponomarenko, “Mining genome variation to associate genetic disease with mutation alterations and ortho/paralogous polimorphysms in transcription factor binding site,” International Journal on Artificial Intelligence Tools, vol. 14, no. 4, pp. 599–619, 2005. View at Publisher · View at Google Scholar · View at Scopus
  150. Y. Ni, A. W. Hall, A. Battenhouse, and V. R. Iyer, “Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data,” BMC Genetics, vol. 13, article 46, 2012. View at Publisher · View at Google Scholar · View at Scopus
  151. S. Leschner, I. V. Deyneko, S. Lienenklaus et al., “Identification of tumor-specific Salmonella Typhimurium promoters and their regulatory logic,” Nucleic Acids Research, vol. 40, no. 7, pp. 2984–2994, 2012. View at Publisher · View at Google Scholar · View at Scopus
  152. J. Hu, J. W. Locasale, J. H. Bielas et al., “Heterogeneity of tumor-induced gene expression changes in the human metabolic network,” Nature Biotechnology, vol. 31, no. 6, pp. 522–529, 2013. View at Publisher · View at Google Scholar · View at Scopus
  153. M. Hein and S. Graver, “Tumor cell response to bevacizumab single agent therapy in vitro,” Cancer Cell International, vol. 13, no. 1, article 94, 2013. View at Publisher · View at Google Scholar · View at Scopus
  154. M. P. Ponomarenko, J. V. Ponomarenko, A. S. Frolov et al., “Oligonucleotide frequency matrices addressed to recognizing functional DNA sites,” Bioinformatics, vol. 15, no. 7-8, pp. 631–643, 1999. View at Publisher · View at Google Scholar · View at Scopus
  155. M. G. Dozmorov, L. R. Cara, C. B. Giles, and J. D. Wren, “GenomeRunner web server: regulatory similarity and differences define the functional impact of SNP sets,” Bioinformatics, vol. 32, 2016. View at Publisher · View at Google Scholar
  156. C. Liu, B. Ho, C. Chen et al., “ePIANNO: ePIgenomics ANNOtation tool,” PLOS ONE, vol. 11, no. 2, article e0148321, 2016. View at Publisher · View at Google Scholar
  157. J. Bendl, M. Musil, J. Štourač et al., “PredictSNP2: a unified platform for accurately evaluating SNP effects by exploiting the different characteristics of variants in distinct genomic regions,” PLoS Computational Biology, vol. 12, no. 5, Article ID e1004962, 2016. View at Publisher · View at Google Scholar
  158. S. S. Yoo, C. Jin, D. K. Jung et al., “Putative functional variants of XRCC1 identified by RegulomeDB were not associated with lung cancer risk in a Korean population,” Cancer Genetics, vol. 208, no. 1-2, pp. 19–24, 2015. View at Publisher · View at Google Scholar · View at Scopus