Table of Contents Author Guidelines Submit a Manuscript
Table of Contents Alerts

To receive news and publication updates for Autoimmune Diseases, enter your email address in the box below.

Autoimmune Diseases
Volume 2012, Article ID 792106, 10 pages
http://dx.doi.org/10.1155/2012/792106
Research Article

The Autoimmune Tautology: An In Silico Approach

Ricardo A. Cifuentes,1 Daniel Restrepo-Montoya,2 and Juan-Manuel Anaya1

1Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24, No. 63-69 piso 3, Bogotá, Colombia
2Bioinformatics and Intelligent Systems Research Laboratory (BIOLISI), Universidad Nacional, Avenida Carrera 30, No. 45-03, Bogotá, Colombia

Received 13 October 2011; Accepted 26 November 2011

Academic Editor: Adriana Rojas-Villarraga

Copyright © 2012 Ricardo A. Cifuentes 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. J. M. Anaya, “The autoimmune tautology,” Arthritis Research & Therapy, vol. 12, no. 6, p. 147, 2010. View at Publisher · View at Google Scholar · View at Scopus
  2. J. M. Anaya, R. Corena, J. Castiblanco, A. Rojas-Villarraga, and Y. Shoenfeld, “The kaleidoscope of autoimmunity: multiple autoimmune syndromes and familial autoimmunity,” Expert Review of Clinical Immunology, vol. 3, no. 4, pp. 623–635, 2007. View at Publisher · View at Google Scholar · View at Scopus
  3. J. Gutierrez-Achury, R. Coutinho de Almeida, and C. Wijmenga, “Shared genetics in coeliac disease and other immune-mediated diseases,” Journal of Internal Medicine, vol. 269, no. 6, pp. 591–603, 2011. View at Publisher · View at Google Scholar
  4. J. M. Anaya, Y. Shoenfeld, P. A. Correa, M. García-Carrasco, and R. Cervera, Autoinmunidad y Enfermedad Autoinmune, Corporación para Investigaciones Biológicas, Medellin, Colombia, 1st edition, 2005.
  5. C. Cotsapas, B. F. Voight, E. Rossin et al., “Pervasive sharing of genetic effects in autoimmune disease,” PLoS Genetics, vol. 7, no. 8, Article ID e1002254, 2011. View at Publisher · View at Google Scholar
  6. A. Delgado-Vega, E. Sánchez, S. Löfgren, C. Castillejo-López, and M. E. Alarcón-Riquelme, “Recent findings on genetics of systemic autoimmune diseases,” Current Opinion in Immunology, vol. 22, no. 6, pp. 698–705, 2010. View at Publisher · View at Google Scholar
  7. M. Sirota, M. A. Schaub, S. Batzoglou, W. H. Robinson, and A. J. Butte, “Autoimmune disease classification by inverse association with SNP alleles,” PLoS Genetics, vol. 5, no. 12, Article ID e1000792, 2009. View at Publisher · View at Google Scholar · View at Scopus
  8. M. Weeber, J. A. Kors, and B. Mons, “Online tools to support literature-based discovery in the life sciences,” Briefings in Bioinformatics, vol. 6, no. 3, pp. 277–286, 2005. View at Publisher · View at Google Scholar · View at Scopus
  9. Y. Tsuruoka, M. Miwa, K. Hamamoto, J. Tsujii, and S. Ananiadou, “Discovering and visualizing indirect associations between biomedical concepts,” Bioinformatics, vol. 27, no. 13, pp. i111–i119, 2011. View at Publisher · View at Google Scholar
  10. E. Tjioe, M. W. Berry, and R. Homayouni, “Discovering gene functional relationships using FAUN (Feature Annotation Using Nonnegative matrix factorization),” BMC Bioinformatics, vol. 11, no. 6, article 14, 2010. View at Publisher · View at Google Scholar · View at Scopus
  11. R. Rodriguez-Esteban, “Biomedical text mining and its applications,” PLoS Computational Biology, vol. 5, no. 12, Article ID e1000597, 2009. View at Publisher · View at Google Scholar · View at Scopus
  12. I. Spasic, S. Ananiadou, J. McNaught, and A. Kumar, “Text mining and ontologies in biomedicine: making sense of raw text,” Briefings in Bioinformatics, vol. 6, no. 3, pp. 239–251, 2005. View at Publisher · View at Google Scholar · View at Scopus
  13. R. Jelier, M. J. Schuemie, P. J. Roes, E. M. van Mulligen, and J. A. Kors, “Literature-based concept profiles for gene annotation: the issue of weighting,” International Journal of Medical Informatics, vol. 77, no. 5, pp. 354–362, 2008. View at Publisher · View at Google Scholar · View at Scopus
  14. M. S. Siadaty and W. A. Knaus, “Locating previously unknown patterns in data-mining results: a dual data- and knowledge-mining method,” BMC Medical Informatics and Decision Making, vol. 6, article 13, 2006. View at Publisher · View at Google Scholar · View at Scopus
  15. A. Ma'ayan, R. D. Blitzer, and R. Iyengar, “Toward predictive models of mammalian cells,” Annual Review of Biophysics and Biomolecular Structure, vol. 34, pp. 319–349, 2005. View at Publisher · View at Google Scholar · View at Scopus
  16. T. Aittokallio and B. Schwikowski, “Graph-based methods for analysing networks in cell biology,” Briefings in Bioinformatics, vol. 7, no. 3, pp. 243–255, 2006. View at Publisher · View at Google Scholar · View at Scopus
  17. M. Hecker, S. Lambeck, S. Toepfer, E. van Someren, and R. Guthke, “Gene regulatory network inference: data integration in dynamic models-A review,” BioSystems, vol. 96, no. 1, pp. 86–103, 2009. View at Publisher · View at Google Scholar · View at Scopus
  18. P. Shannon, A. Markiel, O. Ozier et al., “Cytoscape: a software environment for integrated models of biomolecular interaction networks,” Genome Research, vol. 13, no. 11, pp. 2498–2504, 2003. View at Publisher · View at Google Scholar · View at Scopus
  19. E. G. Cerami, G. D. Bader, B. E. Gross, and C. Sander, “cPath: open source software for collecting, storing, and querying biological pathways,” BMC Bioinformatics, vol. 7, article 497, 2006. View at Publisher · View at Google Scholar · View at Scopus
  20. H. Hermjakob, L. Montecchi-Palazzi, G. Bader et al., “The HUPO PSI's molecular Interaction format—a community standard for the representation of protein interaction data,” Nature Biotechnology, vol. 22, no. 2, pp. 177–183, 2004. View at Publisher · View at Google Scholar · View at Scopus
  21. J. Garcia-Garcia, E. Guney, R. Aragues, J. Planas-Iglesias, and B. Oliva, “Biana: a software framework for compiling biological interactions and analyzing networks,” BMC Bioinformatics, vol. 11, article 56, 2010. View at Publisher · View at Google Scholar · View at Scopus
  22. A. Nikitin, S. Egorov, N. Daraselia, and I. Mazo, “Pathway studio—the analysis and navigation of molecular networks,” Bioinformatics, vol. 19, no. 16, pp. 2155–2157, 2003. View at Publisher · View at Google Scholar · View at Scopus
  23. A. Yuryev, Z. Mulyukov, E. Kotelnikova et al., “Automatic pathway building in biological association networks,” BMC Bioinformatics, vol. 7, article 171, 2006. View at Publisher · View at Google Scholar · View at Scopus
  24. U. Dogrusoz, A. Cetintas, E. Demir, and O. Babur, “Algorithms for effective querying of compound graph-based pathway databases,” BMC Bioinformatics, vol. 10, article 376, 2009. View at Publisher · View at Google Scholar · View at Scopus
  25. J. Chen, B. J. Aronow, and A. G. Jegga, “Disease candidate gene identification and prioritization using protein interaction networks,” BMC Bioinformatics, vol. 10, article 73, 2009. View at Publisher · View at Google Scholar · View at Scopus
  26. X. Zhu, M. Gerstein, and M. Snyder, “Getting connected: analysis and principles of biological networks,” Genes and Development, vol. 21, no. 9, pp. 1010–1024, 2007. View at Publisher · View at Google Scholar · View at Scopus
  27. R. Jelier, G. Jenster, L. C. J. Dorssers et al., “Text-derived concept profiles support assessment of DNA microarray data for acute myeloid leukemia and for androgen receptor stimulation,” BMC Bioinformatics, vol. 8, article 14, 2007. View at Publisher · View at Google Scholar · View at Scopus
  28. R. Jelier, M. J. Schuemie, A. Veldhoven, L. C. J. Dorssers, G. Jenster, and J. A. Kors, “Anni 2.0: a multipurpose text-mining tool for the life sciences,” Genome Biology, vol. 9, no. 6, article R96, 2008. View at Publisher · View at Google Scholar · View at Scopus
  29. S. I. Berger, J. M. Posner, and A. Ma'ayan, “Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases,” BMC Bioinformatics, vol. 8, article 372, 2007. View at Publisher · View at Google Scholar · View at Scopus
  30. R. A. Cifuentes, A. Rojas-Villarraga, and J. M. Anaya, “Human leukocyte antigen class II and type 1 diabetes in Latin America: a combined meta-analysis of association and family-based studies,” Human Immunology, vol. 72, no. 7, pp. 581–586, 2011. View at Publisher · View at Google Scholar
  31. A. E. Handel, L. Handunnetthi, A. J. Berlanga, C. T. Watson, J. M. Morahan, and S. V. Ramagopalan, “The effect of single nucleotide polymorphisms from genome wide association studies in multiple sclerosis on gene expression,” PLoS ONE, vol. 5, no. 4, Article ID e10142, 2010. View at Publisher · View at Google Scholar · View at Scopus
  32. D. Plant, E. Flynn, H. Mbarek et al., “Investigation of potential non-HLA rheumatoid arthritis susceptibility loci in a European cohort increases the evidence for nine markers,” Annals of the Rheumatic Diseases, vol. 69, no. 8, pp. 1548–1553, 2010. View at Publisher · View at Google Scholar · View at Scopus
  33. P. K. Gregersen, C. I. Amos, A. T. Lee et al., “REL, encoding a member of the NF-B family of transcription factors, is a newly defined risk locus for rheumatoid arthritis,” Nature Genetics, vol. 41, no. 7, pp. 820–823, 2009. View at Publisher · View at Google Scholar · View at Scopus
  34. V. Gateva, J. K. Sandling, G. Hom et al., “A large-scale replication study identifies TNIP1, PRDM1, JAZF1, UHRF1BP1 and IL10 as risk loci for systemic lupus erythematosus,” Nature Genetics, vol. 41, no. 11, pp. 1228–1233, 2009. View at Publisher · View at Google Scholar · View at Scopus
  35. L. Zhang, W. Li, L. Song, and L. Chen, “A towards-multidimensional screening approach to predict candidate genes of rheumatoid arthritis based on SNP, structural and functional annotations,” BMC Medical Genomics, vol. 3, article 38, 2010. View at Publisher · View at Google Scholar · View at Scopus
  36. Y. M. Hussein, S. A. El Tarhouny, R. H. Mohamed, A. S. El-Shal, A. M. Abul-Saoud, and M. Abdo, “Association of CD4 enhancer gene polymorphisms with rheumatoid arthritis in Egyptian female patients,” Rheumatology International. In press. View at Publisher · View at Google Scholar
  37. S. F. Lo, L. Wan, H. C. Lin, C. M. Huang, and F. J. Tsai, “Association of CD4 enhancer gene polymorphisms with rheumatoid arthritis and systemic lupus erythematosus in Taiwan,” Journal of Rheumatology, vol. 35, no. 11, pp. 2113–2118, 2008. View at Publisher · View at Google Scholar · View at Scopus
  38. J. Schulte-Pelkum, M. Fritzler, and M. Mahler, “Latest update on the Ro/SS-A autoantibody system,” Autoimmunity Reviews, vol. 8, no. 7, pp. 632–637, 2009. View at Publisher · View at Google Scholar · View at Scopus
  39. M. Dugar, S. Cox, V. Limaye, T. P. Gordon, and P. J. Roberts-Thomson, “Diagnostic utility of anti-Ro52 detection in systemic autoimmunity,” Postgraduate Medical Journal, vol. 86, no. 1012, pp. 79–82, 2010. View at Publisher · View at Google Scholar · View at Scopus
  40. M. Tanaka, K. Tanji, M. Niida, and T. Kamitani, “Dynamic movements of Ro52 cytoplasmic bodies along microtubules,” Histochemistry and Cell Biology, vol. 133, no. 3, pp. 273–284, 2010. View at Publisher · View at Google Scholar · View at Scopus
  41. A. Espinosa, V. Dardalhon, S. Brauner et al., “Loss of the lupus autoantigen Ro52/Trim21 induces tissue inflammation and systemic autoimmunity by disregulating the IL-23-Th17 pathway,” Journal of Experimental Medicine, vol. 206, no. 8, pp. 1661–1671, 2009. View at Publisher · View at Google Scholar · View at Scopus
  42. A. P. M. Verhagen and G. J. M. Pruijn, “Are the Ro RNP-associated Y RNAs concealing microRNAs? Y RNA-derived miRNAs may be involved in autoimmunity,” BioEssays, vol. 33, no. 9, pp. 674–682, 2011. View at Publisher · View at Google Scholar
  43. A. Reich, M. Meurer, A. Viehweg, and D. J. Muller, “Narrow-band UVB-induced externalization of selected nuclear antigens in keratinocytes: implications for lupus erythematosus pathogenesis,” Photochemistry and Photobiology, vol. 85, no. 1, pp. 1–7, 2009. View at Publisher · View at Google Scholar · View at Scopus
  44. H. Park, L. Yu, T. Kim, B. Cho, J. Kang, and Y. Park, “Antigenic determinants to GAD autoantibodies in patients with type 1 diabetes with and without autoimmune thyroid disease,” Annals of the New York Academy of Sciences, vol. 1079, pp. 213–219, 2006. View at Publisher · View at Google Scholar · View at Scopus
  45. A. Rojas-Villarraga, D. Botello-Corzo, and J. M. Anaya, “HLA-Class II in Latin American patients with type 1 diabetes,” Autoimmunity Reviews, vol. 9, no. 10, pp. 666–673, 2010. View at Publisher · View at Google Scholar · View at Scopus
  46. N. Castaño-Rodríguez, L. M. Diaz-Gallo, R. Pineda-Tamayo, A. Rojas-Villarraga, and J. M. Anaya, “Meta-analysis of HLA-DRB1 and HLA-DQB1 polymorphisms in Latin American patients with systemic lupus erythematosus,” Autoimmunity Reviews, vol. 7, no. 4, pp. 322–330, 2008. View at Publisher · View at Google Scholar · View at Scopus
  47. O. L. Rojas, A. Rojas-Villarraga, P. Cruz-Tapias et al., “HLA class II polymorphism in Latin American patients with multiple sclerosis,” Autoimmunity Reviews, vol. 9, no. 6, pp. 407–413, 2010. View at Publisher · View at Google Scholar · View at Scopus
  48. T. Kamradt and N. Avrion Mitchison, “Tolerance and autoimmunity,” New England Journal of Medicine, vol. 344, no. 9, pp. 655–664, 2001. View at Publisher · View at Google Scholar · View at Scopus
  49. A. Korb, H. Pavenstädt, and T. Pap, “Cell death in rheumatoid arthritis,” Apoptosis, vol. 14, no. 4, pp. 447–454, 2009. View at Publisher · View at Google Scholar · View at Scopus
  50. A. Pawlik, M. Herczyńska, M. Kurzawski et al., “IL-1β, IL-6 and TNF gene polymorphisms do not affect the treatment outcome of rheumatoid arthritis patients with leflunomide,” Pharmacological Reports, vol. 61, no. 2, pp. 281–287, 2009. View at Google Scholar · View at Scopus
  51. I. N. Sarkar, “Biomedical informatics and translational medicine,” Journal of Translational Medicine, vol. 8, article 22, 2010. View at Publisher · View at Google Scholar · View at Scopus