A new methodology to associate snps with human diseases according to their pathway related context

PLoS ONE

Volumn 6, Issue 10, 2011, Pages

  Bakir Gungor, Burcu ^a,b   Sezerman, Osman Ugur ^a  

^a SABANCI UNIVERSITY   (Turkey)

^b BAHCESEHIR UNIVERSITY   (Turkey)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMOKINE; HLA C ANTIGEN; HLA G ANTIGEN; JANUS KINASE; MITOGEN ACTIVATED PROTEIN KINASE; NEUROTROPHIN; STAT PROTEIN; TOLL LIKE RECEPTOR; TRANSPORTER ASSOCIATED WITH ANTIGEN PROCESSING 1;

ANTIGEN PRESENTATION; ARTICLE; CONTROLLED STUDY; GENE FUNCTION; GENE IDENTIFICATION; GENE SEQUENCE; GENE TARGETING; GENETIC ASSOCIATION; GENETIC DATABASE; INFORMATION RETRIEVAL; LEUKOCYTE MIGRATION; MOLECULAR PATHOLOGY; RHEUMATOID ARTHRITIS; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM; TIGHT JUNCTION; BIOLOGY; DISEASES; GENETICS; HUMAN; METABOLISM; METHODOLOGY; MOLECULARLY TARGETED THERAPY; PHYSIOLOGY; PROCEDURES;

ARTHRITIS, RHEUMATOID; COMPUTATIONAL BIOLOGY; DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; METHODS; MOLECULAR TARGETED THERAPY; POLYMORPHISM, SINGLE NUCLEOTIDE; SIGNAL TRANSDUCTION;

EID: 80055031911     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0026277     Document Type: Article

References (70)

1. Hardy J, Singleton A, (2009) CURRENT CONCEPTS Genomewide Association Studies and Human Disease. New England Journal of Medicine 360: 1759-1768.
2. Elbers CC, van Eijk KR, Franke L, Mulder F, van der Schouw YT, et al. (2009) Using Genome-Wide Pathway Analysis to Unravel the Etiology of Complex Diseases. Genetic Epidemiology 33: 419-431.
3. Altshuler D, Hirschhorn JN, Klannemark M, Lindgren CM, Vohl MC, et al. (2000) The common PPAR gamma Pro12Ala polymorphism is associated with decreased risk of type 2 diabetes. Nature Genetics 26: 76-80.
4. Frayling TM, (2007) Genome-wide association studies provide new insights into type 2 diabetes aetiology. Nature Reviews Genetics 8: 657-662.
5. Baranzini SE, Galwey NW, Wang J, Khankhanian P, Lindberg R, et al. (2009) Pathway and network-based analysis of genome-wide association studies in multiple sclerosis. Human Molecular Genetics 18: 2078-2090.
6. Peng G, Luo L, Siu HC, Zhu Y, Hu PF, et al. (2010) Gene and pathway-based second-wave analysis of genome-wide association studies. European Journal of Human Genetics 18: 111-117.
7. Askland K, Read C, Moore J, (2009) Pathways-based analyses of whole-genome association study data in bipolar disorder reveal genes mediating ion channel activity and synaptic neurotransmission. Human genetics 125: 63-79.
8. Torkamani A, Topol EJ, Schork NJ, (2008) Pathway analysis of seven common diseases assessed by genome-wide association. Genomics 92: 265-272.
9. Wang K, Li M, Bucan M, (2007) Pathway-Based Approaches for Analysis of Genomewide Association Studies. American journal of human genetics 81.
10. Lesnick TG, Papapetropoulos S, Mash DC, Ffrench-Mullen J, Shehadeh L, et al. (2007) A genomic pathway approach to a complex disease: axon guidance and Parkinson disease. PLoS genetics 3: e98.
11. Pattin KA, Moore JH, (2008) Exploiting the proteome to improve the genome-wide genetic analysis of epistasis in common human diseases. Human genetics 124: 19-29.
12. Wilke RA, Mareedu RK, Moore JH, (2008) The Pathway Less Traveled: Moving from Candidate Genes to Candidate Pathways in the Analysis of Genome-Wide Data from Large Scale Pharmacogenetic Association Studies. Current pharmacogenomics and personalized medicine 6: 150-159.
13. Franke L, van Bakel H, Fokkens L, de Jong ED, Egmont-Petersen M, et al. (2006) Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. American journal of human genetics 78: 1011-1025.
14. Lage K, Karlberg EO, Storling ZM, Olason PI, Pedersen AG, et al. (2007) A human phenome-interactome network of protein complexes implicated in genetic disorders. Nature Biotechnology 25: 309-316.
15. Tu ZD, Wang L, Arbeitman MN, Chen T, Sun FZ, (2006) An integrative approach for causal gene identification and gene regulatory pathway inference. Bioinformatics 22: E489-E496.
16. Suthram S, Beyer A, Karp RM, Eldar Y, Ideker T, (2008) eQED: an efficient method for interpreting eQTL associations using protein networks. Molecular Systems Biology 4:-.
17. Roeder K, Bacanu SA, Wasserman L, Devlin B, (2006) Using linkage genome scans to improve power of association in genome scans. American journal of human genetics 78: 243-252.
18. Roeder K, Devlin B, Wasserman L, (2007) Improving power in genome-wide association studies: weights tip the scale. Genetic Epidemiology 31: 741-747.
19. Saccone SF, Bolze R, Thomas P, Quan JX, Mehta G, et al. (2010) SPOT: a web-based tool for using biological databases to prioritize SNPs after a genome-wide association study. Nucleic Acids Research 38: W201-W209.
20. Lee PH, Shatkay H, (2008) F-SNP: computationally predicted functional SNPs for disease association studies. Nucleic Acids Research 36: D820-D824.
21. Lee PH, Shatkay H, (2009) An integrative scoring system for ranking SNPs by their potential deleterious effects. Bioinformatics 25: 1048-1055.
22. Wingender E, Chen X, Hehl R, Karas H, Liebich I, et al. (2000) TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Research 28: 316-319.
23. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research 13: 2498-2504.
24. Ideker T, Ozier O, Schwikowski B, Siegel AF, (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics 18 (Suppl 1): S233-240.
25. Karchin R, (2009) Next generation tools for the annotation of human SNPs. Briefings in bioinformatics 10: 35-52.
26. Ramensky V, Bork P, Sunyaev S, (2002) Human non-synonymous SNPs: server and survey. Nucleic Acids Research 30: 3894-3900.
27. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, et al. (2010) A method and server for predicting damaging missense mutations. Nature Methods 7: 248-249.
28. Loots G, Ovcharenko I, (2007) ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes. Bioinformatics 23: 122-124.
29. Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, et al. (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449: 851-U853.
30. Saccone SF, Saccone NL, Swan GE, Madden PAF, Goate AM, et al. (2008) Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence. Bioinformatics 24: 1805-1811.
31. Chelala C, Khan A, Lemoine NR, (2009) SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms. Bioinformatics 25: 655-661.
32. Bandyopadhyay S, Kelley R, Ideker T, (2006) Discovering regulated networks during HIV-1 latency and reactivation. Pacific Symposium on Biocomputing Pacific Symposium on Biocomputing pp. 354-366.
33. Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, et al. (2009) ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 25: 1091-1093.
34. Boyle EI, Weng SA, Gollub J, Jin H, Botstein D, et al. (2004) GO::TermFinder- open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 20: 3710-3715.
35. Huang DW, Sherman BT, Tan Q, Collins JR, Alvord WG, et al. (2007) The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biology 8:-.
36. Maere S, Heymans K, Kuiper M, (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks. Bioinformatics 21: 3448-3449.
37. Ramos H, Shannon P, Aebersold R, (2008) The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data. Bioinformatics 24: 2110-2111.
38. Zeeberg BR, Feng WM, Wang G, Wang MD, Fojo AT, et al. (2003) GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biology 4.
39. Bali D, Gourley S, Kostyu DD, Goel N, Bruce I, et al. (1999) Genetic analysis of multiplex rheumatoid arthritis families. Genes and Immunity 1: 28-36.
40. MacGregor AJ, Snieder H, Rigby AS, Koskenvuo M, Kaprio J, et al. (2000) Characterizing the quantitative genetic contribution to rheumatoid arthritis using data from twins. Arthritis and Rheumatism 43: 30-37.
41. Raychaudhuri S, Remmers EF, Lee AT, Hackett R, Guiducci C, et al. (2008) Common variants at CD40 and other loci confer risk of rheumatoid arthritis. Nature Genetics 40: 1216-1223.
42. Raychaudhuri S, Thomson BP, Remmers EF, Eyre S, Hinks A, et al. (2009) Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk. Nature Genetics 41: 1313-U1376.
43. Suzuki M, Tetsuka T, Yoshida S, Watanabe N, Kobayashi M, et al. (2000) The role of p38 mitogen-activated protein kinase in IL-6 and IL-8 production from the TNF-alpha- or IL-1 beta-stimulated rheumatoid synovial fibroblasts. Febs Letters 465: 23-27.
44. Begovich AB, Carlton VEH, Honigberg LA, Schrodi SJ, Chokkalingam AP, et al. (2004) A missense single-nucleotide polymorphism in a gene encoding a protein tyrosine phosphatase (PTPN22) is associated with rheumatoid arthritis. American journal of human genetics 75: 330-337.
45. Kurreeman FAS, Padyukov L, Marques RB, Schrodi SJ, Seddighzadeh M, et al. (2007) A candidate gene approach identifies the TRAF1/C5 region as a risk factor for rheumatoid arthritis. Plos Medicine 4: 1515-1524.
46. Plenge RM, Cotsapas C, Davies L, Price AL, Bakker PIW, et al. (2007) Two independent alleles at 6q23 associated with risk of rheumatoid arthritis. Nature Genetics 39: 1477-1482.
47. Remmers EF, Plenge RM, Lee AT, Graham RR, Hom G, et al. (2007) STAT4 and the risk of rheumatoid arthritis and systemic lupus erythematosus. New England Journal of Medicine 357: 977-986.
48. Thomson W, Barton A, Ke X, Eyre S, Hinks A, et al. (2007) Rheumatoid arthritis association at 6q23. Nature Genetics 39: 1431-1433.
49. Zhernakova A, Alizadeh BZ, Bevova M, van Leeuwen MA, Coenen MJH, et al. (2007) Novel association in chromosome 4q27 region with rheumatoid arthritis and confirmation of type 1 diabetes point to a general risk locus for autoimmune diseases. American journal of human genetics 81: 1284-1288.
50. Gregersen PK, Amos CI, Lee AT, Lu Y, Remmers EF, et al. (2009) REL, encoding a member of the NF-kappa B family of transcription factors, is a newly defined risk locus for rheumatoid arthritis. Nature Genetics 41: 820-U877.
51. Barton A, Eyre S, Ke XY, Hinks A, Bowes J, et al. (2009) Identification of AF4/FMR2 family, member 3 (AFF3) as a novel rheumatoid arthritis susceptibility locus and confirmation of two further pan-autoimmune susceptibility genes. Human Molecular Genetics 18: 2518-2522.
52. Goh KI, Cusick ME, Valle D, Childs B, Vidal M, et al. (2007) The human disease network. Proceedings of the National Academy of Sciences of the United States of America 104: 8685-8690.
53. Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, et al. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437: 1173-1178.
54. Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, et al. (2005) A human protein-protein interaction network: A resource for annotating the proteome. Cell 122: 957-968.
55. Albert R, (2005) Scale-free networks in cell biology. Journal of Cell Science 118: 4947-4957.
56. Jeong H, Tombor B, Albert R, Oltvai ZN, Barabasi AL, (2000) The large-scale organization of metabolic networks. Nature 407: 651-654.
57. Barabasi AL, (2009) Scale-Free Networks: A Decade and Beyond. Science 325: 412-413.
58. Vallabhajosyula RR, Chakravarti D, Lutfeali S, Ray A, Raval A, (2009) Identifying Hubs in Protein Interaction Networks. Plos One 4:-.
59. Barabasi AL, Oltvai ZN, (2004) Network biology: understanding the cell's functional organization. Nature reviews Genetics 5: 101-113.
60. Shahrara S, Castro-Rueda HP, Haines GK, Koch AE, (2007) Differential expression of the FAK family kinases in rheumatoid arthritis and osteoarthritis synovial tissues. Arthritis Research & Therapy 9: R112.
61. Wu G, Zhu L, Dent JE, Nardini C, (2010) A comprehensive molecular interaction map for rheumatoid arthritis. Plos One 5: e10137.
62. Calzone L, Gelay A, Zinovyev A, Radvanyi F, Barillot E, (2008) A comprehensive modular map of molecular interactions in RB/E2F pathway. Molecular Systems Biology 4: 173.
63. Zinovyev A, Viara E, Calzone L, Barillot E, (2008) BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. Bioinformatics 24: 876-877.
64. Martin JE, Alizadeh BZ, Gonzalez-Gay MA, Balsa A, Pascual-Salcedo D, et al. (2010) Identification of the Oxidative Stress-Related Gene MSRA as a Rheumatoid Arthritis Susceptibility Locus by Genome-Wide Pathway Analysis. Arthritis and Rheumatism 62: 3183-3190.
65. Zhang LC, Li W, Song LL, Chen LN, (2010) A towards-multidimensional screening approach to predict candidate genes of rheumatoid arthritis based on SNP, structural and functional annotations. Bmc Medical Genomics 3:-.
66. Couzin J, Kaiser J, (2007) Genome-wide association. Closing the net on common disease genes. Science 316: 820-822.
67. Williams SM, Canter JA, Crawford DC, Moore JH, Ritchie MD, et al. (2007) Problems with genome-wide association studies. Science 316: 1840-1842.
68. Joosten LA, Koenders MI, Smeets RL, Heuvelmans-Jacobs M, Helsen MM, et al. (2003) Toll-like receptor 2 pathway drives streptococcal cell wall-induced joint inflammation: critical role of myeloid differentiation factor 88. Journal of Immunology 171: 6145-6153.
69. Liacini A, Sylvester J, Li WQ, Huang W, Dehnade F, et al. (2003) Induction of matrix metalloproteinase-13 gene expression by TNF-alpha is mediated by MAP kinases, AP-1, and NF-kappaB transcription factors in articular chondrocytes. Experimental cell research 288: 208-217.
70. Schett G, Tohidast-Akrad M, Smolen JS, Schmid BJ, Steiner CW, et al. (2000) Activation, differential localization, and regulation of the stress-activated protein kinases, extracellular signal-regulated kinase, c-JUN N-terminal kinase, and p38 mitogen-activated protein kinase, in synovial tissue and cells in rheumatoid arthritis. Arthritis and Rheumatism 43: 2501-2512.