Lost in the space of bioinformatic tools: A constantly updated survival guide for genetic epidemiology. The GenEpi Toolbox

Atherosclerosis

Volumn 209, Issue 2, 2010, Pages 321-335

  Coassin, Stefan ^a   Brandstätter, Anita ^a   Kronenberg, Florian ^a  

^a INNSBRUCK MEDICAL UNIVERSITY   (Austria)

Author keywords

Association study; Bioinformatic tools; Functional relevance; Genetic epidemiology; Genome wide association study

Indexed keywords

MESSENGER RNA; MICRORNA; NUCLEOTIDE;

AMINO ACID SEQUENCE; ARTICLE; AUTOMATION; BIOINFORMATICS; COMPUTER MODEL; DATA MINING; GENE CONTROL; GENE LOCUS; GENE MUTATION; GENETIC CODE; GENETIC CONSERVATION; GENETIC DATABASE; GENETIC DISORDER; GENETIC EPIDEMIOLOGY; GENETIC SCREENING; GENETIC TRAIT; GENETIC VARIABILITY; GENOMICS; INTERNET; PHENOTYPE; PREDICTION; PRIORITY JOURNAL; RNA SPLICING; SINGLE NUCLEOTIDE POLYMORPHISM;

COMPUTATIONAL BIOLOGY; DATA MINING; DATABASES, GENETIC; DECISION TREES; GENE EXPRESSION REGULATION; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MICRORNAS; MOLECULAR EPIDEMIOLOGY; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE;

EID: 77950044558     PISSN: 00219150     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.atherosclerosis.2009.10.026     Document Type: Review

References (90)

1. Kronenberg F. Genome-wide association studies in aging-related processes such as diabetes mellitus, atherosclerosis and cancer. Exp. Gerontol 2008, 43:39-43.
2. Manolio T.A., Brooks L.D., Collins F.S. A HapMap harvest of insights into the genetics of common disease. J Clin Invest 2008, 118:1590-1605.
3. Kronenberg F. Emerging risk factors and markers of chronic kidney disease progression. Nat Rev Nephrol 2009, 5:677-689.
4. Samani N.J., Erdmann J., Hall A.S., et al. Genomewide association analysis of coronary artery disease. N Engl J Med 2007, 357:443-453.
5. Heid I.M., Boes E., Müller M., et al. Genome-wide association analysis of high-density lipoprotein cholesterol in the population-based KORA study sheds new light on intergenic regions. Circ Cardiovasc Genet 2008, 1:10-20.
6. Lettre G., Rioux J.D. Autoimmune diseases: insights from genome-wide association studies. Hum Mol Genet 2008, 17:R116-R121.
7. Psychiatric GWAS Consortium Coordinating Committee Genomewide association studies: history, rationale, and prospects for psychiatric disorders. Am J Psychiatry 2009, 166:540-556.
8. Chorley B.N., Wang X., Campbell M.R., et al. Discovery and verification of functional single nucleotide polymorphisms in regulatory genomic regions: current and developing technologies. Mutat Res 2008, 659:147-157.
9. Sugatani J., Yamakawa K., Yoshinari K., et al. Identification of a defect in the UGT1A1 gene promoter and its association with hyperbilirubinemia. Biochem Biophys Res Commun 2002, 292:492-497.
10. Knight J.C. Regulatory polymorphisms underlying complex disease traits. J Mol Med 2005, 83:97-109.
11. De Gobbi M., Anguita E., Hughes J., et al. Tissue-specific histone modification and transcription factor binding in {alpha} globin gene expression. Blood 2007, 110:4503-4510.
12. Mishra P.J., Banerjee D., Bertino J.R. MiRSNPs or MiR-polymorphisms, new players in microRNA mediated regulation of the cell: introducing microRNA pharmacogenomics. Cell Cycle 2008, 7:853-858.
13. Parker S.C., Hansen L., Abaan H.O., Tullius T.D., Margulies E.H. Local DNA topography correlates with functional noncoding regions of the human genome. Science 2009, 324:389-392.
14. Birnbaum S., Ludwig K.U., Reutter H., et al. Key susceptibility locus for nonsyndromic cleft lip with or without cleft palate on chromosome 8q24. Nat Genet 2009, 41:473-477.
15. Cohen J.C., Kiss R.S., Pertsemlidis A., et al. Multiple rare alleles contribute to low plasma levels of HDL cholesterol. Science 2004, 305:869-872.
16. Pritchard J.K. Are rare variants responsible for susceptibility to complex diseases?. Am. J Hum Genet 2001, 69:124-137.
17. Bodmer W., Bonilla C. Common and rare variants in multifactorial susceptibility to common diseases. Nat Genet 2008, 40:695-701.
18. Coassin S., Brandstätter A., Kronenberg F. An optimized procedure for the design and evaluation of Ecotilling assays. BMC Genomics 2008, 9:510-520.
19. Bhatti P., Church D.M., Rutter J.L., Struewing J.P., Sigurdson A.J. Candidate single nucleotide polymorphism selection using publicly available tools: a guide for epidemiologists. Am J Epidemiol 2006, 164:794-804.
20. Mooney S. Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis. Brief Bioinform 2005, 6:44-56.
21. Teufel A., Krupp M., Weinmann A., Galle P.R. Current bioinformatics tools in genomic biomedical research (Review). Int J Mol Med 2006, 17:967-973.
22. Ng P.C., Henikoff S: S.I.F.T. Predicting amino acid changes that affect protein function. Nucleic Acids Res 2003, 31:3812-3814.
23. Sunyaev S., Ramensky V., Koch I., et al. Prediction of deleterious human alleles. Hum Mol Genet 2001, 10:591-597.
24. Cartharius K., Frech K., Grote K., et al. MatInspector and beyond: promoter analysis based on transcription factor binding sites. Bioinformatics 2005, 21:2933-2942.
25. Heinemeyer T., Wingender E., Reuter I., et al. Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL. Nucleic Acids Res 1998, 26:362-367.
26. Marinescu V.D., Kohane I.S., Riva A. The MAPPER database: a multi-genome catalog of putative transcription factor binding sites. Nucleic Acids Res 2005, 33:D91-D97.
27. Reumers J., Schymkowitz J., Ferkinghoff-Borg J., et al. SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs. Nucleic Acids Res 2005, 33:D527-D532.
28. Brazas M.D., Yamada J.T., Ouellette B.F. Evolution in bioinformatic resources: 2009 update on the Bioinformatics Links Directory. Nucleic Acids Res 2009, 37:W3-W5.
29. McWilliam H., Valentin F., Goujon M., et al. Web services at the European Bioinformatics Institute-2009. Nucleic Acids Res 2009, 37:W6-10.
30. Sayers E.W., Barrett T., Benson D.A., et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2009, 37:D5-15.
31. Hubbard T.J., Aken B.L., Ayling S., et al. Ensembl 2009. Nucleic Acids Res 2009, 37:D690-D697.
32. Kuhn R.M., Karolchik D., Zweig A.S., et al. The UCSC Genome Browser Database: update 2009. Nucleic Acids Res 2009, 37:D755-D761.
33. Maher B. Personal genomes: the case of the missing heritability. Nature 2008, 456:18-21.
34. Iafrate A.J., Feuk L., Rivera M.N., et al. Detection of large-scale variation in the human genome. Nat Genet 2004, 36:949-951.
35. Visel A., Minovitsky S., Dubchak I., Pennacchio L.A. VISTA Enhancer Browser-a database of tissue-specific human enhancers. Nucleic Acids Res 2007, 35:D88-D92.
36. Uhlen M., Bjorling E., Agaton C., et al. A Human Protein Atlas for normal and cancer tissues based on antibody proteomics. Mol Cell Proteomics 2005, 4:1920-1932.
37. Dixon A.L., Liang L., Moffatt M.F., et al. A genome-wide association study of global gene expression. Nat Genet 2007, 39:1202-1207.
38. Chen Y.H., Liu C.K., Chang S.C., et al. GenoWatch: a disease gene mining browser for association study. Nucleic Acids Res 2008, 36:W336-W340.
39. Frazer K.A., Pachter L., Poliakov A., Rubin E.M., Dubchak I. VISTA: computational tools for comparative genomics. Nucleic Acids Res 2004, 32:W273-W279.
40. Taylor J., Tyekucheva S., King D.C., et al. ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements. Genome Res 2006, 16:1596-1604.
41. Yang M.Q., Taylor J., Elnitski L. Comparative analyses of bidirectional promoters in vertebrates. BMC Bioinformatics 2008, 9(Suppl. 6):S9.
42. King D.C., Taylor J., Elnitski L., et al. Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences. Genome Res 2005, 15:1051-1060.
43. Chelala C., Khan A., Lemoine N.R. SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms. Bioinformatics 2009, 25:655-661.
44. Lee P.H., Shatkay H. F-SNP: computationally predicted functional SNPs for disease association studies. Nucleic Acids Res 2008, 36:D820-D824.
45. Reumers J., Conde L., Medina I., et al. Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases. Nucleic Acids Res 2008, 36:D825-D829.
46. Yuan H.Y., Chiou J.J., Tseng W.H., et al. FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization. Nucleic Acids Res 2006, 34:W635-W641.
47. Jegga A.G., Gowrisankar S., Chen J., Aronow B.J. PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease. Nucleic Acids Res 2007, 35:D700-D706.
48. Hemminger B.M., Saelim B., Sullivan P.F. TAMAL: an integrated approach to choosing SNPs for genetic studies of human complex traits. Bioinformatics 2006, 22:626-627.
49. Kang H.J., Choi K.O., Kim B.D., Kim S., Kim Y.J. FESD: a functional element SNPs database in human. Nucleic Acids Res 2005, 33:D518-D522.
50. Liu C.K., Chen Y.H., Tang C.Y., et al. Functional analysis of novel SNPs and mutations in human and mouse genomes. BMC Bioinformatics 2008, 9(Suppl. 12):S10.
51. Conde L., Vaquerizas J.M., Dopazo H., et al. PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes. Nucleic Acids Res 2006, 34:W621-W625.
52. Ng P.C., Henikoff S. Predicting the effects of amino acid substitutions on protein function. Annu Rev Genomics Hum Genet 2006, 7:61-80.
53. Baralle D., Baralle M. Splicing in action: assessing disease causing sequence changes. J Med Genet 2005, 42:737-748.
54. Desmet F.O., Hamroun D., Lalande M., et al. Human splicing finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Res 2009, 37:e67.
55. Wasserman W.W., Sandelin A. Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet 2004, 5:276-287.
56. Bao L., Zhou M., Wu L., et al. PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits. Nucleic Acids Res 2007, 35:D51-D54.
57. Georges M., Clop A., Marcq F., et al. Polymorphic microRNA-target interactions: a novel source of phenotypic variation. Cold Spring Harb Symp Quant Biol 2006, 71:343-350.
58. Griffiths-Jones S., Saini H.K., van D.S., Enright A.J. miRBase: tools for microRNA genomics. Nucleic Acids Res 2008, 36:D154-D158.
59. Lewis B.P., Burge C.B., Bartel D.P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005, 120:15-20.
60. Papadopoulos G.L., Reczko M., Simossis V.A., Sethupathy P., Hatzigeorgiou A.G. The database of experimentally supported targets: a functional update of TarBase. Nucleic Acids Res 2009, 37:D155-D158.
61. Jimenez R.C., Quinn A.F., Garcia A., et al. Dasty2, an Ajax protein DAS client. Bioinformatics 2008, 24:2119-2121.
62. Bradshaw C.R., Surendranath V., Habermann B. ProFAT: a web-based tool for the functional annotation of protein sequences. BMC Bioinformatics 2006, 7:466.
63. Frisch M., Klocke B., Haltmeier M., Frech K. LitInspector: literature and signal transduction pathway mining in PubMed abstracts. Nucleic Acids Res 2009, 37:W135-W140.
64. Hoffmann R., Valencia A. A gene network for navigating the literature. Nat Genet 2004, 36:664.
65. Doms A., Schroeder M. GoPubMed: exploring PubMed with the Gene Ontology. Nucleic Acids Res 2005, 33:W783-W786.
66. Jensen L.J., Kuhn M., Stark M., et al. STRING 8-a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res 2009, 37:D412-D416.
67. Köhler S., Bauer S., Horn D., Robinson P.N. Walking the interactome for prioritization of candidate disease genes. Am J Hum Genet 2008, 82:949-958.
68. Bottillo I., De L.A., Schirinzi A., et al. Functional analysis of splicing mutations in exon 7 of NF1 gene. BMC Med Genet 2007, 8:4.
69. Sun C., Southard C., Di R.A. Characterization of a novel splicing variant in the RAPTOR gene. Mutat Res 2009, 662:88-92.
70. Armendariz A.D., Krauss R.M. Hepatic nuclear factor 1-alpha: inflammation, genetics, and atherosclerosis. Curr Opin Lipidol 2009, 20:106-111.
71. The International HapMap Consortium The international HapMap project. Nature 2003, 426:789-796.
72. Li S., Ma L., Li H., et al. Snap: an integrated SNP annotation platform. Nucleic Acids Res 2007, 35:D707-D710.
73. Ferrer-Costa C., Gelpi J.L., Zamakola L., et al. PMUT: a web-based tool for the annotation of pathological mutations on proteins. Bioinformatics 2005, 21:3176-3178.
74. Yue P., Melamud E., Moult J. SNPs3D: candidate gene and SNP selection for association studies. BMC Bioinformatics 2006, 7:166.
75. Karchin R., Diekhans M., Kelly L., et al. LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics 2005, 21:2814-2820.
76. Cartegni L., Wang J., Zhu Z., Zhang M.Q., Krainer A.R. ESEfinder: a web resource to identify exonic splicing enhancers. Nucleic Acids Res 2003, 31:3568-3571.
77. Fairbrother W.G., Yeh R.F., Sharp P.A., Burge C.B. Predictive identification of exonic splicing enhancers in human genes. Science 2002, 297:1007-1013.
78. Wang Z., Rolish M.E., Yeo G., et al. Systematic identification and analysis of exonic splicing silencers. Cell 2004, 119:831-845.
79. Zhang X.H., Chasin L.A. Computational definition of sequence motifs governing constitutive exon splicing. Genes Dev 2004, 18:1241-1250.
80. Chekmenev D.S., Haid C., Kel A.E. P-Match: transcription factor binding site search by combining patterns and weight matrices. Nucleic Acids Res 2005, 33:W432-W437.
81. Kim B.C., Kim W.Y., Park D., et al. SNP@Promoter: a database of human SNPs (single nucleotide polymorphisms) within the putative promoter regions. BMC Bioinformatics 2008, 9(Suppl. 1):S2.
82. Rebhan M., Chalifa-Caspi V., Prilusky J., Lancet D. GeneCards: integrating information about genes, proteins and diseases. Trends Genet 1997, 13:163.
83. Hindorff L.A., Sethupathy P., Junkins H.A., et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 2009, 106:9362-9367.
84. Yu W., Gwinn M., Clyne M., Yesupriya A., Khoury M.J. A navigator for human genome epidemiology. Nat Genet 2008, 40:124-125.
85. Thorisson G.A., Lancaster O., Free R.C., et al. HGVbaseG2P: a central genetic association database. Nucleic Acids Res 2009, 37:D797-D802.
86. Becker K.G., Barnes K.C., Bright T.J., Wang S.A. The genetic association database. Nat Genet 2004, 36:431-432.
87. Rhee H., Lee J.S. MedRefSNP: a database of medically investigated SNPs. Hum Mutat 2009, 30:E460-E466.
88. Singh A., Olowoyeye A., Baenziger P.H., et al. MutDB: update on development of tools for the biochemical analysis of genetic variation. Nucleic Acids Res 2008, 36:D815-D819.
89. Boutet E., Lieberherr D., Tognolli M., Schneider M., Bairoch A. UniProtKB/Swiss-Prot. Methods Mol Biol 2007, 406:89-112.
90. Ryan M., Diekhans M., Lien S., Liu Y., Karchin R. LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures. Bioinformatics 2009, 25:1431-1432.