ArchiLD: Hierarchical visualization of linkage disequilibrium in human populations

PLoS ONE

Volumn 9, Issue 1, 2014, Pages

  Melchiotti, Rossella ^a,b   Rötzschke, Olaf ^a   Poidinger, Michael ^a  

^a AGENCY FOR SCIENCE   (Singapore)

^b UNIVERSITY OF MILANO BICOCCA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHILD DATA BASE; ARTICLE; COMPUTER PROGRAM; DATA BASE; GENE CONTROL; GENE EXPRESSION; GENE LINKAGE DISEQUILIBRIUM; GENETIC CONSERVATION; GENOMICS; GENOTYPE; HUMAN; SINGLE NUCLEOTIDE POLYMORPHISM;

GENETIC LINKAGE; GENOME, HUMAN; GENOTYPE; HUMANS; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE;

EID: 84904126622     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0086761     Document Type: Article

References (20)

1. Kofler R, Schlötterer C (2012) Gowinda: unbiased analysis of gene set enrichment for genome-wide association studies. Bioinformatics 28: 2084-2085.
2. The International HapMap Consortium (2003) The International HapMap Project. Nature 426: 789-796.
3. The International HapMap Consortium (2005) A haplotype map of the human genome. Nature 437: 1299-1320.
4. The International HapMap Consortium (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449: 851-861.
5. The International HapMap Consortium (2010) Integrating common and rare genetic variation in diverse human populations. Nature 467: 52-58.
6. The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing. Nature 467: 1061-1073.
7. Barrett JC, Fry B, Maller J, Daly MJ (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21: 263-265. (Pubitemid 40202029)
8. Bush WS, Dudek SM, Ritchie MD (2010) Visualizing SNP statistics in the context of linkage disequilibrium using LD-Plus. Bioinformatics 26: 578-579.
9. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, et al. (2002) The Human Genome Browser at UCSC. Genome Res 12: 996-1006. (Pubitemid 34662293)
10. Johnson AD, Handsaker RE, Pulit SL, Nizzari MM, O'Donnell CJ, et al. (2008) SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap. Bioinformatics 24: 2938-2939.
11. The 1000 Genomes Project Consortium (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491: 56-65.
12. R Development Core Team (2012) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. p.
13. UCSC Genome Bioinformatics (n.d.). Available:http://genome.ucsc.edu/FAQ/ FAQformat.html. Accessed 20 December 2013.
14. Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, et al. (2013) The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res 41: D64-D69.
15. Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, et al. (2006) The UCSC Genome Browser Database: update 2006. Nucleic Acids Res 34: D590-D598.
16. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, et al. (2007) PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses. Am J Hum Genet 81: 559-575. (Pubitemid 47330214)
17. Qt Jambi (n.d.). Available:http://qt-jambi.org/. Accessed 20 December 2013.
18. Pruim RJ, Welch RP, Sanna S, Teslovich TM, Chines PS, et al. (2010) LocusZoom: regional visualization of genome-wide association scan results. Bioinformatics 26: 2336-2337.
19. Ricopili (2010). Available:http://www.broadinstitute.org/mpg/ricopili/. Accessed 20 December 2013.
20. ArchiLD (2013). Available:http://archild.sign.a-star.edu.sg/. Accessed 20 December 2013.