Information-theoretic identification of predictive SNPs and supervised visualization of genome-wide association studies
The size, dimensionality and the limited range of the data values makes visualization of single nucleotide polymorphism (SNP) datasets challenging. The purpose of this study is to evaluate the usefulness of 3D VizStruct, a novel multi-dimensional data visualization technique for SNP datasets capable...
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| Veröffentlicht in: | Nucleic acids research 2006-01, Vol.34 (14), p.e101-e101 |
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| creator | Bhasi, Kavitha Zhang, Li Brazeau, Daniel Zhang, Aidong Ramanathan, Murali |
| description | The size, dimensionality and the limited range of the data values makes visualization of single nucleotide polymorphism (SNP) datasets challenging. The purpose of this study is to evaluate the usefulness of 3D VizStruct, a novel multi-dimensional data visualization technique for SNP datasets capable of identifying informative SNPs in genome-wide association studies. VizStruct is an interactive visualization technique that reduces multi-dimensional data to three dimensions using a combination of the discrete Fourier transform and the Kullback-Leibler divergence. The performance of 3D VizStruct was challenged with several diverse, biologically relevant published datasets including the human lipoprotein lipase (LPL) gene locus, the human Y-chromosome in several populations and a multi-locus genotype dataset of coral samples from four populations. In every case, the SNPs and or polymorphic markers identified by the 3D VizStruct mapping were predictive of the underlying biology. |
| doi_str_mv | 10.1093/nar/gkl520 |
| format | Article |
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In every case, the SNPs and or polymorphic markers identified by the 3D VizStruct mapping were predictive of the underlying biology.</description><subject>Animals</subject><subject>Anthozoa - genetics</subject><subject>Chromosomes, Human, Y</subject><subject>Computer Graphics</subject><subject>Gene Frequency</subject><subject>Genomics - methods</subject><subject>Genotype</subject><subject>Haplotypes</subject><subject>Humans</subject><subject>Information Theory</subject><subject>Linkage Disequilibrium</subject><subject>Lipoprotein Lipase - genetics</subject><subject>Male</subject><subject>Methods Online</subject><subject>Polymorphism, Single Nucleotide</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2006</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqF0ctu1DAUBmALgehQ2PAAELFggRR6fEucDRKquFSqAKl0bfk6dUnswU6mgqfHkFG5bNjYi_Ppl49_hB5jeIlhoCdR5ZPtl5ETuIM2mHakZUNH7qINUOAtBiaO0INSrgEww5zdR0e4E8PAmNigm7PoU57UHFJs5yuXspuDaYJ1cQ4-mF-DJvlml50NZg5711x8-FQaFW1Tlp3L-1Ccbeq5qDF8v_VbF9Pk2pua1KhSkgnrqMyLDa48RPe8Got7dLiP0eXbN59P37fnH9-dnb4-bw3jYm47TgcwFpxWVhtPhBZWqUFhTAnuqBHc-151DhhU2YPCvSBE91pzrDnV9Bi9WnN3i56cNXWtrEa5y2FS-ZtMKsi_JzFcyW3aS8x5L0DUgOeHgJy-Lq7McgrFuHFU0aWlyE4IQgVh_4V4oLQyXOGzf-B1WnKsvyAJAO-7gUNFL1ZkciolO3_7ZAzyZ-uyti7X1it-8ueSv-mh5gqersCrJNU2hyIvLwhgCjWqLiDoDxPGth4</recordid><startdate>20060101</startdate><enddate>20060101</enddate><creator>Bhasi, Kavitha</creator><creator>Zhang, Li</creator><creator>Brazeau, Daniel</creator><creator>Zhang, Aidong</creator><creator>Ramanathan, Murali</creator><general>Oxford Publishing Limited (England)</general><general>Oxford University Press</general><scope>FBQ</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7QO</scope><scope>7QP</scope><scope>7QR</scope><scope>7SS</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20060101</creationdate><title>Information-theoretic identification of predictive SNPs and supervised visualization of genome-wide association studies</title><author>Bhasi, Kavitha ; Zhang, Li ; Brazeau, Daniel ; Zhang, Aidong ; Ramanathan, Murali</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c458t-65390cd0ebadbcf28b8daa9a1132163c85ff7a6e04053970a17822b7bb51b53b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2006</creationdate><topic>Animals</topic><topic>Anthozoa - genetics</topic><topic>Chromosomes, Human, Y</topic><topic>Computer Graphics</topic><topic>Gene Frequency</topic><topic>Genomics - methods</topic><topic>Genotype</topic><topic>Haplotypes</topic><topic>Humans</topic><topic>Information Theory</topic><topic>Linkage Disequilibrium</topic><topic>Lipoprotein Lipase - genetics</topic><topic>Male</topic><topic>Methods Online</topic><topic>Polymorphism, Single Nucleotide</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Bhasi, Kavitha</creatorcontrib><creatorcontrib>Zhang, Li</creatorcontrib><creatorcontrib>Brazeau, Daniel</creatorcontrib><creatorcontrib>Zhang, Aidong</creatorcontrib><creatorcontrib>Ramanathan, Murali</creatorcontrib><collection>AGRIS</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Bhasi, Kavitha</au><au>Zhang, Li</au><au>Brazeau, Daniel</au><au>Zhang, Aidong</au><au>Ramanathan, Murali</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Information-theoretic identification of predictive SNPs and supervised visualization of genome-wide association studies</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2006-01-01</date><risdate>2006</risdate><volume>34</volume><issue>14</issue><spage>e101</spage><epage>e101</epage><pages>e101-e101</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><coden>NARHAD</coden><abstract>The size, dimensionality and the limited range of the data values makes visualization of single nucleotide polymorphism (SNP) datasets challenging. The purpose of this study is to evaluate the usefulness of 3D VizStruct, a novel multi-dimensional data visualization technique for SNP datasets capable of identifying informative SNPs in genome-wide association studies. VizStruct is an interactive visualization technique that reduces multi-dimensional data to three dimensions using a combination of the discrete Fourier transform and the Kullback-Leibler divergence. The performance of 3D VizStruct was challenged with several diverse, biologically relevant published datasets including the human lipoprotein lipase (LPL) gene locus, the human Y-chromosome in several populations and a multi-locus genotype dataset of coral samples from four populations. In every case, the SNPs and or polymorphic markers identified by the 3D VizStruct mapping were predictive of the underlying biology.</abstract><cop>England</cop><pub>Oxford Publishing Limited (England)</pub><pmid>16899448</pmid><doi>10.1093/nar/gkl520</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Animals Anthozoa - genetics Chromosomes, Human, Y Computer Graphics Gene Frequency Genomics - methods Genotype Haplotypes Humans Information Theory Linkage Disequilibrium Lipoprotein Lipase - genetics Male Methods Online Polymorphism, Single Nucleotide |
| title | Information-theoretic identification of predictive SNPs and supervised visualization of genome-wide association studies |
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