GWAS in a box: statistical and visual analytics of structured associations via GenAMap.
With the continuous improvement in genotyping and molecular phenotyping technology and the decreasing typing cost, it is expected that in a few years, more and more clinical studies of complex diseases will recruit thousands of individuals for pan-omic genetic association analyses. Hence, there is a...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2014-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC4048179?pdf=render |
| _version_ | 1819108427719245824 |
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| author | Eric P Xing Ross E Curtis Georg Schoenherr Seunghak Lee Junming Yin Kriti Puniyani Wei Wu Peter Kinnaird |
| author_facet | Eric P Xing Ross E Curtis Georg Schoenherr Seunghak Lee Junming Yin Kriti Puniyani Wei Wu Peter Kinnaird |
| author_sort | Eric P Xing |
| collection | DOAJ |
| description | With the continuous improvement in genotyping and molecular phenotyping technology and the decreasing typing cost, it is expected that in a few years, more and more clinical studies of complex diseases will recruit thousands of individuals for pan-omic genetic association analyses. Hence, there is a great need for algorithms and software tools that could scale up to the whole omic level, integrate different omic data, leverage rich structure information, and be easily accessible to non-technical users. We present GenAMap, an interactive analytics software platform that 1) automates the execution of principled machine learning methods that detect genome- and phenome-wide associations among genotypes, gene expression data, and clinical or other macroscopic traits, and 2) provides new visualization tools specifically designed to aid in the exploration of association mapping results. Algorithmically, GenAMap is based on a new paradigm for GWAS and PheWAS analysis, termed structured association mapping, which leverages various structures in the omic data. We demonstrate the function of GenAMap via a case study of the Brem and Kruglyak yeast dataset, and then apply it on a comprehensive eQTL analysis of the NIH heterogeneous stock mice dataset and report some interesting findings. GenAMap is available from http://sailing.cs.cmu.edu/genamap. |
| first_indexed | 2024-12-22T03:09:46Z |
| format | Article |
| id | doaj.art-4bc064869a404720b64a362d94f3ef7d |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-22T03:09:46Z |
| publishDate | 2014-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-4bc064869a404720b64a362d94f3ef7d2022-12-21T18:40:57ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0196e9752410.1371/journal.pone.0097524GWAS in a box: statistical and visual analytics of structured associations via GenAMap.Eric P XingRoss E CurtisGeorg SchoenherrSeunghak LeeJunming YinKriti PuniyaniWei WuPeter KinnairdWith the continuous improvement in genotyping and molecular phenotyping technology and the decreasing typing cost, it is expected that in a few years, more and more clinical studies of complex diseases will recruit thousands of individuals for pan-omic genetic association analyses. Hence, there is a great need for algorithms and software tools that could scale up to the whole omic level, integrate different omic data, leverage rich structure information, and be easily accessible to non-technical users. We present GenAMap, an interactive analytics software platform that 1) automates the execution of principled machine learning methods that detect genome- and phenome-wide associations among genotypes, gene expression data, and clinical or other macroscopic traits, and 2) provides new visualization tools specifically designed to aid in the exploration of association mapping results. Algorithmically, GenAMap is based on a new paradigm for GWAS and PheWAS analysis, termed structured association mapping, which leverages various structures in the omic data. We demonstrate the function of GenAMap via a case study of the Brem and Kruglyak yeast dataset, and then apply it on a comprehensive eQTL analysis of the NIH heterogeneous stock mice dataset and report some interesting findings. GenAMap is available from http://sailing.cs.cmu.edu/genamap.http://europepmc.org/articles/PMC4048179?pdf=render |
| spellingShingle | Eric P Xing Ross E Curtis Georg Schoenherr Seunghak Lee Junming Yin Kriti Puniyani Wei Wu Peter Kinnaird GWAS in a box: statistical and visual analytics of structured associations via GenAMap. PLoS ONE |
| title | GWAS in a box: statistical and visual analytics of structured associations via GenAMap. |
| title_full | GWAS in a box: statistical and visual analytics of structured associations via GenAMap. |
| title_fullStr | GWAS in a box: statistical and visual analytics of structured associations via GenAMap. |
| title_full_unstemmed | GWAS in a box: statistical and visual analytics of structured associations via GenAMap. |
| title_short | GWAS in a box: statistical and visual analytics of structured associations via GenAMap. |
| title_sort | gwas in a box statistical and visual analytics of structured associations via genamap |
| url | http://europepmc.org/articles/PMC4048179?pdf=render |
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