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Mapsnp: an R package to plot a genomic map for single nucleotide polymorphisms.

Zhang F, Xu Y, Cao H, Jin C, Cheng Z, Wang G, Shugart YY - PLoS ONE (2015)

Bottom Line: Visualizing genomic coordinates of SNPs, including their physical location relative to their host gene, and the structure of the relevant transcripts, may provide intuitive supplements to the understanding of their functions.Nevertheless, to date, no such easy-to-use programming tools exist.Therefore, we developed an R package, "mapsnp", to plot genomic map for a panel of SNPs within a genome region of interest, including the relative chromosome location and the transcripts in the region. mapsnp is a simple and flexible software package which can be used to visualize a genomic map for SNPs, integrating a chromosome ideogram, genomic coordinates, SNP locations and SNP labels.

View Article: PubMed Central - PubMed

Affiliation: Wuxi Mental Health Center of Nanjing Medical University, Wuxi, Jiangsu Province, China; Unit on Statistical Genomics, Intramural Research Program, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, United States of America.

ABSTRACT
Single-nucleotide polymorphism (SNP) is one of the most common sources of genetic variations of the genome. Currently, SNPs are a main target for most genetic association studies. Visualizing genomic coordinates of SNPs, including their physical location relative to their host gene, and the structure of the relevant transcripts, may provide intuitive supplements to the understanding of their functions. Nevertheless, to date, no such easy-to-use programming tools exist. Therefore, we developed an R package, "mapsnp", to plot genomic map for a panel of SNPs within a genome region of interest, including the relative chromosome location and the transcripts in the region. mapsnp is a simple and flexible software package which can be used to visualize a genomic map for SNPs, integrating a chromosome ideogram, genomic coordinates, SNP locations and SNP labels.

No MeSH data available.


A detailed genomic map for seven SNPs within ATXN2 using Ensembl database.At the top, the relevant chromosome is drawn with the subregion of interest marked in red. The ‘Transcript’ track shows all the alternative transcripts within the region, retrieved from Ensembl database, including a non-ATXN2 transcript U7. At the bottom, the SNPs’ location and ID are plotted along the same genomic coordinate.
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pone.0123609.g001: A detailed genomic map for seven SNPs within ATXN2 using Ensembl database.At the top, the relevant chromosome is drawn with the subregion of interest marked in red. The ‘Transcript’ track shows all the alternative transcripts within the region, retrieved from Ensembl database, including a non-ATXN2 transcript U7. At the bottom, the SNPs’ location and ID are plotted along the same genomic coordinate.

Mentions: The above command plots a genomic map for the ATXN2 SNPs, with multiple alternative transcripts (Fig 1). Please note that users need an established internet connection for the package to work, and that fetching data from UCSC can take some time. Usually, there might be dozens of transcripts for a gene, and the longer a gene is, the more transcripts it has. Therefore, the transcript track may seem redundant for large genes. In many situations, it may be more desirable to create a concise map with all the transcripts stacking together. Nevertheless, there is a caveat in doing so, as there are some transcripts for other overlapping genes within the genomic region, for instance U7 and AC230095.1 in Fig 1. When combining multiple transcripts together, the intended transcript ATXN2 will contain other ‘noisy’ transcripts as well.


Mapsnp: an R package to plot a genomic map for single nucleotide polymorphisms.

Zhang F, Xu Y, Cao H, Jin C, Cheng Z, Wang G, Shugart YY - PLoS ONE (2015)

A detailed genomic map for seven SNPs within ATXN2 using Ensembl database.At the top, the relevant chromosome is drawn with the subregion of interest marked in red. The ‘Transcript’ track shows all the alternative transcripts within the region, retrieved from Ensembl database, including a non-ATXN2 transcript U7. At the bottom, the SNPs’ location and ID are plotted along the same genomic coordinate.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4390227&req=5

pone.0123609.g001: A detailed genomic map for seven SNPs within ATXN2 using Ensembl database.At the top, the relevant chromosome is drawn with the subregion of interest marked in red. The ‘Transcript’ track shows all the alternative transcripts within the region, retrieved from Ensembl database, including a non-ATXN2 transcript U7. At the bottom, the SNPs’ location and ID are plotted along the same genomic coordinate.
Mentions: The above command plots a genomic map for the ATXN2 SNPs, with multiple alternative transcripts (Fig 1). Please note that users need an established internet connection for the package to work, and that fetching data from UCSC can take some time. Usually, there might be dozens of transcripts for a gene, and the longer a gene is, the more transcripts it has. Therefore, the transcript track may seem redundant for large genes. In many situations, it may be more desirable to create a concise map with all the transcripts stacking together. Nevertheless, there is a caveat in doing so, as there are some transcripts for other overlapping genes within the genomic region, for instance U7 and AC230095.1 in Fig 1. When combining multiple transcripts together, the intended transcript ATXN2 will contain other ‘noisy’ transcripts as well.

Bottom Line: Visualizing genomic coordinates of SNPs, including their physical location relative to their host gene, and the structure of the relevant transcripts, may provide intuitive supplements to the understanding of their functions.Nevertheless, to date, no such easy-to-use programming tools exist.Therefore, we developed an R package, "mapsnp", to plot genomic map for a panel of SNPs within a genome region of interest, including the relative chromosome location and the transcripts in the region. mapsnp is a simple and flexible software package which can be used to visualize a genomic map for SNPs, integrating a chromosome ideogram, genomic coordinates, SNP locations and SNP labels.

View Article: PubMed Central - PubMed

Affiliation: Wuxi Mental Health Center of Nanjing Medical University, Wuxi, Jiangsu Province, China; Unit on Statistical Genomics, Intramural Research Program, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, United States of America.

ABSTRACT
Single-nucleotide polymorphism (SNP) is one of the most common sources of genetic variations of the genome. Currently, SNPs are a main target for most genetic association studies. Visualizing genomic coordinates of SNPs, including their physical location relative to their host gene, and the structure of the relevant transcripts, may provide intuitive supplements to the understanding of their functions. Nevertheless, to date, no such easy-to-use programming tools exist. Therefore, we developed an R package, "mapsnp", to plot genomic map for a panel of SNPs within a genome region of interest, including the relative chromosome location and the transcripts in the region. mapsnp is a simple and flexible software package which can be used to visualize a genomic map for SNPs, integrating a chromosome ideogram, genomic coordinates, SNP locations and SNP labels.

No MeSH data available.