A Survey of Genomic Properties for the Detection of Regulatory Polymorphisms
Publication Date
June 08, 2007
Journal
PLOS Computational Biology
Authors
Stephen B Montgomery, Obi L Griffith, Johanna M Schuetz, Angela Brooks Wilson, et al
Volume
3
Issue
6
Pages
e106
DOI
https://dx.plos.org/10.1371/journal.pcbi.0030106
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.0030106
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/17559298
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1892352
Europe PMC
http://europepmc.org/abstract/MED/17559298
Web of Science
000249105500010
Scopus
34347342903
Mendeley
http://www.mendeley.com/research/survey-genomic-properties-detection-regulatory-polymorphisms
Events
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CiteULike | Further Information

Mendeley | Further Information

{"title"=>"A survey of genomic properties for the detection of regulatory polymorphisms", "type"=>"journal", "authors"=>[{"first_name"=>"Stephen B.", "last_name"=>"Montgomery", "scopus_author_id"=>"8708455800"}, {"first_name"=>"Obi L.", "last_name"=>"Griffith", "scopus_author_id"=>"7102837839"}, {"first_name"=>"Johanna M.", "last_name"=>"Schuetz", "scopus_author_id"=>"16686855400"}, {"first_name"=>"Angela", "last_name"=>"Brooks-Wilson", "scopus_author_id"=>"6701511300"}, {"first_name"=>"Steven J M", "last_name"=>"Jones", "scopus_author_id"=>"55732380600"}], "year"=>2007, "source"=>"PLoS Computational Biology", "identifiers"=>{"sgr"=>"34347342903", "doi"=>"10.1371/journal.pcbi.0030106", "pui"=>"47015836", "issn"=>"1553734X", "pmid"=>"17559298", "isbn"=>"1553-734X\\r1553-7358", "scopus"=>"2-s2.0-34347342903"}, "id"=>"102bda99-cfd8-3b08-bbce-05e98160f08c", "abstract"=>"Advances in the computational identification of functional noncoding polymorphisms will aid in cataloging novel determinants of health and identifying genetic variants that explain human evolution. To date, however, the development and evaluation of such techniques has been limited by the availability of known regulatory polymorphisms. We have attempted to address this by assembling, from the literature, a computationally tractable set of regulatory polymorphisms within the ORegAnno database (http://www.oreganno.org). We have further used 104 regulatory single-nucleotide polymorphisms from this set and 951 polymorphisms of unknown function, from 2-kb and 152-bp noncoding upstream regions of genes, to investigate the discriminatory potential of 23 properties related to gene regulation and population genetics. Among the most important properties detected in this region are distance to transcription start site, local repetitive content, sequence conservation, minor and derived allele frequencies, and presence of a CpG island. We further used the entire set of properties to evaluate their collective performance in detecting regulatory polymorphisms. Using a 10-fold cross-validation approach, we were able to achieve a sensitivity and specificity of 0.82 and 0.71, respectively, and we show that this performance is strongly influenced by the distance to the transcription start site.", "link"=>"http://www.mendeley.com/research/survey-genomic-properties-detection-regulatory-polymorphisms", "reader_count"=>43, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>7, "Researcher"=>16, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>2, "Other"=>1, "Student > Master"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>7, "Researcher"=>16, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>2, "Other"=>1, "Student > Master"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>7, "Mathematics"=>1, "Agricultural and Biological Sciences"=>29, "Medicine and Dentistry"=>2, "Philosophy"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>29}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>2}, "Philosophy"=>{"Philosophy"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>5, "Italy"=>1, "United Kingdom"=>2, "Germany"=>1, "Spain"=>1}, "group_count"=>2}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/948719"], "description"=>"<p>Representative ROC curves were calculated by training an SVM on a 90% subset of the 104-rSNP and ufSNP datasets. Here, 93 rSNPs and 882 ufSNPs were used for training, followed by testing on the held-out 10%. The ALL SVM approach was used for training. Furthermore, each curve had one tested property held out to demonstrate the impact of various properties on training. Notably, many curves are the same except for a marked reduction in performance when the “Distance to TSS” property is held out. The area under the “all” curve is 0.830. The dot on the “all” curve marks the location of the decision boundary selected by the SVM. At this boundary, the SVM identifies nine of 11 true positives and 56 of 69 true negatives. (Plots for each tested partition are available at <a href=\"http://www.bcgsc.ca/chum/gistplots.html\" target=\"_blank\">http://www.bcgsc.ca/chum/gistplots.html</a>).</p>", "links"=>[], "tags"=>["curves", "discriminating", "rsnps"], "article_id"=>619045, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Stephen B Montgomery", "Obi L Griffith", "Johanna M Schuetz", "Angela Brooks-Wilson", "Steven J. M Jones"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0030106.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_ROC_Curves_for_Discriminating_Known_rSNPs_from_ufSNPs_/619045", "title"=>"ROC Curves for Discriminating Known rSNPs from ufSNPs", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-06-08 02:30:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/948631"], "description"=>"<p>CpG island expectancy is plotted for each chromosome as a function of the distance from the TSS. This type of data was used to normalize many of the features in this study for distance from the TSS. In this figure, the expectancy of being in a CpG island at position −1 for any promoter region is ~0.5.</p>", "links"=>[], "tags"=>["positional"], "article_id"=>618955, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Stephen B Montgomery", "Obi L Griffith", "Johanna M Schuetz", "Angela Brooks-Wilson", "Steven J. M Jones"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0030106.g001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_CpG_Island_Positional_Bias_/618955", "title"=>"CpG Island Positional Bias", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-06-08 02:29:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/475365", "https://ndownloader.figshare.com/files/475415", "https://ndownloader.figshare.com/files/475562", "https://ndownloader.figshare.com/files/475584"], "description"=>"<div><p>Advances in the computational identification of functional noncoding polymorphisms will aid in cataloging novel determinants of health and identifying genetic variants that explain human evolution. To date, however, the development and evaluation of such techniques has been limited by the availability of known regulatory polymorphisms. We have attempted to address this by assembling, from the literature, a computationally tractable set of regulatory polymorphisms within the ORegAnno database (<a href=\"http://www.oreganno.org\">http://www.oreganno.org</a>). We have further used 104 regulatory single-nucleotide polymorphisms from this set and 951 polymorphisms of unknown function, from 2-kb and 152-bp noncoding upstream regions of genes, to investigate the discriminatory potential of 23 properties related to gene regulation and population genetics. Among the most important properties detected in this region are distance to transcription start site, local repetitive content, sequence conservation, minor and derived allele frequencies, and presence of a CpG island. We further used the entire set of properties to evaluate their collective performance in detecting regulatory polymorphisms. Using a 10-fold cross-validation approach, we were able to achieve a sensitivity and specificity of 0.82 and 0.71, respectively, and we show that this performance is strongly influenced by the distance to the transcription start site.</p></div>", "links"=>[], "tags"=>["genomic", "properties", "detection", "polymorphisms"], "article_id"=>153697, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Stephen B Montgomery", "Obi L Griffith", "Johanna M Schuetz", "Angela Brooks-Wilson", "Steven J. M Jones"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.0030106.sg001", "https://dx.doi.org/10.1371/journal.pcbi.0030106.st001", "https://dx.doi.org/10.1371/journal.pcbi.0030106.st002", "https://dx.doi.org/10.1371/journal.pcbi.0030106.sd001"], "stats"=>{"downloads"=>3, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Survey_of_Genomic_Properties_for_the_Detection_of_Regulatory_Polymorphisms/153697", "title"=>"A Survey of Genomic Properties for the Detection of Regulatory Polymorphisms", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2007-06-08 01:01:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/948831"], "description"=>"<p>The positions of rSNPs are plotted in a histogram for bin sizes of 10 bp for the first 300 bp of sequence from the TSS. A blip is seen at position 21–31, where it is likely that TATA and CCAAT box–binding sites are located. These types of rSNPs, however, are only slightly overrepresented in this study and from this graph are not expected to significantly bias the outcome.</p>", "links"=>[], "tags"=>["positional", "rsnps", "300", "bp"], "article_id"=>619153, "categories"=>["Biological Sciences", "Genetics", "Evolutionary Biology"], "users"=>["Stephen B Montgomery", "Obi L Griffith", "Johanna M Schuetz", "Angela Brooks-Wilson", "Steven J. M Jones"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.0030106.g003", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Histogram_of_Positional_Bias_of_rSNPs_for_the_First_300_bp_of_Sequence_/619153", "title"=>"Histogram of Positional Bias of rSNPs for the First 300 bp of Sequence", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-06-08 02:32:33"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"4", "full-text"=>"2", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"8"}
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Relative Metric

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