iPiG: Integrating Peptide Spectrum Matches into Genome Browser Visualizations
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{"title"=>"iPiG: Integrating Peptide Spectrum Matches into Genome Browser Visualizations", "type"=>"journal", "authors"=>[{"first_name"=>"Mathias", "last_name"=>"Kuhring", "scopus_author_id"=>"55515324200"}, {"first_name"=>"Bernhard Y.", "last_name"=>"Renard", "scopus_author_id"=>"25931246300"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84870751362", "pmid"=>"23226516", "isbn"=>"1932-6203 (Linking)", "scopus"=>"2-s2.0-84870751362", "issn"=>"19326203", "pui"=>"366222101", "doi"=>"10.1371/journal.pone.0050246"}, "id"=>"8c9e43a9-9fc7-387f-9a71-b71b94f80787", "abstract"=>"Proteogenomic approaches have gained increasing popularity, however it is still difficult to integrate mass spectrometry identifications with genomic data due to differing data formats. To address this difficulty, we introduce iPiG as a tool for the integration of peptide identifications from mass spectrometry experiments into existing genome browser visualizations. Thereby, the concurrent analysis of proteomic and genomic data is simplified and proteomic results can directly be compared to genomic data. iPiG is freely available from https://sourceforge.net/projects/ipig/. It is implemented in Java and can be run as a stand-alone tool with a graphical user-interface or integrated into existing workflows. Supplementary data are available at PLOS ONE online.", "link"=>"http://www.mendeley.com/research/ipig-integrating-peptide-spectrum-matches-genome-browser-visualizations", "reader_count"=>25, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>3, "Researcher"=>5, "Student > Ph. D. Student"=>8, "Other"=>5, "Student > Master"=>1, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>3, "Researcher"=>5, "Student > Ph. D. Student"=>8, "Other"=>5, "Student > Master"=>1, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>12, "Chemistry"=>2, "Computer Science"=>2, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Chemistry"=>{"Chemistry"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>12}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"Turkey"=>1, "France"=>1, "India"=>1}, "group_count"=>2}

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/289282"], "description"=>"<div><p>Proteogenomic approaches have gained increasing popularity, however it is still difficult to integrate mass spectrometry identifications with genomic data due to differing data formats. To address this difficulty, we introduce iPiG as a tool for the integration of peptide identifications from mass spectrometry experiments into existing genome browser visualizations. Thereby, the concurrent analysis of proteomic and genomic data is simplified and proteomic results can directly be compared to genomic data. iPiG is freely available from <a href=\"https://sourceforge.net/projects/ipig/\">https://sourceforge.net/projects/ipig/</a>. It is implemented in Java and can be run as a stand-alone tool with a graphical user-interface or integrated into existing workflows. Supplementary data are available at PLOS ONE online.</p> </div>", "links"=>[], "tags"=>["integrating", "peptide", "matches", "genome", "browser", "visualizations"], "article_id"=>116961, "categories"=>["Biochemistry", "Biological Sciences", "Information And Computing Sciences", "Genetics"], "users"=>["Mathias Kuhring", "Bernhard Y. Renard"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0050246", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/iPiG_Integrating_Peptide_Spectrum_Matches_into_Genome_Browser_Visualizations__/116961", "title"=>"iPiG: Integrating Peptide Spectrum Matches into Genome Browser Visualizations", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-12-04 01:56:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/530842"], "description"=>"<p>Custom annotation tracks showing mapped peptides from an iPiG BED file imported into the UCSC Genome Browser. The peptide tracks only contain unique peptides that are mapped to referenced genes (annotation-filtered mapping). The peptides can be easily shown in context with other annotations such as the UCSC Genes (blue track). In particular, here PSMs are shown that mapped to the region of the gene CELA2A on chromosome one. The first PSM track (squish) shows all PSMs individually, where the different colors (grey, orange, green) code for different identification scores (low, mid, high). The second PSM track (dense) shows the PSMs overlapping and thus indicating a contiguous object. Both PSM tracks accurately represent the exon-intron structure of the corresponding gene, where thick blocks indicate exon parts and thin lines and arrows indicate intron parts resp. strand orientation.</p>", "links"=>[], "tags"=>["genome"], "article_id"=>201345, "categories"=>["Biochemistry", "Biological Sciences", "Information And Computing Sciences", "Genetics"], "users"=>["Mathias Kuhring", "Bernhard Y. Renard"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0050246.g002", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PSMs_in_a_genome_browser_/201345", "title"=>"PSMs in a genome browser.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-04 00:22:25"}

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Relative Metric

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