Harbin: a quantitation PCR analysis tool
Objectives To enable analysis and comparisons of different relative quantitation experiments, a web-browser application called Harbin was created that uses a quantile-based scoring system for the comparison of samples at different time points and between experiments. Results Harbin uses the standard...
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| Veröffentlicht in: | Biotechnology letters 2017, Vol.39 (1), p.171-178 |
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| container_title | Biotechnology letters |
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| creator | Bester, Rachelle Pepler, Pieter T. Aldrich, Dirk J. Maree, Hans J. |
| description | Objectives
To enable analysis and comparisons of different relative quantitation experiments, a web-browser application called Harbin was created that uses a quantile-based scoring system for the comparison of samples at different time points and between experiments.
Results
Harbin uses the standard curve method for relative quantitation to calculate concentration ratios (CRs). To evaluate if different datasets can be combined the Harbin quantile bootstrap test is proposed. This test is more sensitive in detecting distributional differences between data sets than the Kolmogorov–Smirnov test. The utility of the test is demonstrated in a comparison of three grapevine leafroll associated virus 3 (GLRaV-3) RT-qPCR data sets.
Conclusions
The quantile-based scoring system of CRs will enable the monitoring of virus titre or gene expression over different time points and be useful in other genomic applications where the combining of data sets are required. |
| doi_str_mv | 10.1007/s10529-016-2221-1 |
| format | Article |
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To enable analysis and comparisons of different relative quantitation experiments, a web-browser application called Harbin was created that uses a quantile-based scoring system for the comparison of samples at different time points and between experiments.
Results
Harbin uses the standard curve method for relative quantitation to calculate concentration ratios (CRs). To evaluate if different datasets can be combined the Harbin quantile bootstrap test is proposed. This test is more sensitive in detecting distributional differences between data sets than the Kolmogorov–Smirnov test. The utility of the test is demonstrated in a comparison of three grapevine leafroll associated virus 3 (GLRaV-3) RT-qPCR data sets.
Conclusions
The quantile-based scoring system of CRs will enable the monitoring of virus titre or gene expression over different time points and be useful in other genomic applications where the combining of data sets are required.</description><identifier>ISSN: 0141-5492</identifier><identifier>EISSN: 1573-6776</identifier><identifier>DOI: 10.1007/s10529-016-2221-1</identifier><identifier>PMID: 27695982</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Applied Microbiology ; Biochemistry ; Biomedical and Life Sciences ; Biotechnology ; Genetic diversity ; Life Sciences ; Mathematical analysis ; Microbiology ; Monitoring ; Original Research Paper ; Polymerase chain reaction ; Quantiles ; Real-Time Polymerase Chain Reaction ; Scoring ; Software ; Utilities ; Viruses ; Vitaceae</subject><ispartof>Biotechnology letters, 2017, Vol.39 (1), p.171-178</ispartof><rights>Springer Science+Business Media Dordrecht 2016</rights><rights>Biotechnology Letters is a copyright of Springer, 2017.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c475t-a523eec7a010cbb5e57ab53522908900b48639910f0b577e0a72ac18c76096c33</citedby><cites>FETCH-LOGICAL-c475t-a523eec7a010cbb5e57ab53522908900b48639910f0b577e0a72ac18c76096c33</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s10529-016-2221-1$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10529-016-2221-1$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27695982$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Bester, Rachelle</creatorcontrib><creatorcontrib>Pepler, Pieter T.</creatorcontrib><creatorcontrib>Aldrich, Dirk J.</creatorcontrib><creatorcontrib>Maree, Hans J.</creatorcontrib><title>Harbin: a quantitation PCR analysis tool</title><title>Biotechnology letters</title><addtitle>Biotechnol Lett</addtitle><addtitle>Biotechnol Lett</addtitle><description>Objectives
To enable analysis and comparisons of different relative quantitation experiments, a web-browser application called Harbin was created that uses a quantile-based scoring system for the comparison of samples at different time points and between experiments.
Results
Harbin uses the standard curve method for relative quantitation to calculate concentration ratios (CRs). To evaluate if different datasets can be combined the Harbin quantile bootstrap test is proposed. This test is more sensitive in detecting distributional differences between data sets than the Kolmogorov–Smirnov test. The utility of the test is demonstrated in a comparison of three grapevine leafroll associated virus 3 (GLRaV-3) RT-qPCR data sets.
Conclusions
The quantile-based scoring system of CRs will enable the monitoring of virus titre or gene expression over different time points and be useful in other genomic applications where the combining of data sets are required.</description><subject>Applied Microbiology</subject><subject>Biochemistry</subject><subject>Biomedical and Life Sciences</subject><subject>Biotechnology</subject><subject>Genetic diversity</subject><subject>Life Sciences</subject><subject>Mathematical analysis</subject><subject>Microbiology</subject><subject>Monitoring</subject><subject>Original Research Paper</subject><subject>Polymerase chain reaction</subject><subject>Quantiles</subject><subject>Real-Time Polymerase Chain Reaction</subject><subject>Scoring</subject><subject>Software</subject><subject>Utilities</subject><subject>Viruses</subject><subject>Vitaceae</subject><issn>0141-5492</issn><issn>1573-6776</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqNkU1Lw0AQhhdRbK3-AC8S8NLL6uxXJutNilqhoIiel826lZQ0abPJof_erakigtDTHOZ5n4F5CTlncMUA8DowUFxTYCnlnDPKDsiQKRQ0RUwPyRCYZFRJzQfkJIQFAGgEPCYDjqlWOuNDMp7aJi-qm8Qm685WbdHatqir5HnyktjKlptQhKSt6_KUHM1tGfzZbo7I2_3d62RKZ08Pj5PbGXUSVUut4sJ7hxYYuDxXXqHNlVCca8g0QC6zVGjNYA65QvRgkVvHMocp6NQJMSLj3rtq6nXnQ2uWRXC-LG3l6y4YlqHWmdJiH1TpeE4i3wMVSuj4SBnRyz_oou6a-IovoUQppNoKWU-5pg6h8XOzaoqlbTaGgdmWY_pyTHSabTmGxczFztzlS__-k_huIwK8B0JcVR---XX6X-snjcOU8Q</recordid><startdate>2017</startdate><enddate>2017</enddate><creator>Bester, 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J.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Harbin: a quantitation PCR analysis tool</atitle><jtitle>Biotechnology letters</jtitle><stitle>Biotechnol Lett</stitle><addtitle>Biotechnol Lett</addtitle><date>2017</date><risdate>2017</risdate><volume>39</volume><issue>1</issue><spage>171</spage><epage>178</epage><pages>171-178</pages><issn>0141-5492</issn><eissn>1573-6776</eissn><abstract>Objectives
To enable analysis and comparisons of different relative quantitation experiments, a web-browser application called Harbin was created that uses a quantile-based scoring system for the comparison of samples at different time points and between experiments.
Results
Harbin uses the standard curve method for relative quantitation to calculate concentration ratios (CRs). To evaluate if different datasets can be combined the Harbin quantile bootstrap test is proposed. This test is more sensitive in detecting distributional differences between data sets than the Kolmogorov–Smirnov test. The utility of the test is demonstrated in a comparison of three grapevine leafroll associated virus 3 (GLRaV-3) RT-qPCR data sets.
Conclusions
The quantile-based scoring system of CRs will enable the monitoring of virus titre or gene expression over different time points and be useful in other genomic applications where the combining of data sets are required.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><pmid>27695982</pmid><doi>10.1007/s10529-016-2221-1</doi><tpages>8</tpages></addata></record> |
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| subjects | Applied Microbiology Biochemistry Biomedical and Life Sciences Biotechnology Genetic diversity Life Sciences Mathematical analysis Microbiology Monitoring Original Research Paper Polymerase chain reaction Quantiles Real-Time Polymerase Chain Reaction Scoring Software Utilities Viruses Vitaceae |
| title | Harbin: a quantitation PCR analysis tool |
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