Quantitative comparison of EST libraries requires compensation for systematic biases in cDNA generation
<p>Abstract</p> <p>Background</p> <p>Publicly accessible EST libraries contain valuable information that can be utilized for studies of tissue-specific gene expression and processing of individual genes. This information is, however, confounded by multiple systematic ef...
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| Format: | Article |
| Language: | English |
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BMC
2006-02-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/7/77 |
| _version_ | 1818759088601825280 |
|---|---|
| author | Graber Joel H Liu Donglin |
| author_facet | Graber Joel H Liu Donglin |
| author_sort | Graber Joel H |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Publicly accessible EST libraries contain valuable information that can be utilized for studies of tissue-specific gene expression and processing of individual genes. This information is, however, confounded by multiple systematic effects arising from the procedures used to generate these libraries.</p> <p>Results</p> <p>We used alignment of ESTs against a reference set of transcripts to estimate the size distributions of the cDNA inserts and sampled mRNA transcripts in individual EST libraries and show how these measurements can be used to inform quantitative comparisons of libraries. While significant attention has been paid to the effects of normalization and substraction, we also find significant biases in transcript sampling introduced by the combined procedures of reverse transcription and selection of cDNA clones for sequencing. Using examples drawn from studies of mRNA 3'-processing (cleavage and polyadenylation), we demonstrate effects of the transcript sampling bias, and provide a method for identifying libraries that can be safely compared without bias. All data sets, supplemental data, and software are available at our supplemental web site <abbrgrp><abbr bid="B1">1</abbr></abbrgrp>.</p> <p>Conclusion</p> <p>The biases we characterize in the transcript sampling of EST libraries represent a significant and heretofore under-appreciated source of false positive candidates for tissue-, cell type-, or developmental stage-specific activity or processing of genes. Uncorrected, quantitative comparison of dissimilar EST libraries will likely result in the identification of statistically significant, but biologically meaningless changes.</p> |
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| format | Article |
| id | doaj.art-d9a9b6bd9a684107a05e84b2aebc2064 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-18T06:37:10Z |
| publishDate | 2006-02-01 |
| publisher | BMC |
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| spelling | doaj.art-d9a9b6bd9a684107a05e84b2aebc20642022-12-21T21:17:45ZengBMCBMC Bioinformatics1471-21052006-02-01717710.1186/1471-2105-7-77Quantitative comparison of EST libraries requires compensation for systematic biases in cDNA generationGraber Joel HLiu Donglin<p>Abstract</p> <p>Background</p> <p>Publicly accessible EST libraries contain valuable information that can be utilized for studies of tissue-specific gene expression and processing of individual genes. This information is, however, confounded by multiple systematic effects arising from the procedures used to generate these libraries.</p> <p>Results</p> <p>We used alignment of ESTs against a reference set of transcripts to estimate the size distributions of the cDNA inserts and sampled mRNA transcripts in individual EST libraries and show how these measurements can be used to inform quantitative comparisons of libraries. While significant attention has been paid to the effects of normalization and substraction, we also find significant biases in transcript sampling introduced by the combined procedures of reverse transcription and selection of cDNA clones for sequencing. Using examples drawn from studies of mRNA 3'-processing (cleavage and polyadenylation), we demonstrate effects of the transcript sampling bias, and provide a method for identifying libraries that can be safely compared without bias. All data sets, supplemental data, and software are available at our supplemental web site <abbrgrp><abbr bid="B1">1</abbr></abbrgrp>.</p> <p>Conclusion</p> <p>The biases we characterize in the transcript sampling of EST libraries represent a significant and heretofore under-appreciated source of false positive candidates for tissue-, cell type-, or developmental stage-specific activity or processing of genes. Uncorrected, quantitative comparison of dissimilar EST libraries will likely result in the identification of statistically significant, but biologically meaningless changes.</p>http://www.biomedcentral.com/1471-2105/7/77 |
| spellingShingle | Graber Joel H Liu Donglin Quantitative comparison of EST libraries requires compensation for systematic biases in cDNA generation BMC Bioinformatics |
| title | Quantitative comparison of EST libraries requires compensation for systematic biases in cDNA generation |
| title_full | Quantitative comparison of EST libraries requires compensation for systematic biases in cDNA generation |
| title_fullStr | Quantitative comparison of EST libraries requires compensation for systematic biases in cDNA generation |
| title_full_unstemmed | Quantitative comparison of EST libraries requires compensation for systematic biases in cDNA generation |
| title_short | Quantitative comparison of EST libraries requires compensation for systematic biases in cDNA generation |
| title_sort | quantitative comparison of est libraries requires compensation for systematic biases in cdna generation |
| url | http://www.biomedcentral.com/1471-2105/7/77 |
| work_keys_str_mv | AT graberjoelh quantitativecomparisonofestlibrariesrequirescompensationforsystematicbiasesincdnageneration AT liudonglin quantitativecomparisonofestlibrariesrequirescompensationforsystematicbiasesincdnageneration |