Quantitative comparison of EST libraries requires compensation for systematic biases in cDNA generation

BMC Bioinformatics
Donglin Liu, Joel H Graber

Abstract

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. 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. The biases we characterize in the transcript sampling of EST libraries represent a significant an...Continue Reading

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Citations

Apr 4, 2008·Molecular Genetics and Genomics : MGG·Joachim JacobGodelieve Gheysen
Jul 3, 2009·Neuropsychopharmacology : Official Publication of the American College of Neuropsychopharmacology·Amélie SoumierAnnie Daszuta
Dec 13, 2006·Nucleic Acids Research·Donglin LiuJoel H Graber
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Nov 22, 2018·Langmuir : the ACS Journal of Surfaces and Colloids·Jie YangYi-Tao Long

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Software Mentioned

BLAT
ExQuest
dbEST
BodyMap
ENSEMBL
MathType
PACdb
Tissuelnfo

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