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

Background: 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. Results: 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...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Donglin Liu, Joel H. Graber
• Keywords: Accessible Est Libraries, BMCBI 2006, Cdna Clone, EST Libraries