Discarding duplicate ditags in LongSAGE analysis may introduce significant error

Background: During gene expression analysis by Serial Analysis of Gene Expression (SAGE), duplicate ditags are routinely removed from the data analysis, because they are suspected to stem from artifacts during SAGE library construction. As a consequence, naturally occurring duplicate ditags are also removed from the analysis leading to an error of measurement. Results: An algorithm was developed to analyze the differential occurrence of SAGE tags in different ditag combinations. Analysis of a pancreatic acinar cell LongSAGE library showed no sign of a general amplification bias that justified the removal of all duplicate ditags. Extending the analysis to 10 additional LongSAGE libraries showed no justification for removal of all duplicate ditags either. On the contrary, while the error introduced in original SAGE by removal of naturally occurring duplicate ditags is insignificant, it leads to an error of up to 3 fold in LongSAGE. However, the algorithm developed for the analysis of du...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Jeppe Emmersen, Anna M. Heidenblut, Annabeth Laursen Høgh, Stephan A. Hahn, Karen G. Welinder, Kåre L. Nielsen
• Keywords: Analysis, BMCBI 2007, Gene Expression, Gene Expression Analysis