ArticleBMC bioinformatics2007
Discarding duplicate ditags in LongSAGE analysis may introduce significant error.
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Palindromic sequence impedes sequencing-by-ligation mechanism.BMC systems biology · 2012Article
- Identification of novel androgen-responsive genes by sequencing of LongSAGE libraries.BMC genomics · 2009Article
- Gene expression profiling via LongSAGE in a non-model plant species: a case study in seeds of Brassica napus.BMC genomics · 2009Article
- A human glomerular SAGE transcriptome database.BMC nephrology · 2009Article
- Functional analysis of MmeI from methanol utilizer Methylophilus methylotrophus, a subtype IIC restriction-modification enzyme related to type I enzymes.Applied and environmental microbiology · 2009Article
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Authors and funding
6 authors.
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Abstract
backgroundDuring 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.
resultsAn 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 duplicate ditags was able to identify individual artifact ditags that originated from rare nucleotide variations of tags and vector contamination.
conclusionThe removal of all duplicate ditags was unfounded for the datasets analyzed and led to large errors. This may also be the case for other LongSAGE datasets already present in databases. Analysis of the ditag population, however, can identify artifact tags that should be removed from analysis or have their tag count adjusted.
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