What are the technical biases that may affect the analysis of a particular gene?
Several problems can prevent identification of a specific gene in the libraries. These are all sequence-specific and so only affect a small percentage of the total genes. However, if your gene is one of those that are affected, you’re out of luck. (Sorry!) The potential problems are: 1) Not all genes (including 3’UTRs) contain Sau3A sites (GATC), which was used for our libraries and hence is necessary for your gene of interest to appear in this MPSS analysis. Lynx may use other restriction sites, but for this database, no Sau3A site = no signature. 2) Some signatures identified from the mRNA may span splice sites in the genomic sequence. Currently, we cannot insert gaps in signatures to span these sites. The only way to remedy this is to extract potential signatures from a full-length cDNA, then compare these to the genomic sequence to see if any of them occur close to splice sites. The 5′ and 3′ ends can be obtained from the RIKEN full-length cDNA collection; the 3′ ends may be useful
