Gene prediction and modelling were performed by automatic gene assignment programs that employ ab initio gene finding and similarity searches.
The new method of EST to gene assignment improved accuracy enabling a higher percentage of ESTs to be unambiguously assigned compared to the Huminiecki and Bicknell method [8].
Gene assignment was performed using featureCounts.
Expression of the gene product in functional form and biochemical characterization of the product is therefore necessary before the gene assignment is finally established.
Source code for our target gene assignment program is available on request.
Another mapped locus (CHL2) with contradictory mapping information and a questionable gene assignment was also removed.
This was used to calculate the estimated probability of presence that gives a statistical validation of the gene assignment.
Gene assignment was based on the levels of naming specificity used by the Manetee project (The Institute for Genomic Research TIGRR) http://manatee.sourceforge.net).net
As shown in Table 2, the percentage of clones for which we identified a peak was much lower among the clones with no assignment to an Entrez gene than those with a gene assignment.
To perform a statistical test not biased by the redundancy of the probe sets (more probe sets for the same gene), the computation of p-value of functional enrichment was based on the Entrez Gene assignment.
Table 2 summarises the SNP to gene assignment.
