Although snpEff does annotate each SNP and indel with the gene that they fall into, we reannotated the VCF files using the latest annotations of the M129 and FH genomes downloaded from NCBI.
To annotate the probes in the Affymetrix array we used the latest annotation file available [ 17].
This feature requires manual curation of the data based on Affymetrix instructions to use the latest annotation, which is also the most relevant.
Probes were annotated using the latest Affymetrix annotation file available (http://www.affymetrix.com/catalog/131488/AFFY/Porcine-Genome-Array#1_1).
The first goal of this study was to rebuild the alternative splicing database using the latest genome annotation and newly acquired 454 sequencing data as transcript evidence.
By using the latest Affymetrix annotation file (dated November 30 , 2008, we found that a total of 33,752 (61.73%) probe sets correspond to unique genes, whereas the remaining probe sets do not and were thus excluded from our statistical analysis.
Therefore, we compared and contrasted human and mouse co-expression maps, obtained from GeneFriends [ 26], an online tool entailing a co-expression analysis of over 60,000 microarray samples, using the latest homology annotation on approximately 16,000 genes.
SNP and indel effects were annotated with snpEff, and we manually re-annotated gene symbols for the SNPs using the latest gene annotations of the M129 and FH reference strains from NCBI.
Gene expression analysis was carried out with GeneSpring GX v10.0.2 software (Agilent Technologies), using the latest gene annotations available.
