Park et al. BMC Genomics 2012, 13:473 http://www.biomedcentral.com/1471-2164/13/473 oxide synthase (iNOS; ENSECAT00000026843) [41], were upregulated in horse muscle after exercise. Among the 1,285 DEGs from the two tissues, we iden- tified 91 transcription factors, which might regulate downstream components of exercise-triggered signal- ing pathways (Additional file 1: Table S19). GATA2, which can interact with AP1 transcription factors to regulate MAPK and NF-κB signaling [42], was under- expressed in blood, while CREB5, whose zinc-finger and bZIP domain can specifically bind to the CRE with c-Jun or CRE-BP1 [43], was overexpressed in muscle. Upregulation of CREB5 might be explained by the fact that CREB5 and c-Jun genes are involved in calcium- dependent transcriptional pathways in skeletal muscle [44]. At least 56 uncharacterized transcription factors could be candidates for novel primary transcriptional regula- tors accompanying exercise. We validated the expression levels of seven randomly chosen transcription factors using quantitative RT-PCR from the remaining sample materials (Additional file 1: Tables S20 and S21). Page 5 of 8 Switching the expression pattern of alternative splicing forms of the gene before and after exercising Four genes (three from muscle, one from blood) showed interesting RNA expression patterns, in which two dif- ferent alternative splicing forms of the same gene showed reversed expression patterns before and after ex- ercising, similar to that of the SXL gene in Drosophila [45]. This observation suggested a cost-effective method of regulation: the cells do not have to produce com- pletely new exons and proteins, but merely change the composition of the existing exons [46]. The genes with reversed expression are: AXL, DYNC1, PLEKHG1, and COBLL1 (Additional file 1: Table S22 and Additional file 1: Figure S11). Figure 2 shows cytoplasmic dynein inter- mediate chain (ENSECAG00000020218) protein (DYNC1) [47] as an example of the reversed expression pattern in muscle before and after exercising. Conclusion We generated a large amount of horse transcriptome data. Their analyses provided candidate genes that are Figure 2 Switching expressions of alternatively spliced forms before and after exercise. (A) Red bars are the exons of the two transcripts of the DYNC1 gene: ENSECAT00000021919 and ENSECAT00000021863. (B) Each plot shows the gene expression level (FPKM value; fragments per kilobase of exon per million fragments mapped) of the two transcripts (Blue lines represent the ENSECAT00000021919 transcript and red lines represent the ENSECAT00000021863 transcript) in each individual horse, whose name is shown as the plot title. Percentages inside the plots are the coverages of the transcripts.