Transcriptome Analysis of Spermophilus lateralis and Spermophilus tridecemlineatus Liver Does Not Suggest the Presence of Spermophilus liver specific Reference Genes.

Citation: Keng, BMH, Chan, OYW, Heng, SSJ, Ling, MHT. 2013. Transcriptome Analysis of Spermophilus lateralis and Spermophilus tridecemlineatus Liver Does Not Suggest the Presence of Spermophilus-liver-specific Reference Genes. ISRN Bioinformatics 2013, Article ID 361321.

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The expressions of reference genes used in gene expression studies are assumed to be stable under most circumstances. However, studies had demonstrated that genes assumed to be stably expressed in a species are not necessarily stably expressed in other organisms and some studies suggested the possibility for reference genes that are both genus-specific and organ-specific. This study aims to evaluate the likelihood of genus-specific reference genes for liver using comparable microarray datasets from Spermophilus lateralis and Spermophilus tridecemlineatus. The coefficient of variance (CV) of each probe was calculated and there were 178 probes common between the lowest 10% CV of both datasets (n = 1258). All 3 lists were analysed by NormFinder. Correlation between the NormFinder ranks of the common CV-identified stable probes of both species suggests good correlation (p-value = 1e-5). This is consistent with previous studies indicating that the liver transcriptomes of S. lateralis and S. tridecemlineatus are comparable. NormFinder analysis suggests that the most invariant probe for S. tridecemlineatus was 02n12, while the most invariant probe for S. lateralis was 24j21. However, our results showed that Probes 02n12 and 24j21 are ranked 8644 and 926 in terms of invariancy for S. lateralis and S. tridecemlineatus respectively. This suggests the lack of common liver-specific reference probes for both S. lateralis and S. tridecemlineatus. Given that S. lateralis and S. tridecemlineatus are closely related species and the datasets are comparable, our results do not support the presence of genus- specific reference genes.