Gene expression of functionally-related genes coevolves across fungal species: detecting coevolution of gene expression using phylogenetic comparative methods

Table 1 Highlighting issues with not correcting for phylogeny

Method	Correlation	TPR (S.D)	FPR (S.D)	FDR (S.D)	Overall Accuracy (S.D)
multivariate BM PCM (p<0.05)	ρ_C	0.476 (0.0004)	0.026 (0.0030)	0.053 (0.0056)	0.725 (0.0013)
cor.test() (p<0.05)	ρ_U	0.574 (0.0006)	0.209 (0.0075)	0.267 (0.0068)	0.682 (0.0035)
Fraser et. al. [8]	ρ_C	0.567 (0.0363)	0.053 (0.0152)	0.084 (0.0212)	0.757 (0.0148)
	ρ_U	0.511 (0.0432)	0.097 (0.0285)	0.156 (0.0316)	0.708 (0.0144)
Martin and Fraser [12]	ρ_C	0.476 (0.0108)	0.025 (0.0008)	0.050 (0.0010)	0.726 (0.0051)
	ρ_U	0.305 (0.0155)	0.016 (0.0010)	0.050 (0.0015)	0.644 (0.0073)

Comparison of 4 methods for detecting coevolution of gene expression using data simulated under Brownian Motion. The 4 methods represent the multivariate Brownian Motion (BM) PCM described in this manuscript, hypothesis testing with the phylogenetically-uncorrected correlation, the method described in Fraser et. al. [8], and the method described in Martin and Fraser [12]. Mean and standard deviations for true positive rates (TPR), false positive rates (FPR), false discovery rate (FDR), and overall accuracy are reported

ISSN: 1471-2164