Identification of co-regulated transcripts affecting male body size in Drosophila

Table 1 Gene expression simulations

Number of genotypes	Number of factors	Number of genes		Correlation (ρ)	Effect size	Factors clearly identified	Proportion correct
		Noise	Each factor
2	3	100	30	0.8	0.2,0.4,0.6	Y	1.00
					0.02,0.04,0.06	Y	1.00
				0.4	0.2,0.4,0.6	Y	0.84
					0.02,0.04,0.06	Y	0.66
2	3	1000	300	0.8	0.2,0.4,0.6	Y	1.00
				0.4	0.2,0.4,0.6	Y	0.66
10	3	100	30	0.8	1,2,3	N	0.81
				0.4	1,2,3	N	0.64
		0	30	0.8	1,2,3	Y	1.00
				0.4	1,2,3	N	0.63
10	20	100	30	0.4	1,2,...,20	N	-
					0.1,0.2,...,2	N	-

The number of genotypes simulated is given in the first column. The number of underlying latent factors is given in the second column, followed by the number of genes simulated that are not a part of any underlying factor. The number of genes on each factor is given next, and are simulated as a multivariate normal with pairwise correlation among genes within the factor of ρ. The mean for the first genotype is drawn from a gamma distribution, and the subsequent means were drawn from a multivariate normal, with standard deviation of one such that the maximum difference between the means can be interpreted as the genotypic effect size. Thus, for each underlying factor the simulated genotypic effect is the maximum difference in transcript abundance among genotypes for the first, second, and third factor, respectively. Factors are considered to be clearly identified if there is a substantial drop in the eigenvalues of the correlation matrix, and a reasonable proportion of the total variation is explained. The proportion correct is the proportion of genes correctly identified when setting the number of factors in the factor analysis to be the simulated number of latent factors. For the simulation with 20 latent factors we cannot compute the proportion correctly identified, as there are more simulated factors than possible factors.

ISSN: 1474-760X