First, we apply the weighted log-likelihood method, where the model parameters are estimated from the log-likelihood function, summed up with each log-likelihood weighted in proportion to the reliability of the data set.
Unfortunately, there was no practical way to determine what proportion of studies in the data set might have qualified from this exemption.
d The numbers in parentheses indicate the prior probability that such protein localized to a given site is equal to the proportion of proteins in the data set [ 65].
Owing to the large size of the data set, all proportions were found to be surrounded by very tight 95% CIs, and differences between proportions were all highly significant (p<0.001), even when the proportions were very similar.
The expected number of N-mt genes was obtained by calculating the product of the proportion of all genes in the data set with mitochondrial annotations (matching GO 0005739) and the number of annotated genes in a given gene set.
However, this motif was not the top-scored one (rank = 11), which may be the result of a large proportion of false positives in the data set.
The expected number of X-linked MBG (or FBG) for each data set was determined by multiplying the proportion of all genes in the data set that were X-linked by the total number of genes detected as male-biased (or female-biased) in that data set.
