Sentence examples for genes we calculated from inspiring English sources

To analyze the evolutionary selection after the duplication events of the five pairs of OsOPT genes, we calculated Ka, Ks and Ka/Ks ratios for the seven duplicated pairs in the OsOPT family (Table 2).

Based on the presence/absence matrix of T3E genes, we calculated frequencies of association between T3E genes within X. axonopodis strains.

Based on the TILLING of 11 genes, we calculated the overall mutation rate of one mutation every 573 kb and identified 8 alleles per tilled kilobase.

To define functional context associations of kinase genes we calculated a genomic co-expression network across 5712 samples (31 samples included here were omitted from transcriptional activity level calculations due to the incomplete annotation) for each of the kinase genes.

To obtain a subset of variable genes, we calculated the coefficient of variation (CV) for each transcript and generated a set of 5095 "active genes" containing the transcripts with the highest (15% of the total) CV scores.

For these genes we calculated Pearson's product moment correlation coefficient between log2 ratios in both experiments.

For these genes, we calculated the average substitutional rate asymmetry ω.

For those genes we calculated the Spearman rank correlation between each of the four data sets.

To analyze for co-expressed genes we calculated an all against all Pearson correlation matrix.

For each of the transition genes, we calculated the number of shortest paths that crossed it.

To identify cooperation response genes, we calculated synergy scores according to (McMurray et al, 2008).