These genes have been defined as those for which the non-silent mutation rate is significantly greater than a background mutation rate estimated from silent mutations.
We sample each sample ID with the probability proportional to the number of passenger mutations (silent mutations and non-silent mutations observed in genes with at most one non-silent mutations) that occurred in the sample.
Differences between DNA and protein phylogenies often arise from silent DNA mutations, which ensure protein sequence conservation, but produce phylogenetic divergence at the level of DNA.
It is possible that one of the alleles in 3PN embryo No.16 (group 3) (Fig. 2E), which only contained 4 of the 6 silent mutations from the ssDNA oligo, might have been generated by non-crossover pathway as well (Fig. 4A).
In addition to non-synonymous mutations from cBioPortal, we retrieved silent mutations directly from the TCGA Data Portal (https://tcga-data.nci.nih.gov/tcga/).
It outputs summary reports and annotates detected variants with additional information for discrimination of silent mutations from variants that are potentially causing diseases.
Overall, 879 "missense" and "coding silent" mutations from COSMIC database [ 49, 50] are mapped onto 29 target proteins (40 target PDB structures) in the IL-10 centered network (Table 1 and Additional file 3).
Though undoubtedly useful, both technologies are limited in the number of loci they examine and they lack capacity to differentiate silent mutations from those that effect drug efficacy, leading to false positive results [ 11- 13].
Gene ontology analysis with Database for Annotation, Visualisation and Integrated Discovery using the data set of 856 genes with non-silent mutations from 22 patients showed significant enrichment of two classical CRC-related signalling pathways, namely ErbB signalling and cadherin/Wnt signalling (p<0.01, false discovery rate (FDR) <5%).
The WKZ isolates differs in 423 single nucleotide polymorphisms or SNPs from MRSA252 (181 missense mutations, 97 silent mutations 85 mutations at intergenic regions, and 60 indels) in the core genome of S. aureus.
