Sharma Y*, Miladi M*, Dukare S*, Boulay K*, Caudron-Herger M, Groß M, Backofen R, Diederichs S: A pan-cancer analysis of synonymous mutations
Nature Communications (2019) 10:2569
https://www.nature.com/articles/s41467-019-10489-2
SynMICdb aims to facilitate the study of synonymous mutations in cancer. These mutations alter the nucleotide sequence of the gene and the mRNA, but not the amino acid sequence of the respective protein. Synonymous mutations can change mRNA structure, stability, splicing, translation efficiency or impact cis-regulatory sequences. These mutations can be recurrent and conserved and mirror many aspects of cancer driving mutations.
Search options
- Search by Gene: Here, the user can search for synonymous mutations present in gene of interest (HGNC gene symbol, gene name and Ensembl IDs are accepted).
- Search by Position in CDS: Here, the user can search for mutations on the basis of their location within the coding sequence (CDS) relative to the 5' or 3' end of the gene.
- Search by Region: Here, the user can search for mutations at genomic coordinates (GRCh38).
- Search by Organ: Here, the user can search for synonymous mutations by organ system, site and histology.
- Advanced Search: This allows the combination of different search options. Here, the user can search for mutations on the basis of gene name, Cancer Gene Census genes (CGC), conservation, primary site and/or histology and location within the coding region.
References
- Diederichs S et al., The dark matter of the cancer genome: aberrations in regulatory elements, untranslated regions, splice sites, non-coding RNA and synonymous mutations. EMBO Mol Med (2016) 8:442:57.
Tutorial
A detailed and user-friendly documentation can be downloaded here:
Read more
Contact
The authors of the SYNMICdb can be contacted at the following email address:
databases.diederichslab(at)dkfz.de
- Search by Gene: Here, the user can search for synonymous mutations present in gene of interest (HGNC gene symbol, gene name and Ensembl IDs are accepted).
- Search by Position in CDS: Here, the user can search for mutations on the basis of their location within the coding sequence (CDS) relative to the 5' or 3' end of the gene.
- Search by Region: Here, the user can search for mutations at genomic coordinates (GRCh38).
- Search by Organ: Here, the user can search for synonymous mutations by organ system, site and histology.
- Advanced Search: This allows the combination of different search options. Here, the user can search for mutations on the basis of gene name, Cancer Gene Census genes (CGC), conservation, primary site and/or histology and location within the coding region.