The dark matter of the cancer genome: aberrations in regulatory elements, untranslated regions, splice sites, non‐coding RNA and synonymous mutations
S Diederichs, L Bartsch, JC Berkmann… - EMBO molecular …, 2016 - embopress.org
Cancer is a disease of the genome caused by oncogene activation and tumor suppressor
gene inhibition. Deep sequencing studies including large consortia such as TCGA and …
gene inhibition. Deep sequencing studies including large consortia such as TCGA and …
The rules and impact of nonsense-mediated mRNA decay in human cancers
Premature termination codons (PTCs) cause a large proportion of inherited human genetic
diseases. PTC-containing transcripts can be degraded by an mRNA surveillance pathway …
diseases. PTC-containing transcripts can be degraded by an mRNA surveillance pathway …
REVIGO summarizes and visualizes long lists of gene ontology terms
Outcomes of high-throughput biological experiments are typically interpreted by statistical
testing for enriched gene functional categories defined by the Gene Ontology (GO). The …
testing for enriched gene functional categories defined by the Gene Ontology (GO). The …
[HTML][HTML] Synonymous mutations frequently act as driver mutations in human cancers
Synonymous mutations change the sequence of a gene without directly altering the
sequence of the encoded protein. Here, we present evidence that these" silent" mutations …
sequence of the encoded protein. Here, we present evidence that these" silent" mutations …
A pan-cancer analysis of synonymous mutations
Synonymous mutations have been viewed as silent mutations, since they only affect the
DNA and mRNA, but not the amino acid sequence of the resulting protein. Nonetheless …
DNA and mRNA, but not the amino acid sequence of the resulting protein. Nonetheless …
The code of silence: widespread associations between synonymous codon biases and gene function
F Supek - Journal of molecular evolution, 2016 - Springer
Some mutations in gene coding regions exchange one synonymous codon for another, and
thus do not alter the amino acid sequence of the encoded protein. Even though they are …
thus do not alter the amino acid sequence of the encoded protein. Even though they are …
[HTML][HTML] A role for tRNA modifications in genome structure and codon usage
Transfer RNA (tRNA) gene content is a differentiating feature of genomes that contributes to
the efficiency of the translational apparatus, but the principles sha** tRNA gene copy …
the efficiency of the translational apparatus, but the principles sha** tRNA gene copy …
Genome-wide methylation profiling in Crohn's disease identifies altered epigenetic regulation of key host defense mechanisms including the Th17 pathway
Background Germline variation in the 71 Crohn's disease (CD) loci implicated by genome-
wide association studies (GWAS) only accounts for approximately 25% of estimated …
wide association studies (GWAS) only accounts for approximately 25% of estimated …
The landscape of microbial phenotypic traits and associated genes
Bacteria and Archaea display a variety of phenotypic traits and can adapt to diverse
ecological niches. However, systematic annotation of prokaryotic phenotypes is lacking. We …
ecological niches. However, systematic annotation of prokaryotic phenotypes is lacking. We …
Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles
M Botzman, H Margalit - Genome biology, 2011 - Springer
Background It is widely acknowledged that synonymous codons are used unevenly among
genes in a genome. In organisms under translational selection, genes encoding highly …
genes in a genome. In organisms under translational selection, genes encoding highly …