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We consider one of these genes to be easy to discover (acrB, mutated in most strains), one somewhat harder (marC, mutated in a quarter of the strains), and the third hardest (acrA, mutated in less than a fifth of the strains).
The experimental data deviate from this model mainly in two respects: acrB appears to be considerably easier to find (mutated in most strains), whereas our model assumed an equal split among the three target genes (implying each would be found mutated in approximately a third of the strains); conversely, acrA appears to be harder to identify (mutated in less than a fifth of the strains).
Personalized drivers mutated in less than 2% of patients will be considered personalized rare drivers.
FAT4 has been recently established as a tumor suppressor [ 31], generally mutated in less than 10% of epithelial cancers (Additional file 3: Table S12).
We notice that TP53 is the most commonly mutated gene and is present in more than 80% of the high-grade serous ovarian carcinomas while all other genes are mutated in less than 27% of samples.
RUNX1 (a TF required for differentiation of blood cells) is another example of a lineage-specific TF that is preferentially mutated in AML (~9% of cases) compared with other cancer types (mutated in less than 4% of cases for other cancer types) [ 122].
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Initial reports on the p53 tumor suppressor gene suggested it was mutated in 10% or less of medulloblastomas [ 5- 8].
A gene that is mutated in the melanin-less cavefish is OCA2, encoding an endoplasmic reticulum (ER -localized transportER -localizedgene has been shown transporterulocutheeousamebinism type II in humans (Protas et al., 2006).
The critical protein targets identified by the integrated approach were also shown to have clinically relevant mutation frequencies in patients with various cancer subtypes, including not only well-established pan-cancer genes, such as PTEN tumor suppressor, but also a number of targets that are less frequently mutated in specific cancer types, including ABL1 oncoprotein in acute myeloid leukemia.
In addition, p53 protein, less frequently mutated in ILC than in IDC (Marchetti et al, 1993), is able to down-regulate the promoter activity of VEGF in a dose-dependent manner (Mukhopadhyay et al, 1995) and to inactivate the HIF-1α protein (Blagosklonny et al, 1998).
Although recent studies have analysed the importance of codon 61 (less frequently found mutated in CRC) [ 18], at the time we started our study mutational analysis of KRAS codons 12 and 13 was standard for patients with mCRC.
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