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A statistical analysis of the robustness of alternate genetic coding tables.

ABSTRACT: The rules that specify how the information contained in DNA is translated into amino acid "language" during protein synthesis are called "the genetic code", commonly called the "Standard" or "Universal" Genetic Code Table. As a matter of fact, this coding table is not at all "universal": in addition to different genetic code tables used by different organisms, even within the same organism the nuclear and mitochondrial genes may be subject to two different coding tables. Results In an attempt to understand the advantages and disadvantages these coding tables may bring to an organism, we have decided to analyze various coding tables on genes subject to mutations, and have estimated how these genes "survive" over generations. We have used this as indicative of the "evolutionary" success of that particular coding table. We find that the "standard" genetic code is not actually the most robust of all coding tables, and interestingly, Flatworm Mitochondrial Code (FMC) appears to be the highest ranking coding table given our assumptions. Conclusions It is commonly hypothesized that the more robust a genetic code, the better suited it is for maintenance of the genome. Our study shows that, given the assumptions in our model, Standard Genetic Code is quite poor when compared to other alternate code tables in terms of robustness. This brings about the question of why Standard Code has been so widely accepted by a wider variety of organisms instead of FMC, which needs to be addressed for a thorough understanding of genetic code evolution.

SUBMITTER: Kurnaz ML

PROVIDER: S-EPMC2635705 | biostudies-literature | 2008 May

REPOSITORIES: biostudies-literature

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A statistical analysis of the robustness of alternate genetic coding tables.

Kurnaz Mehmet Levent ML Kurnaz Isil Aksan IA

International journal of molecular sciences 20080502 5

The rules that specify how the information contained in DNA is translated into amino acid "language" during protein synthesis are called "the genetic code", commonly called the "Standard" or "Universal" Genetic Code Table. As a matter of fact, this coding table is not at all "universal": in addition to different genetic code tables used by different organisms, even within the same organism the nuclear and mitochondrial genes may be subject to two different coding tables. Results In an attempt to ...[more]

PMID: 19325778

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Project description:PurposeEvidenced-based decision-making is rooted in comparative clinical studies; however, a small number of outcome event reversals have the potential to change study significance. The purpose of this study was to determine the utility of applying fragility analysis to comparative studies in the published orthopaedic shoulder literature.MethodsComparative clinical shoulder research studies reporting 1:1 dichotomous categorical data were analyzed in 6 leading orthopaedic journals between 2006 and 2016. Statistical significance was defined as a P value of less than .05. The fragility index (FI) for each study outcome was determined by the number of event reversals required to change the P value to either greater or less than 0.05, thus changing the study conclusions. The associated fragility quotient (FQ) was determined by dividing the FI by the total population comprising a particular outcome.ResultsOf the 23,897 studies screened, 3,591 met search criteria, with 198 comparative studies ultimately included for analysis, 67 of which were randomized controlled trials. There were 357 total outcome events with 74 reported as significant and 283 as not significant. The FI was 4 (IQR 2-6) with an associated FQ of 0.066 (interquartile range [IQR] 0.038-0.102). There was no difference in statistical fragility between randomized and nonrandomized trials with both revealing a FI of 4 and FQ of 0.068 (IQR 0.044-0.107) and 0.065 (IQR 0.031-0.101), respectively.ConclusionsThis current analysis reveals that comparative shoulder studies published in six leading orthopaedic journals are at risk of statistical fragility. As such, contemporary clinical shoulder literature may not be as robust as traditionally perceived with the reversal of only a few outcome events required to change study significance. Therefore, we advocate the reporting of both FI and FQ in addition to the P value as statistical complements to all comparative investigations to provide a more comprehensive understanding of trial stability and significance in the published shoulder literature.Clinical relevanceComparative study designs are commonly employed in shoulder research. Several studies in both the general medical and orthopaedic literature have identified a lack of statistical robustness through comprehensive fragility analysis. Our findings demonstrate the P value may be an inadequate independent statistical metric requiring the complement of a FI and FQ to aid in the interpretation and understanding of study significance for clinical decision-making.

Project description:Changing the information format from probabilities into frequencies as well as employing appropriate visualizations such as tree diagrams or 2 × 2 tables are important tools that can facilitate people's statistical reasoning. Previous studies have shown that despite their widespread use in statistical textbooks, both of those visualization types are only of restricted help when they are provided with probabilities, but that they can foster insight when presented with frequencies instead. In the present study, we attempt to replicate this effect and also examine, by the method of eye tracking, why probabilistic 2 × 2 tables and tree diagrams do not facilitate reasoning with regard to Bayesian inferences (i.e., determining what errors occur and whether they can be explained by scan paths), and why the same visualizations are of great help to an individual when they are combined with frequencies. All ten inferences of N = 24 participants were based solely on tree diagrams or 2 × 2 tables that presented either the famous "mammography context" or an "economics context" (without additional textual wording). We first asked participants for marginal, conjoint, and (non-inverted) conditional probabilities (or frequencies), followed by related Bayesian tasks. While solution rates were higher for natural frequency questions as compared to probability versions, eye-tracking analyses indeed yielded noticeable differences regarding eye movements between correct and incorrect solutions. For instance, heat maps (aggregated scan paths) of distinct results differed remarkably, thereby making correct and faulty strategies visible in the line of theoretical classifications. Moreover, the inherent structure of 2 × 2 tables seems to help participants avoid certain Bayesian mistakes (e.g., "Fisherian" error) while tree diagrams seem to help steer them away from others (e.g., "joint occurrence"). We will discuss resulting educational consequences at the end of the paper.

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A statistical analysis of the robustness of alternate genetic coding tables.

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A statistical analysis of the robustness of alternate genetic coding tables.

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