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Given the qualitative nature of these growth phenotypes, two types of inconsistencies may arise: false viable predictions – growth was predicted yet not observed experimentally – and false lethal predictions – growth was not predicted yet observed experimentally.
While the full gene complement in iMM904 greatly increased the number of true viable predictions, the full model also made significantly more false viable predictions compared with reduced iMM904 and iLL672 predictions.
Analysis of the initial positive, or viable, predictions of mutant phenotypes of SpoMBEL1693 resulted in 65.4% of the positive predictions matching the observed in vivo phenotypes (296 false positives and 560 true positives).
The growth rate threshold for considering a prediction viable was chosen for each condition and method separately to optimize the tradeoff between true viable and false viable predictions (maximum Matthews correlation coefficient, see Methods).
Conversely, false viable predictions can help detect missing essential biomass components, genes falsely annotated as encoding isozymes or reactions that were wrongly assigned or are inactive in the experimental conditions (Duarte et al., 2004; Joyce et al., 2006).
These dead-ends are considered "knowledge gaps" in pathways that have not been fully characterized and, as a result, lead to false viable predictions when determining gene essentiality if the pathway is in fact required for growth under a certain condition [ 2, 26].
Similar(54)
The predictive algorithm for the ORIT generates a viable prediction of the minimum number of vaccines required to stop an outbreak in real time.
This study suggests a viable prediction of the effects offshore wind farms could create to the naturally occurring macrobenthos on a large-scale.
This technique enables not only viable prediction of physicochemical properties of the molecules, but also effective database mining, being particularly useful tool in search for ligands of desired activity.
However, these prognostic factors do not allow viable prediction of the outcome for the individual patient.
As more of these pathways are elucidated and included in the model to fill in existing network gaps, we can expect false viable prediction rates to consequently decrease.
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