GTestimate: Improving relative gene expression estimation in scRNA-seq using the Good-Turing estimator
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE268930 | GEO | 2024/07/31
REPOSITORIES: GEO
Similar Datasets
Project description:BACKGROUND:To define a new coefficient to be used in the formula (Volume?=?L x H x W x Coefficient) that better estimates prostate volume using dimensions of fresh prostates from patients who had transrectal ultrasound (TRUS) imaging prior to prostatectomy. METHODS:The prostate was obtained from 153 patients, weighed and measured to obtain length (L), height (H), and width (W). The density was determined by water displacement to calculate volume. TRUS data were retrieved from patient charts. Linear regression analyses were performed to compare various prostate volume formulas, including the commonly used ellipsoid formula and newly introduced bullet-shaped formula. RESULTS:By relating measured prostate volumes from fresh prostates to TRUS-estimated prostate volumes, 0.66 was the best fitting coefficient in the (L x H x W x Coefficient) equation. This newfound coefficient combined with outlier removal yielded a linear equation with an R2 of 0.64, compared to 0.55 and 0.60, for the ellipsoid and bullet, respectively. By comparing each of the measured vs. estimated dimensions, we observed that the mean prostate height and length were overestimated by 11.1 and 10.8% using ultrasound (p?<?0.05), respectively, while the mean width was similar (p?>?0.05). Overall, the ellipsoid formula underestimates prostate volumes by 18%, compared to an overestimation of 4.6 and 5.7% for the bullet formula and the formula using our coefficient, respectively. CONCLUSIONS:This study defines, for the first time, a coefficient based on freshly resected prostates as a reference to estimate volumes by imaging. Our findings support a bullet rather than an ellipsoid prostate shape. Moreover, substituting the coefficient commonly used in the ellipsoid formula by our calculated coefficient in the equation estimating prostate volume by TRUS, provides a more accurate value of the true prostate volume.
| S-EPMC6657110 | biostudies-literature
Project description:The present study sought to determine whether witness memory for duration could be improved. In three studies, we examined the effects of unpacking (breaking an event into its component parts), anchoring (supplying participants with a reference duration), and summation (summing component estimates). Participants watched a video-recorded mock crime and provided duration estimates for components of the crime (e.g., casing the car, unlocking the door, etc.) and for the total crime. Results indicate that bias in estimated duration was less for the sum of the parts than it was for the overall duration estimate. Further, the sum of the individual parts did not equal the total estimate, even though all estimates were given in sequence. Summing the component parts could be a more successful intervention than anchoring or unpacking and is easy to employ with witnesses.
| S-EPMC6621925 | biostudies-literature
Project description:Direct targeting of oncogenic MYC proteins has been an elusive goal of many cancer drug development efforts. In this issue of Cancer Discovery, Stegmaier and colleagues demonstrate that pharmacologically interfering with the bromodomain and extraterminal (BET) class of proteins potently depletes MYCN in neuroblastoma cells, resulting in cellular cytotoxicity and thus providing a novel approach with a potential impact on a previously undruggable major oncogene.
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Project description: Not available
| S-EPMC8172148 | biostudies-literature
Project description:BackgroundThe main goal of the whole transcriptome analysis is to correctly identify all expressed transcripts within a specific cell/tissue--at a particular stage and condition--to determine their structures and to measure their abundances. RNA-seq data promise to allow identification and quantification of transcriptome at unprecedented level of resolution, accuracy and low cost. Several computational methods have been proposed to achieve such purposes. However, it is still not clear which promises are already met and which challenges are still open and require further methodological developments.ResultsWe carried out a simulation study to assess the performance of 5 widely used tools, such as: CEM, Cufflinks, iReckon, RSEM, and SLIDE. All of them have been used with default parameters. In particular, we considered the effect of the following three different scenarios: the availability of complete annotation, incomplete annotation, and no annotation at all. Moreover, comparisons were carried out using the methods in three different modes of action. In the first mode, the methods were forced to only deal with those isoforms that are present in the annotation; in the second mode, they were allowed to detect novel isoforms using the annotation as guide; in the third mode, they were operating in fully data driven way (although with the support of the alignment on the reference genome). In the latter modality, precision and recall are quite poor. On the contrary, results are better with the support of the annotation, even though it is not complete. Finally, abundance estimation error often shows a very skewed distribution. The performance strongly depends on the true real abundance of the isoforms. Lowly (and sometimes also moderately) expressed isoforms are poorly detected and estimated. In particular, lowly expressed isoforms are identified mainly if they are provided in the original annotation as potential isoforms.ConclusionsBoth detection and quantification of all isoforms from RNA-seq data are still hard problems and they are affected by many factors. Overall, the performance significantly changes since it depends on the modes of action and on the type of available annotation. Results obtained using complete or partial annotation are able to detect most of the expressed isoforms, even though the number of false positives is often high. Fully data driven approaches require more attention, at least for complex eucaryotic genomes. Improvements are desirable especially for isoform quantification and for isoform detection with low abundance.
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Project description:Molecular analysis of the spatio-temporal dynamics of destabilization and self-reorganization underscore the crucial role of WNT and BMP signaling modulators as part of the Turing system.
2024-08-30 | GSE275783 | GEO
Project description:Molecular analysis of the spatio-temporal dynamics of destabilization and self-reorganization underscore the crucial role of WNT and BMP signaling modulators as part of the Turing system.
2024-08-30 | GSE275782 | GEO
Project description:The marginal likelihood is commonly used for comparing different evolutionary models in Bayesian phylogenetics and is the central quantity used in computing Bayes Factors for comparing model fit. A popular method for estimating marginal likelihoods, the harmonic mean (HM) method, can be easily computed from the output of a Markov chain Monte Carlo analysis but often greatly overestimates the marginal likelihood. The thermodynamic integration (TI) method is much more accurate than the HM method but requires more computation. In this paper, we introduce a new method, steppingstone sampling (SS), which uses importance sampling to estimate each ratio in a series (the "stepping stones") bridging the posterior and prior distributions. We compare the performance of the SS approach to the TI and HM methods in simulation and using real data. We conclude that the greatly increased accuracy of the SS and TI methods argues for their use instead of the HM method, despite the extra computation needed.
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Project description:Models of evolution by genome rearrangements are prone to two types of flaws: One is to ignore the diversity of susceptibility to breakage across genomic regions, and the other is to suppose that susceptibility values are given. Without necessarily supposing their precise localization, we call "solid" the regions that are improbably broken by rearrangements and "fragile" the regions outside solid ones. We propose a model of evolution by inversions where breakage probabilities vary across fragile regions and over time. It contains as a particular case the uniform breakage model on the nucleotidic sequence, where breakage probabilities are proportional to fragile region lengths. This is very different from the frequently used pseudouniform model where all fragile regions have the same probability to break. Estimations of rearrangement distances based on the pseudouniform model completely fail on simulations with the truly uniform model. On pairs of amniote genomes, we show that identifying coding genes with solid regions yields incoherent distance estimations, especially with the pseudouniform model, and to a lesser extent with the truly uniform model. This incoherence is solved when we coestimate the number of fragile regions with the rearrangement distance. The estimated number of fragile regions is surprisingly small, suggesting that a minority of regions are recurrently used by rearrangements. Estimations for several pairs of genomes at different divergence times are in agreement with a slowly evolvable colocalization of active genomic regions in the cell.
| S-EPMC4898800 | biostudies-other
Project description:The goal was to obtain the differential transcriptome in the deep cones fibroblasts between shallow and deep wounds in Duroc breeds at 20 wks. We made shallow and deep wounds on the backs 2 Duroc pigs, biopsied the wounds at 20 weeks, cultured fibroblasts, extracted and the RNA from the cultured fibroblasts, and hybridized the Affymetrix GeneChip. We compared wound depth, the system included 1 factors (depth). The system also included repeated measures since the same pigs were used at each time. It also included paired data since the shallow and deep wounds compared were located on the same pig.
2011-09-29 | E-GEOD-29768 | biostudies-arrayexpress