Background: X chromosome inactivation (XCI) is an epigenetic phenomenon that one of two X chromosomes in females is transcriptionally silenced during early embryonic development. Skewed XCI has been reported to be associated with some X-linked diseases. There have been several methods measuring the degree of the skewness of XCI. However, these methods may still have several limitations.
Results: We propose a Bayesian method to obtain the point estimate and the credible interval of the degree of XCI skewing by incorporating its prior information of being between 0 and 2. We consider a normal prior and a uniform prior for it (respectively denoted by BN and BU). We also propose a penalized point estimate based on the penalized Fieller's method and derive the corresponding confidence interval. Simulation results demonstrate that the BN and BU methods can solve the problems of extreme point estimates, noninformative intervals, empty sets and discontinuous intervals. The BN method generally outperforms other methods with the lowest mean squared error in the point estimation, and well controls the coverage probability with the smallest median and the least variation of the interval width in the interval estimation. We apply all the methods to the Graves' disease data and the Minnesota Center for Twin and Family Research data, and find that SNP rs3827440 in the Graves' disease data may undergo skewed XCI towards the allele C.
Conclusions: We recommend the BN method for measuring the degree of the skewness of XCI in practice. The R package BEXCIS is publicly available at https://github.com/Wen-YiYu/BEXCIS .
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http://dx.doi.org/10.1186/s12859-022-04721-y | DOI Listing |
Sci Rep
January 2025
Department of Statistics, Federal Govt. Quaid-i-Azam Degree College, Hamd Ullah, National University of Pakistan, Rawalpindi, Pakistan.
The study has investigated the implications of three estimation methods, namely L-moments, Maximum Likelihood, and Maximum Product of Spacing (MPS), for fitting the four-parameter Kappa Distribution (KAPD) in extreme value analysis using Monte Carlo simulations. The accuracy of the estimates has been evaluated using root mean square error (RMSE) and bias. The paper also includes an analysis of the effect of the estimation method on the estimated quantiles considering a real-life example of annual maximum peak flows and the Generalized Normal Distribution as the error distribution.
View Article and Find Full Text PDFPLoS One
December 2024
Department of Mathematics and Statistics, University of Lahore, Sargodha, Pakistan.
Extreme-cum-median ranked set sampling has been developed to address the problem of heterogeneity and outliers / extreme values. Double ranked set sampling has been suggested to obtain more reliable samples using the concept of degree of distinguishability. Dealing with heterogeneous and non-normal populations seems to be an area with a dearth of research.
View Article and Find Full Text PDFJ Speech Lang Hear Res
December 2024
Department of Communicative Disorders and Deaf Education, Utah State University, Logan.
Purpose: When using the spatiotemporal index (STI) to measure variability across repetitions of the same stimulus, researchers will typically screen and remove productions that contain errors or disfluencies. However, this screening process is highly subjective, reduces the amount of data available, and may generate samples that are less representative of true speech difficulties. In this study, we quantify the degree to which the STI is skewed by the inclusion of highly deviating productions and whether alternative calculations could better facilitate their inclusion.
View Article and Find Full Text PDFEJNMMI Rep
November 2024
Division of Nuclear Medicine, Department of Radiology-Room 3820-AJPP, University of Iowa Carver College of Medicine, 200 Hawkins Drive, Iowa City, IA, 52242, USA.
Background: Indices of tumor heterogeneity on somatostatin receptor PET/CT scans may potentially serve as predictive biomarkers of treatment efficacy in neuroendocrine tumor (NET) patients undergoing [Lu]Lu-DOTA-TATE PRRT.
Methods: NET patients who underwent [Lu]Lu-DOTA-TATE therapy at the University of Iowa from August 2018 to February 2021 were retrospectively evaluated. Radiomic features on the pre-PRRT somatostatin receptor PET/CT were evaluated using a custom MIM Software® LesionID workflow.
Diagnostics (Basel)
November 2024
Department of Radiology and Nuclear Medicine, Xuanwu Hospital, Capital Medical University, Beijing 100053, China.
Isocitrate dehydrogenase (IDH) and O-methylguanine-DNA methyltransferase (MGMT) genes are critical molecular markers in determining treatment options and predicting the prognosis of adult-type diffuse gliomas. : this study aimed to investigate whether multimodal MRI enables the differentiation of genotypes in adult-type diffuse gliomas. : a total of 116 adult-type diffuse glioma patients (61 males, 51.
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