Epitranscriptomic subtyping, visualization, and denoising by global motif visualization

Abstract Advances in sequencing technologies have empowered epitranscriptomic profiling at the single-base resolution. Putative RNA modification sites identified from a single high-throughput experiment may contain one type of modification deposited by different writers or different types of modifications, along with false positive results because of the challenge of distinguishing signals from noise. However, current tools are insufficient for subtyping, visualization, and denoising these signals. Here, we present iMVP, which is an interactive framework for epitranscriptomic analysis with a nonlinear dimension reduction technique and density-based partition. As exemplified by the analysis of mRNA m5C and ModTect variant data, we show that iMVP allows the identification of previously unknown RNA modification motifs and writers and the discovery of false positives that are undetectable by traditional methods. Using putative m6A/m6Am sites called from 8 profiling approaches, we illustrate that iMVP enables comprehensive comparison of different approaches and advances our understanding of the difference and pattern of true positives and artifacts in these methods. Finally, we demonstrate the ability of iMVP to analyze an extremely large human A-to-I editing dataset that was previously unmanageable. Our work provides a general framework for the visualization and interpretation of epitranscriptomic data

The effect of scattered neutrons on the ion temperature measurement with different line-of-sight on the SGIII laser facility

Two neutron time-of-flight (nToF) detectors have been employed to measure the neutron time-of-flight spectrum in different lines-of-sight, i.e., at the equator plane and the south pole, on Shenguang-III (SG-III) laser facility. The contribution of scattered neutrons has been calculated with the Monte Carlo code JMCT for each nToF detector. The results show that the scattered neutron spectrum is dominated by neutrons scattered on materials in the experiment hall, including the vacuum chamber. The shape of the scattered neutron spectrum depends on the view line, which has been observed with nToF detectors located in the experiment hall of the SG-III laser facility. A method based on the convolution of the calculated neutron time-of-flight spectrum and the instrument response function has been developed for the ion temperature determination. The calculated neutron spectra with the contribution of scattered neutrons can fit the measured results. No obvious ion temperature anisotropy has been observed on the SG-III laser facility at present