Abstract：
:Mutations that cause an error in the splicing of a messenger RNA (mRNA) can lead to diseases in humans. Various computational models have been developed to recognize the sequence pattern of the splice sites. In recent studies, Convolutional Neural Network (CNN) architectures were shown to outperform other existing models in predicting the splice sites. However, an insufficient effort has been put into extending the CNN model to predict the effect of the genomic variants on the splicing of mRNAs. This study proposes a framework to elaborate on the utility of CNNs to assess the effect of splice variants on the identification of potential disease-causing variants that disrupt the RNA splicing process. Five models, including three CNN-based and two non-CNN machine learning based, were trained and compared using two existing splice site datasets, Genome Wide Human splice sites (GWH) and a dataset provided at the Deep Learning and Artificial Intelligence winter school 2018 (DLAI). The donor sites were also used to test on the HSplice tool to evaluate the predictive models. To improve the effectiveness of predictive models, two datasets were combined. The CNN model with four convolutional layers showed the best splice site prediction performance with an AUPRC of 93.4% and 88.8% for donor and acceptor sites, respectively. The effects of variants on splicing were estimated by applying the best model on variant data from the ClinVar database. Based on the estimation, the framework could effectively differentiate pathogenic variants from the benign variants (p = 5.9 × 10-7). These promising results support that the proposed framework could be applied in future genetic studies to identify disease causing loci involving the splicing mechanism. The datasets and Python scripts used in this study are available on the GitHub repository at https://github.com/smiile8888/rna-splice-sites-recognition.
journal_name
PeerJjournal_title
PeerJauthors
Thanapattheerakul T,Engchuan W,Chan JHdoi
10.7717/peerj.9470subject
Has Abstractpub_date
2020-07-06 00:00:00pages
e9470issn
2167-8359pii
9470journal_volume
8pub_type
杂志文章相关文献
PeerJ文献大全abstract：:Studies on the adverse health effects caused by azo dyes are insufficient and quite contradictory. This work aims to investigate the possible toxic effect of two types of widely used food additives, Sunset Yellow and Allura Red, by assessing the physiological, histopathological and ultrastructural changes in the liver...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.5689
更新日期：2018-09-28 00:00:00
abstract：Background:Foam cells (FCs) play crucial roles in the process of all stages of atherosclerosis. Smooth muscle cells (SMCs) and macrophages are the major sources of FCs. This study aimed to identify the common molecular mechanism in these two types of FCs. Methods:GSE28829, GSE43292, GSE68021, and GSE54666 were include...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.10336
更新日期：2020-11-17 00:00:00
abstract：Background:Much of the shape variation found in animals is based on allometry and heterochrony. Horses represent an excellent model to investigate patterns of size-shape variation among breeds that were intentionally bred for extreme small and large sizes. Methods:We tested whether ponies (wither height < 148 cm) have...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.7678
更新日期：2019-09-16 00:00:00
abstract：Background:Dengue infection represents a global health issue of growing importance. Dengue non-structural protein 1 (NS1) plays a central role in the early detection of the disease. The most common method for NS1 detection is testing by lateral flow immunoassays (LFIAs) with varying sensitivity. In this study, we prese...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.7779
更新日期：2019-09-25 00:00:00
abstract：:Researchers often need to consider the practical significance of a relationship. For example, interpreting the magnitude of an effect size or establishing bounds in equivalence testing requires knowledge of the meaningfulness of a relationship. However, there has been little research exploring the degree of relationsh...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.6853
更新日期：2019-05-14 00:00:00
abstract：:Ticks are globally distributed arthropods and a public health concern due to the many human pathogens they carry and transmit, including the causative agent of Lyme disease, Borrelia burgdorferi. As tick species' ranges increase, so do the number of reported tick related illnesses. The microbiome is a critical part of...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.10424
更新日期：2020-12-02 00:00:00
abstract：:The incorporation of feedback into a person's body schema is well established. The crossmodal congruency task (CCT) is used to objectively quantify incorporation without being susceptible to experimenter biases. This visual-tactile interference task is used to calculate the crossmodal congruency effect (CCE) score as ...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.6976
更新日期：2019-05-22 00:00:00
abstract：Background:Recently, SARS-CoV-2 virus with the D614G mutation has become a public concern due to rapid dissemination of this variant across many countries. Our study aims were (1) to report full-length genome sequences of SARS-CoV-2 collected from four COVID-19 patients in the Special Region of Yogyakarta and Central J...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.10575
更新日期：2020-12-21 00:00:00
abstract：Background:Trace elements are essential for the growth and survival of plants, and their concentrations and distributions in plants are effective reflections of ecological adaptation strategies. However, this aspect has seldom been addressed. Method:Changes in the leaf and branch trace elements of Pinus massoniana Lam...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.9935
更新日期：2020-09-16 00:00:00
abstract：:Diffuse sources of pollution like agricultural or urban runoff are important factors in determining the quality of surface waters, although they are more difficult to monitor than point sources. The objective of our study was to verify assumptions that the inflow from agricultural nutrient sources is higher than from ...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.8381
更新日期：2020-02-06 00:00:00
abstract：Background:It was well known that age has an impact on word processing (word frequency or predictability) in terms of fixating time during reading. However, little is known about whether or not age modulates these impacts on saccade behaviors in Chinese reading (i.e., length of incoming/outgoing saccades for a target w...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.8860
更新日期：2020-04-01 00:00:00
abstract：:Sex differences in some preferences and motivations are well established, but it is unclear whether they persist in selective sub-populations, such as expert financial decision makers, top scientists, or elite athletes. We addressed this issue by studying competitiveness in 1,147 varsity intercollegiate distance runne...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.884
更新日期：2015-04-21 00:00:00
abstract：:Physical exercise is linked to individuals whose affect profiles are invariably positive and it induces anti-apoptotic and anti-excitotoxic effects, buttressing blood-brain barrier intactness in both healthy individuals and those suffering from disorders accompanying overweight and obesity. In this regard, exercise of...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.694
更新日期：2014-12-16 00:00:00
abstract：:[This corrects the article DOI: 10.7717/peerj.4029.]. ...
journal_title：PeerJ
pub_type： 杂志文章,已发布勘误
doi：10.7717/peerj.4029/correction-1
更新日期：2018-02-27 00:00:00
abstract：:We study the glycosylation processes that convert initially toxic substrates to nutritionally valuable metabolites in the flavonoid biosynthesis pathway of tomato (Solanum lycopersicum) seedlings. To estimate the reaction rates we use ordinary differential equations (ODEs) to model the enzyme kinetics. A popular choic...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.2417
更新日期：2016-09-20 00:00:00
abstract：:Rhizoctonia solani AG1 IA is a soil-borne fungal phytopathogen that can significantly harm crops resulting in economic loss. This species overwinters in grass roots and diseased plants, and produces sclerotia that infect future crops. R. solani AG1 IA does not produce spores; therefore, understanding the molecular mec...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.5103
更新日期：2018-06-18 00:00:00
abstract：:A range of diseases is associated with amyloid fibril formation. Despite different proteins being responsible for each disease, all of them share similar features including beta-sheet-rich secondary structure and fibril-like protein aggregates. A number of proteins can form amyloid-like fibrils in vitro, resembling st...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.1271
更新日期：2015-09-24 00:00:00
abstract：:Bacterial populations present in Hg-rich environments have evolved biological mechanisms to detoxify methylmercury and other organometallic mercury compounds. The most common resistance mechanism relies on the H(+)-assisted cleavage of the Hg-C bond of methylmercury by the organomercurial lyase MerB. Although the init...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.1127
更新日期：2015-07-28 00:00:00
abstract：:Because of the environmental sensitivity of the Black Sea, as a semi-enclosed sea, any subsea oil spill can cause destructive impacts on the marine environment and beaches. Employing numerical modeling as a prediction tool is one of the most efficient methods to understand oil spill behavior under various environmenta...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.5448
更新日期：2018-08-29 00:00:00
abstract：:We present the first comprehensive review of the present and past shark and ray diversity in marine waters of Tropical America, examining the patterns of distribution in the Eastern Central Pacific (EP) and Western Central Atlantic (WA) realms. We identified the major regions of diversity and of endemism, and explored...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.5313
更新日期：2018-07-20 00:00:00
abstract：:Objectives. Diabetes mellitus (DM) and hypothyroidism are each associated with increased rate of pregnancy complications. However, their combined morbidity during gestation is poorly studied. Therefore, the aims of this study were to determine the prevalence of the combined morbidity of DM & hypothyroidism and whether...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.52
更新日期：2013-03-19 00:00:00
abstract：Background:Parkinson's disease (PD) is the second most common neurodegenerative disorder. In addition to its highly debilitating motor symptoms, non-motor symptoms may precede their motor counterparts by many years, which may characterize a prodromal phase of PD. A potential pharmacological strategy is to introduce neu...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.4957
更新日期：2018-06-01 00:00:00
abstract：Background:"Quantile-dependent expressivity" occurs when the effect size of a genetic variant depends upon whether the phenotype (e.g. adiponectin) is high or low relative to its distribution. We have previously shown that the heritability (h2 ) of adiposity, lipoproteins, postprandial lipemia, pulmonary function, and ...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.10099
更新日期：2020-10-14 00:00:00
abstract：Background:Type 2 diabetes mellitus (T2DM) had been reported to be associated with tendinopathy. However, the underlying mechanisms of diabetic tendinopathy still remain largely to be discovered. The purpose of this study was to develop insulin resistance (IR) model on primary human tenocytes (hTeno) culture with tumou...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.8740
更新日期：2020-06-08 00:00:00
abstract：:Convergent evolution can provide insights into the predictability of, and constraints on, the evolution of biodiversity. One striking example of convergence is seen in the 'river dolphins'. The four dolphin genera that make up the 'river dolphins' (Inia geoffrensis, Pontoporia blainvillei, Platanista gangetica and Lip...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.4090
更新日期：2017-11-21 00:00:00
abstract：Background:Sex ratio distorting agents (maternally inherited symbionts and meiotically-driving sex chromosomes) are common in insects. When these agents rise to high frequencies they create strong population sex ratio bias and selection then favours mutations that act to restore the rare sex. Despite this strong select...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.7677
更新日期：2019-10-01 00:00:00
abstract：:A new Primulina species from Guangdong, China with an unusual inflorescence is described here. Primulina anisocymosa is vegetatively most similar to P. bobaiensis. It can be distinguished from all species within Primulina morphologically by its unique zigzag monochasial cyme and infructescence. To confirm the phylogen...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.6157
更新日期：2019-01-04 00:00:00
abstract：:Helminths include both parasitic nematodes (roundworms) and platyhelminths (trematode and cestode flatworms) that are abundant, and are of clinical importance. The genetic characterization of parasitic flatworms using advanced molecular tools is central to the diagnosis and control of infections. Although the nuclear ...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.207
更新日期：2013-11-12 00:00:00
abstract：:The Drosophila melanogaster P transposable element provides one of the best cases of horizontal transfer of a mobile DNA sequence in eukaryotes. Invasion of natural populations by the P element has led to a syndrome of phenotypes known as P-M hybrid dysgenesis that emerges when strains differing in their P element com...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.3824
更新日期：2017-09-15 00:00:00
abstract：Background:E-health technology applications are essential tools of modern information technology that improve quality of healthcare delivery in hospitals of both developed and developing countries. However, despite its positive benefits, studies indicate that the rate of the e-health adoption in some developing countri...
journal_title：PeerJ
pub_type： 杂志文章
doi：10.7717/peerj.4436
更新日期：2018-03-01 00:00:00
