MiasDB: A Database of Molecular Interactions Associated with Alternative Splicing of Human Pre-mRNAs

Abstract

Alternative splicing (AS) is pervasive in human multi-exon genes and is a major contributor to expansion of the transcriptome and proteome diversity. The accurate recognition of alternative splice sites is regulated by information contained in networks of protein-protein and protein-RNA interactions. However, the mechanisms leading to splice site selection are not fully understood. Although numerous databases have been built to describe AS, molecular interaction databases associated with AS have only recently emerged. In this study, we present a new database, MiasDB, that provides a description of molecular interactions associated with human AS events. This database covers 938 interactions between human splicing factors, RNA elements, transcription factors, kinases and modified histones for 173 human AS events. Every entry includes the interaction partners, interaction type, experimental methods, AS type, tissue specificity or disease-relevant information, a simple description of the functionally tested interaction in the AS event and references. The database can be queried easily using a web server (http://47.88.84.236/Miasdb). We display some interaction figures for several genes. With this database, users can view the regulation network describing AS events for 12 given genes.

Predicting Functional Effects of Synonymous Variants: A Systematic Review and Perspectives

“…Predictors describe the potential impact of sSNVs on splicing by relying on the identified putative ESE and ESS motifs. Identification of these motifs and the corresponding splicing regulatory proteins has been an ongoing experimental and computational effort (Wang and Burge, 2008; Shepard and Hertel, 2009); identified motifs and regulatory proteins are available via public repositories (Desmet et al, 2009; Giulietti et al, 2013; Xing et al, 2016). Tools such as SPANR (Splicing-based Analysis of Variants) (Xiong et al, 2015), have also been developed to predict the splicing effects of SNVs.…”

Systematics for types and effects of RNA variations

“…SASD [ 18 ] was developed for proteomics studies to detect consequences of alternative splicing. In MiasDB there are data for interactions of molecules involved in alternative splicing [ 19 ].…”

Bioinformatics challenges and perspectives when studying the effect of epigenetic modifications on alternative splicing

“…MiasDB contains interactions between splicing factors, epigenetic marks and cis -regulatory elements as well as the interaction between trans -acting proteins. This resource is currently available only for human interactions and coverage is still incomplete [ 81 ]. In future work, there are plans to integrate MiasDB with established signalling pathway database KEGG [ 82 ].…”

“…This restricts the experimental conditions under which epigenetics and splicing can be analysed [ 76 , 85 ]. Furthermore, the annotation of results requires prior knowledge [ 59 , 79 ] but databases on prior knowledge are not complete and exist only for specific organisms [ 80 , 81 ].…”