GREMET: An integrative tool for the prediction of mutation effects on gene regulation

• Published in: Computer methods and programs in biomedicine Vol. 111; no. 1; pp. 214 - 219
• Main Authors: Athanasiadis, Polykarpos, Malousi, Andigoni, Kouidou, Sofia, Maglaveras, Nicos
• Format: Journal Article
• Language: English
• Published: Kidlington Elsevier Ireland Ltd 01-07-2013; Elsevier
• Subjects: Acetyl-CoA C-Acetyltransferase - deficiency; Acetyl-CoA C-Acetyltransferase - genetics; Applied sciences; Biological and medical sciences; Computer science; control theory; systems; Computer systems and distributed systems. User interface; CpG Islands; DNA methylation; DNA Methylation - genetics; DNA Mutational Analysis - statistics & numerical data; Exact sciences and technology; Exonic splcing enhancers; Fundamental and applied biological sciences. Psychology; Gene Expression Regulation; Genes, p53; Genome, Human; Humans; INDEL Mutation; Internal Medicine; Internet; Molecular and cellular biology; Molecular genetics; Mutation; Mutation effect; Neoplasms - genetics; Online tool; Other; Point Mutation; RNA Splice Sites - genetics; Software; Splicing; Transcription. Transcription factor. Splicing. Rna processing; DNA methylation; Online tool; Splicing; Mutation effect; Exonic splcing enhancers; Regulator gene; Annotation; Exon; User interface; Genetics; Mutation; Genome; Methylation; Time analysis
• ISSN: 0169-2607; 1872-7565
• DOI: 10.1016/j.cmpb.2013.04.002

Abstract The identification of thousands of mutations yearly has put new challenges to researchers who are interested in fast and effective annotation as well as the prediction of potential implications to the gene regulation mechanisms. This work presents an integrative tool, called GREMET, for the prediction of alterations in gene splicing regulation inferred by mutations of the human genome. GREMET supports the characterization of mutations either single-point or indels with respect to their effect on the splicing potential of the neighboring sequences and the binding strength of auxiliary cis-acting splicing enhancers. In addition, GREMET identifies possible consequences of mutations on the DNA methylation through the disruption or creation of CpG sequences. Besides locus-specific mutations, GREMET performs the analyses on newly identified mutations and provides an easy-to-use Web interface helping researchers to save time in routine mutation analyses. GREMET is freely accessible at: http://kedip.med.auth.gr/biotools/gremet/.