Abstract
Integrated analysis of DNA variants and gene expression profiles may facilitate precise identification of gene regulatory networks involved in disease mechanisms. Despite the widespread availability of public resources, we lack databases that are capable of simultaneously providing gene expression profiles, variant annotations, functional prediction scores and pathogenic analyses. VariED is the first web-based querying system that integrates an annotation database and expression profiles for genetic variants. The database offers a user-friendly platform and locates gene/variant names in the literature by connecting to established online querying tools, biological annotation tools and records from free-text literature. VariED acts as a central hub for organized genome information consisting of gene annotation, variant allele frequency, functional prediction, clinical interpretation and gene expression profiles in three species: human, mouse and zebrafish. VariED also provides a novel scoring scheme to predict the functional impact of a DNA variant. With one single entry, all results regarding queried DNA variants can be downloaded. VariED can potentially serve as an efficient way to obtain comprehensive variant knowledge for clinicians and scientists around the world working on important drug discoveries and precision treatments.
Highlights
Advances in microarray and next-generation sequencing (NGS) technologies and the widespread availability of genomic data provide a good opportunity for researchers to simultaneously analyze data from multiple molecular levels
VariED predicts the functional impact of queried DNA variants using a novel index score that is composed of several popular prediction algorithms and scores (REVEL and GERP++), the expression profile of the variant in the target tissue and associated clinical characteristics, furnishing users with a ready-made multidimensional view of the query
The findings suggest that the index score calculated in VariED can serve as an efficient selection tool to rank the possibility of queried variants playing an important role in a biological process (Figure 3D)
Summary
Advances in microarray and next-generation sequencing (NGS) technologies and the widespread availability of genomic data provide a good opportunity for researchers to simultaneously analyze data from multiple molecular levels. The surge in analysis of gene expression data in recent years has led to the development of various web-based tools and databases that help to explore the genetic roots of diseases in different populations [1, 2]. Databases such as ANNOVAR [3], InterVar [4], FUMA [5], Ensembl [6] and UCSC [7] provide gene annotation information, and databases such as ProteinAtlas [8], GeneCards [9], NCBI [10] and UniProt [11] furnish tissue-specific gene expression profile information. We still lack a comprehensive analytical system that integrates different kinds of information, such as the functional impact of DNA variants, allele frequencies in different populations and gene expression levels in specific tissue types
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