Journal: Bioinformatics

Article Title: GENEASE: real time bioinformatics tool for multi-omics and disease ontology exploration, analysis and visualization

doi: 10.1093/bioinformatics/bty182

Figure Lengend Snippet: GENEASE workflows: (a) GENEASE API used to retrieve gene, SNP, disease or CpG site information from local database. (b) Exploration module, begins with reading the input types from the explore screen. Local API used to extract information if the input is found and external database links are included in the final result. (c) Enrichment analysis module, starts with reading the gene/SNP lists from the analysis screen. Functional annotations are accessed and parsed on-the-fly and statistical tests are performed to test for enrichment. Multiple test correction procedures are employed and odds ratio is used to find enrichment/depletion. (d) Overlap analysis module firstly reads the gene/SNP sets supplied by the user. In case of direct overlap, intersections are found and overlap scores are computed directly. For enriched term overlap analysis, enrichment analysis module is used to retrieve the enriched terms in each of the sets and overlap is computed using them (Color version of this figure is available at Bioinformatics online.)

Article Snippet: Results In this study, we present GENEASE, a web-based one-stop bioinformatics tool designed to not only query and explore multi-omics and phenotype databases (e.g. GTEx, ClinVar, dbGaP, GWAS Catalog, ENCODE, Roadmap Epigenomics, KEGG, Reactome, Gene and Phenotype Ontology) in a single web interface but also to perform seamless post genome-wide association downstream functional and overlap analysis for non-coding regulatory variants.

Techniques: Functional Assay

Journal: Bioinformatics

Article Title: GENEASE: real time bioinformatics tool for multi-omics and disease ontology exploration, analysis and visualization

doi: 10.1093/bioinformatics/bty182

Figure Lengend Snippet: GENEASE module procedures: (a) Step-by-step procedures followed in Exploration module including the conditional validation procedure. External references are downloaded and appended to external links to form dynamic requests. (b) All steps of enrichment module including the two-step validation. Annotation data is downloaded in run-time and input ‘hit’ counts processed for significance tests. (c) Summary of procedures followed in overlap analysis. Enrichment analysis performed before computing the overlaps in case of ‘enriched term overlap’ case (Color version of this figure is available at Bioinformatics online.)

Article Snippet: Results In this study, we present GENEASE, a web-based one-stop bioinformatics tool designed to not only query and explore multi-omics and phenotype databases (e.g. GTEx, ClinVar, dbGaP, GWAS Catalog, ENCODE, Roadmap Epigenomics, KEGG, Reactome, Gene and Phenotype Ontology) in a single web interface but also to perform seamless post genome-wide association downstream functional and overlap analysis for non-coding regulatory variants.

Techniques: Biomarker Discovery