GeneAnalytics – An Integrative Gene Set Analysis Tool for Next Generation Sequencing, RNAseq and Microarray Data

Postgenomics data are produced in large volumes by life sciences and clinical applications of novel omics diagnostics and therapeutics for precision medicine. To move from “data-to-knowledge-to-innovation,” a crucial missing step in the current era is, however, our limited understanding of biological and clinical contexts associated with data.

Prominent among the emerging remedies to this challenge are the gene set enrichment tools. GeneAnalytics™ (geneanalytics.genecards.org),is a comprehensive and easy-to-apply gene set analysis tool for rapid contextualization of expression patterns and functional signatures embedded in the postgenomics Big Data domains, such as Next Generation Sequencing (NGS), RNAseq, and microarray experiments. GeneAnalytics’ differentiating features include in-depth evidence-based scoring algorithms, an intuitive user interface and proprietary unified data. GeneAnalytics employs the LifeMap Science’s GeneCards suite, including the GeneCards®-the human gene database; the MalaCards-the human diseases database; and the PathCards-the biological pathways database. Expression-based analysis in GeneAnalytics relies on the LifeMap Discovery®-the embryonic development and stem cells database, which includes manually curated expression data for normal and diseased tissues, enabling advanced matching algorithm for gene-tissue association. This assists in evaluating differentiation protocols and discovering biomarkers for tissues and cells. Results are directly linked to gene, disease, or cell “cards” in the GeneCards suite. Future developments aim to enhance the GeneAnalytics algorithm as well as visualizations, employing varied graphical display items. Such attributes make GeneAnalytics a broadly applicable postgenomics data analyses and interpretation tool for translation of data to knowledge-based innovation in various Big Data fields such as precision medicine, ecogenomics, nutrigenomics, pharmacogenomics, vaccinomics, and others yet to emerge on the postgenomics horizon.

Tissues and Cells results

(A) The Analyzed genes are the queried genes that were identified and included in the analysis. The “Notes” indicate genes in the query that were found to be abundant or defined as housekeeping genes in human. These genes get lower scores in the Tissue and Cells matching analysis. (B) The filters panel allows for filtering genes specifically expressed in Tissue/system, In vivo/In vitro, ‘Expressed in’ (cells, anatomical compartments, organs and tissues, and/or high throughput comparisons and large-scale dataset samples), Prenatal/Postnatal. (C) The detailed results table presents all entities in which at least one of the analyzed genes is expressed, along with links to their cards in LMD. (D) A link to the list of the matched genes and additional information for them (for example, “Mature Rod Cells”). (E) The list of matched genes linked to the specific entity in LMD (connected to “Mature Rod Cells”).

Availability – GeneAnalytics™ is available at: http://geneanalytics.genecards.org