eVITTA

eVITTA provides visualization and inference for transcriptome analysis, enabling retrieval, comparative analysis, and functional profiling of gene expression datasets.

Key Features:

• Integration with NCBI GEO: easyGEO enables systematic retrieval and exploration of studies stored in the National Center for Biotechnology Information's Gene Expression Omnibus (NCBI GEO).
• Functional profiling (easyGSEA): easyGSEA performs molecular- and systems-level functional profiling to identify biological processes and pathways associated with gene expression changes.
• Customizable comparisons (easyVizR): easyVizR supports customizable comparisons among experimental groups to visualize differences and similarities across datasets.
• Species support: Analyses encompass human and model organisms.

Scientific Applications:

• SARS-CoV-2 transcriptome analysis: Applied to human nasopharyngeal swab samples to identify downregulation of olfactory signal transducers consistent with anosmia in COVID-19 patients.
• Caenorhabditis elegans metabolism study: Used to analyze worms with disrupted S-adenosylmethionine metabolism, confirming activation of innate immune responses and feedback induction of one-carbon cycle genes.
• Gene regulation in development and disease: Facilitates functional characterization of gene regulation changes across developmental and disease contexts.

Methodology:

Integrates data from NCBI GEO and applies modules easyGEO for dataset retrieval, easyGSEA for molecular- and systems-level functional profiling, and easyVizR for customizable inter-group comparisons.