SEAweb

SEAweb provides an atlas of small RNA and pathogen expression enabling querying, visualization, and comparative analysis of sRNA profiles across multiple organisms.

Key Features:

• Extensive dataset coverage: Over 4,200 published samples from ten organisms covering microRNAs (miRNA), Piwi-interacting RNAs (piRNA), small nucleolar RNAs (snoRNA), small nuclear RNAs (snRNA), small interfering RNAs (siRNA), and pathogen expression data, standardized with search terms and ontologies.
• Differential expression and classification analyses: Contains 879 differential expression analyses and 514 classification comparisons available for exploration and re-analysis.
• Re-analysis and dataset comparison: Enables comparison and re-analysis of published and user-specific datasets to identify common and distinct sRNA expression patterns and candidate biomarkers.
• Ontology-connected metadata: Metadata is curated and connected to ontologies and standardized search terms to support comparable queries across datasets.
• Interactive reporting: Generates interactive reports for customized analysis and presentation of sRNA expression results.

Scientific Applications:

• Tissue-specific miRNA identification: Generated a set of 591 tissue-specific miRNAs across 29 tissues.
• Pathogen detection: Facilitates identification of known and novel bacterial and viral infections across diseases using sRNA and pathogen expression data.
• Biomarker discovery: Supported identification of a Parkinson's disease-specific blood biomarker signature using novel data.

Methodology:

SEAweb analyzes publicly available sRNA sequencing datasets using the Oasis 2 pipelines; results are curated and stored in a database and integrated with ontology-connected metadata for standardized searches.