piRNAQuest

piRNAQuest V.2 provides a comprehensive database and analysis resource for PIWI-interacting RNAs (piRNAs), enabling cataloging of piRNA sequences, genomic contexts, expression profiles, cluster prediction, target prediction, and structural visualization to support piRNA research.

Key Features:

• Extensive Database Coverage: The updated database contains 92,77,689 piRNA entries across 28 species, including 25 newly added species and previously covered organisms such as humans, mice, and rats.
• Primary piRNA Features: Annotations include genomic locations of piRNAs and their overlaps with repeat elements, pseudogenes, and syntenic regions.
• Novel Functionalities: Implemented features include density-based cluster prediction that avoids parametric distribution assumptions, piRNA expression profiles across 21 disease systems (including cancer) and 32 tissue-specific profiles, and predicted and curated piRNA targets within eight disease systems and mouse testis developmental stages.
• Visualization Tools: Visualization includes piRNA-target duplex structures and ping-pong signature patterns for all ping-pong piRNA partners across species.

Scientific Applications:

• Comparative Genomics: Cross-species piRNA data support comparative and evolutionary analyses of piRNA function.
• Disease Research: Expression profiles across disease systems, including cancer, enable investigations into piRNA roles in disease pathogenesis and progression.
• Functional Genomics: Target predictions and annotations facilitate exploration of piRNA-mediated regulatory networks and functional studies.

Methodology:

piRNAQuest V.2 uses a density-based approach for piRNA cluster identification that does not assume parametric distributions.