LncPheDB

LncPheDB catalogs genome-wide associations between long non-coding RNAs (lncRNAs) and phenotypic traits across nine plant species to support analysis of lncRNA roles in agronomic trait diversity.

Key Features:

• Extensive Data Repository: Contains 203,391 lncRNA sequences, 2,000 phenotypes, and 120,271 variants across nine species: Zea mays, Gossypium barbadense, Triticum aestivum, Lycopersicon esculentum, Oryza sativa, Hordeum vulgare, Sorghum bicolor, Glycine max, and Cucumis sativus.
• lncRNA-Phenotype Correlations: Reports 68,862 lncRNAs linked to agronomic trait diversity via genome-wide association studies (GWAS).
• Target Gene Prediction and Regulatory Networks: Includes predicted lncRNA target genes and constructs regulatory networks by linking phenotypic study pages containing similar lncRNA fragments across species.
• Variant-Trait Associations: Maps genomic positions of variants to trait associations to relate genetic variation to lncRNA-associated phenotypes.
• BLAST Tool Integration: Provides BLAST-based similarity searches across all included species for comparative genomic analyses.

Scientific Applications:

• Functional Characterization: Investigating roles of lncRNAs in plant development, stress responses, and trait improvement using integrated lncRNA annotations and target gene predictions.
• Trait Association Mapping: Linking lncRNAs and genomic variants to agronomic traits using GWAS-derived correlations and mapped variant positions.
• Comparative Genomics: Performing cross-species comparisons of conserved lncRNA sequences and associated phenotypes using BLAST and inter-species network links.
• Regulatory Network Analysis: Elucidating lncRNA-mediated regulatory networks by integrating predicted targets and links between similar lncRNA fragments across species.

Methodology:

Uses genome-wide association studies (GWAS) for lncRNA-phenotype correlations, target gene prediction, BLAST similarity searches, construction of regulatory networks by linking similar lncRNA fragments across species, and mapping variant genomic positions to traits.