SalMotifDB

SalMotifDB annotates transcription factors (TFs) and cis-regulatory binding sites in salmonid genomes to enable prediction of regulatory interactions and interpretation of how non-coding variation affects gene expression and phenotypes.

Key Features:

• Extensive motif compilation: Incorporates 3,072 unique DNA motifs compiled from a wide array of metazoan motif databases for analysis across salmonid species.
• Multi-species regulatory network construction: Constructs putative regulatory networks by leveraging multi-species motif databases to study evolutionary aspects such as gene expression divergence in gene duplicates resulting from whole genome duplications.
• Regulatory annotations: Provides regulatory annotations that link non-coding genomic regions to predicted TF binding and potential effects on gene expression and phenotype.
• Application to lipid metabolism and duplicate divergence: Applied to predict key lipid metabolism regulators influencing gene expression related to lipid and fatty acid content in salmonid feed and to explain a significant portion of expression divergence among duplicated genes after whole genome duplication.

Scientific Applications:

• Life-history and trait variation: Analyze regulatory mechanisms underlying life-history trait variation in salmonids.
• Aquaculture trait investigation: Investigate regulatory bases of economically important traits in aquaculture, including lipid and fatty acid content related to feed.
• Evolutionary genomics: Study the evolutionary consequences of whole genome duplications and resulting expression divergence among gene duplicates in salmonids.

Methodology:

Motif matching and TF prediction are used to construct putative regulatory networks.