SynoR

SynoR identifies synonymous regulatory elements (SREs) in vertebrate genomes by detecting conserved modules of transcription factor binding sites (TFBS) that underlie shared temporal and spatial gene expression.

Key Features:

• De Novo Identification: Performs de novo identification of SREs by scanning vertebrate genomes using known patterns of TFBS from active regulatory elements as initial seeds.
• Conservation-Based Approach: Incorporates multiple-species conservation data and applies differential phylogenetic sequence conservation filters to detect conserved SREs across vertebrates.
• Extensive Annotation: Annotates genes containing predicted SREs with functional classifications including Gene Ontology categories.
• Tissue-Specificity Cataloging: Integrates GNF Expression Atlas 2 expression data to catalog tissue-specific expression patterns linked to predicted SREs.

Scientific Applications:

• Comparative and Evolutionary Genomics: Identifies conserved regulatory mechanisms across vertebrates to inform comparative genomics and evolutionary analyses.
• Functional Genomics: Links predicted SREs to gene function via Gene Ontology and expression data to support functional genomics studies.
• Development and Disease Research: Elucidates regulatory modules underlying shared temporal and spatial expression to inform studies of development and disease mechanisms.

Methodology:

Scans vertebrate genomes for conserved modules of TFBS arranged in predefined configurations using known patterns from active regulatory elements as seeds, applies differential phylogenetic sequence conservation filters across multiple species, annotates genes with Gene Ontology, and integrates GNF Expression Atlas 2 expression data for tissue-specific cataloging.