GenomeTraFaC

GenomeTraFaC identifies and characterizes conserved cis-regulatory element clusters in RefSeq gene orthologs to support comparative genomics analyses of non-coding regulatory regions.

Key Features:

• Cis-Regulatory Element Detection: Scans ortholog gene pairs to detect compositionally similar cis-clusters within conserved non-coding DNA segments and visualizes conserved sequence regions and the relative density of conserved cis-element motif clusters forming distinct graph peak structures.
• Motif Analysis: Mines gene lists to identify frequently represented cis-motifs across orthologs for comparative motif representation analysis.
• Gene Model Consistency Evaluation: Evaluates and visualizes gene model consistency between orthologs to assess how sequence variations in conserved non-coding regions affect complex cis-element structures.
• Cross-Species Comparative Analysis: Performs comparative analysis of microRNA genes and conventional RNA-encoding genes across genomes (for example, mouse and human) using resources such as the NCBI Reference Sequence database and the Sanger Institute miRBase.
• Transcription Factor Target Identification: Identifies validated transcription factor targets within promoter and distal genomic regulatory regions of both conventional and microRNA genes.

Scientific Applications:

• Comparative genomics of non-coding DNA: Characterizes conservation and composition of cis-regulatory clusters across RefSeq orthologs to inform evolutionary and functional studies.
• Regulatory motif discovery: Detects recurrent cis-motifs across gene sets to support identification of candidate regulatory elements influencing gene expression.
• Transcription factor and miRNA regulatory analysis: Maps transcription factor targets and regulatory architectures in promoter and distal regions of protein-coding and microRNA genes.

Methodology:

Uses a systematic gene-centric pipeline that integrates data from multiple genomic databases, focuses on conserved non-coding regions across orthologous genes, and produces visualizations of conserved sequence regions and cis-element motif cluster densities.