ConTra v3

ConTra v3 facilitates visualization and exploration of predicted transcription factor binding sites (TFBSs) across specified genomic regions to support studies of gene regulation, development, cell signaling, and diseases linked to transcription factor dysregulation.

Key Features:

• Broad Organismal Coverage: Supports analysis across nine reference organisms, including humans and yeast, enabling comparative studies.
• Flexible Genomic Region Analysis: Analyzes promoter regions, 5′-UTRs, 3′-UTRs, introns, or other genomic regions of interest for predicted TFBSs.
• Extensive Position Weight Matrices (PWMs): Provides access to thousands of PWMs for detection and characterization of specific TFBS motifs.
• Automated TFBS Prioritization: Automatically detects and ranks predicted TFBSs based on regulatory potential, conservation scores within the covered genomic regions, and co-localization with genomic regions exhibiting regulatory activity.

Scientific Applications:

• Gene regulation analysis: Identification and prioritization of TFBSs to study regulatory elements controlling gene expression.
• Developmental biology: Comparative TFBS analysis across stages or species to investigate developmental regulatory networks.
• Cell signaling pathway analysis: Mapping TFBSs relevant to transcription factors involved in signaling pathways.
• Disease-associated TF dysregulation studies: Prioritizing TFBSs to investigate transcription factor contributions to disease mechanisms.

Methodology:

TFBS prediction using position weight matrices (PWMs) with integration of conservation scores and co-localization data to refine and prioritize predicted TFBSs, and automatic ranking by regulatory potential, conservation, and co-localization.