TPE-OLD

TPE-OLD analyzes the influence of chromosomal positioning—particularly telomere position effects (TPE-OLD)—on gene transcriptional regulation by assessing positional properties of human genes and their orthologs across species.

Key Features:

• Multiple Scoring Methods: Incorporates adjustable scoring methods to quantify positional variation of genes across species.
• Ranking System: Combines positional scores to generate customizable rankings of candidate genes potentially subject to position effects.
• Enrichment Analyses: Performs enrichment analyses of user-provided gene lists against top-ranking candidate genes to identify overrepresented sets.
• Orthologous Position Comparison: Compares chromosomal positions of human genes and their orthologs across species to identify conserved or divergent positional patterns.
• Telomere-Centric Assessment: Evaluates relationships between gene positions and telomeres to assess susceptibility to telomere position effects (TPE-OLD).
• Parameter Customization: Allows adjustment of scoring and ranking parameters to tailor analyses to specific gene sets or comparative settings.

Scientific Applications:

• Study of TPE-OLD: Investigation of telomere-mediated regulation of gene expression over long genomic distances.
• Candidate Gene Identification: Prioritization of genes likely influenced by chromosomal positioning for downstream functional studies.
• Comparative Genomics of Position Effects: Analysis of conserved positional features across species to infer evolutionary or mechanistic aspects of positional regulation.
• Disease and Regulatory Mechanism Research: Exploration of how chromosomal positioning and telomere proximity correlate with gene regulation changes relevant to disease.

Methodology:

The framework integrates multiple adjustable scoring methods to assess positional variation of genes across species, combines those scores to produce rankings of candidate genes, and supports customization via user-defined parameters.