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Updated: Feb 17, 2026
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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
Published on: May 28, 2021
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Network analysis of pseudogene-gene relationships: from pseudogene evolution to their functional potentials.
Travis S Johnson1, Sihong Li, Jonathan R Kho
1Dept. Biomedical Informatics, Ohio State University, 5000 HITS, 410 W. 10th St. Indianapolis, Indiana, 46202, USA, Travis.Johnson@osumc.edu.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
|December 9, 2017
Summary
Pseudogenes, once considered junk DNA, are now recognized for potential functions. This study developed a novel network analysis to reveal pseudogene-gene relationships and their roles in evolution and disease.
Area of Science:
- Genomics
- Evolutionary Biology
- Bioinformatics
Background:
- Pseudogenes were historically dismissed as non-functional DNA.
- Emerging evidence indicates pseudogenes can exhibit transcriptional activity and adopt regulatory roles.
- Some pseudogenes are reactivated in diseases like cancer, suggesting functional potential.
Purpose of the Study:
- To develop and apply a novel computational approach for evaluating pseudogene-gene relationships.
- To explore the evolutionary history and functional potential of pseudogenes.
- To infer the impact of pseudogenes in gene regulatory networks and disease contexts.
Main Methods:
- Integrated graph analysis, sequence alignment, and functional analysis.
- Generated pseudogene-gene (PGG) families and sequence alignment networks.
- Constructed phylogenetic trees and performed gene ontology enrichment analysis.
Main Results:
- Identified 445 PGG families, with 98.4% containing multiple pseudogenes.
- Revealed evolutionary insights into families like the olfactory receptor genes.
- Inferred functional roles and impacts of pseudogenes within identified networks.
Conclusions:
- Pseudogenes possess significant functional potential beyond their protein-coding origins.
- The developed network analysis approach is effective for studying pseudogene evolution and function.
- This work provides a foundation for understanding pseudogene involvement in disease.
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