Using Genetic Markers to Orient Edges in Trait Networks
Author Information
Author(s): Aten Jason E, Fuller Tova F, Lusis Aldons J, Horvath Steve
Primary Institution: University of California, Los Angeles
Hypothesis
Can genetic markers serve as causal anchors for orienting the edges of trait networks?
Conclusion
The NEO software can effectively orient edges of gene co-expression networks using genetic marker data.
Supporting Evidence
- NEO software allows users to carry out robustness analysis regarding genetic marker selection.
- NEO was demonstrated to recover known causal relationships in the sterol homeostasis pathway.
- Local SEM-based Edge Orienting (LEO) scores were proposed to summarize genetic evidence for edge orientation.
Takeaway
Scientists can use special software to figure out how different genes affect each other by looking at their genetic markers.
Methodology
The study developed and implemented Network Edge Orienting (NEO) methods and software to infer directed gene networks from gene expression data and genetic marker data.
Potential Biases
Automatic SNP selection is particularly vulnerable to false positives.
Limitations
The method requires significant genetic markers associated with traits and may produce unreliable scores with spurious associations.
Participant Demographics
The study used data from F2 mouse intercrosses involving two inbred mouse strains.
Digital Object Identifier (DOI)
Want to read the original?
Access the complete publication on the publisher's website