evolSOM: an R Package for evolutionary conservation analysis with SOMs
Santiago Prochetto Renata Reinheimer Georgina Stegmayer
Motivation: Unraveling the connection between genes and traits is crucial for
solving many biological puzzles. Genes provide instructions for building
cellular machinery, directing the processes that sustain life. RNA molecules
and proteins, derived from these genetic instructions, play crucial roles in
shaping cell structures, influencing reactions, and guiding behavior. This
fundamental biological principle links genetic makeup to observable traits, but
integrating and extracting meaningful relationships from this complex,
multimodal data presents a significant challenge. Results: We introduce
evolSOM, a novel R package that utilizes Self-Organizing Maps (SOMs) to explore
and visualize the conservation of biological variables, easing the integration
of phenotypic and genotypic attributes. By constructing species-specific or
condition-specific SOMs that capture non-redundant patterns, evolSOM allows the
analysis of displacement of biological variables between species or conditions.
Variables displaced together suggest membership in the same regulatory network,
and the nature of the displacement may hold biological significance. The
package automatically calculates and graphically presents these displacements,
enabling efficient comparison and revealing conserved and displaced variables.
The package facilitates the integration of diverse phenotypic data types,
enabling the exploration of potential gene drivers underlying observed
phenotypic changes. Its user-friendly interface and visualization capabilities
enhance the accessibility of complex network analyses. Illustratively, we
employed evolSOM to study the displacement of genes and phenotypic traits,
successfully identifying potential drivers of phenotypic differentiation in
grass leaves. Availability: The package is open-source and is available at
https://github.com/sanprochetto/evolSOM.