evolSOM

evolSOM explores and visualizes the conservation or displacement of biological variables, facilitating the integration of phenotypic and genotypic attributes by projecting multi-dimensional expression profiles onto interpretable two-dimensional grids.

Key Features:

• Conservation and Displacement Analysis: evolSOM automatically calculates and graphically presents the conservation or displacement of biological variables across multiple conditions.
• Multi-dimensional Projection: The package enables projection of multi-dimensional expression profiles onto interpretable two-dimensional grids.
• Phenotypic and Genotypic Integration: evolSOM eases the integration of phenotypic and genotypic attributes for exploring relationships between genes and traits.
• Regulatory Network Inference: Variables displaced together suggest membership to the same regulatory network, where the nature of the displacement may hold biological significance.

Scientific Applications:

• Gene-Phenotype Relationship Analysis: evolSOM aids in identifying conserved or displaced genes and phenotypes across multiple conditions, supporting the unraveling of connections between genes and traits.
• Multi-condition Comparative Studies: The package facilitates comparison of RNA and protein expression patterns across different biological conditions to detect conservation or displacement patterns.
• Regulatory Network Analysis: evolSOM supports the identification of co-displaced variables that may belong to the same regulatory network, with displacement patterns potentially indicating biological significance.

Methodology:

evolSOM uses self-organizing maps to project multi-dimensional expression profiles onto two-dimensional grids, with automatic calculation of conservation or displacement of variables.