Resources & Tools
Biological systems are networks and in these networks, we can define nodes (e.g., genes, proteins, metabolites) connected through edges (e.g., enzymatic/chemical reactions, transcription regulation). Networks have properties that can be measured using a mathematical approach, and we can make predictions about the evolution of a system based on some of those properties.
A “pathway” in a biological system can be defined as a relatively discrete (though never completely isolated) portion of a network. Generally, we view a pathway as a sequence of gene regulatory and enzymatic reactions that produce some important biological outcomes (e.g., synthesize an energy storage molecule, sense and regulate blood sugar levels).
In this project we will be using network analysis approaches to better understand the evolution and function of biological pathways. The Pathways Project is focused on annotating genes found in well characterized signaling and metabolic pathways across the Drosophila genus. The current focus is on the insulin signaling pathway which is well conserved across animals and critical to growth and metabolic homeostasis. The long-term goal of the Drosophila Pathways Project is to analyze how the regulatory regions of genes evolve in the context of their positions within a network and we anticipate that other pathways will eventually be part of the analyses.
Interactions across the D. melanogaster insulin signaling pathway elements. Arrows (edges) indicate the direction of signal transduction from one node to another.
This walkthrough illustrates how to apply the GEP annotation strategy for the Pathways Project to construct a gene model for the Ras homolog enriched in brain (Rheb) gene in Drosophila yakuba.
GEP students will use the Report Form document to submit their annotation results for the Pathways Project.
The Pathways Annotation Notebook will help GEP students keep track of their work as they are annotating, and then they can use the notebook to fill out the report form.
The Annotation Workflow is a one page summary of the annotation protocol for the Pathways Project. This workflow provides an overview of the key analysis steps and bioinformatics tools for the annotation of a putative ortholog.