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About the Pathways Project

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 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.

Brief overview of the Pathways Project provided by the Project Leader.

click to enlarge

Interactions across the D. melanogaster insulin signaling pathway elements. Arrows (edges) indicate the direction of signal transduction from one node to another. 

Project Curriculum

Pathways Project: Annotation Walkthrough

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.

Pathways Project: Annotation Notebook

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.

Pathways Project: Annotation Notebook D. pseudoobscura Homework Key

Students can apply what they learned in the Pathways Project: Annotation Walkthrough to construct a gene model for Rheb in D. pseudoobscura by completing the Pathways Project: Annotation Notebook. An answer key is provided to assist in checking the accuracy of the annotation and includes potential areas of confusion throughout.

Pathways Project: Annotation Workflow

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.

Prerequisite Curriculum

completion recommended in order from left to right, top to bottom

Module 1. Introduction to the Genome Browser: What is a gene?

This module introduces students to the UCSC Genome Browser. After completing this module students will be able to navigate to a genomic region and to control the display setting for different evidence tracks. Additionally, students will be able to explain the relationships among DNA, pre-mRNA, and protein.

Module 4. Removal of introns from pre-mRNA by splicing

This module uses mRNA data to identify splice sites. After completing this module students will be able to identify intron-exon boundaries using canonical splice donor and acceptor sequences and determine which are best supported by RNA-Seq and TopHat splice junction predictions.

Module 5. Translation: The need for an Open Reading Frame

In this module students will learn how mRNA is translated into a string of amino acids. After completing this module students will be able to determine the codons for specific amino acids as well as start and stop codons. They will be able to identify open reading frames for a given gene, define the phases of splice donor and acceptor sites and describe how they impact the maintenance of the open reading frame.

Module 6. Alternative splicing

This module explores how multiple different mRNAs and polypeptides can be encoded by the same gene. After completing this module students will be able to explain how alternative splicing of a gene can lead to different mRNAs and illustrate how alternative splicing can lead to the production of different polypeptides and result in drastic changes in phenotype.

RNA-Seq Primer

This PowerPoint presentation provides a brief introduction to the different types of RNA-Seq evidence tracks (e.g. Bowtie, TopHat, Cufflinks) that are on the GEP UCSC Genome Browser.