New & Noteworthy
New Pathway Pages: Comprehensive Views of Yeast Biochemical Pathways
August 11, 2026
We’re excited to announce the release of Pathway Pages at SGD! These new pages provide comprehensive information about the 220 manually curated biochemical pathways in yeast, bringing together pathway diagrams, gene lists, functional networks, and curated experimental data all in one place.
- One-stop resource: All pathway information in a single place
- Rich context: See genes in the context of the pathway they participate in
- Evidence-based: All data tied to primary literature
- Interactive exploration: Multiple ways to explore pathway relationships
Pathway pages offer a complete view of specific biochemical pathways in Saccharomyces cerevisiae. Each page integrates information from multiple sources to help you understand what the pathway does, which genes are involved, how gene products interact, and which chemicals are involved.
What’s Included?
Interactive Pathway Diagrams
Each pathway page features a pathway diagram showing the chemical reactions and metabolic flow. The diagram displays:
- Chemical compounds involved (substrates and products)
- Enzymes catalyzing each reaction
- Reaction directionality and relationships
A “View interactive diagram at YeastPathways” button takes you to the full interactive version where you can explore the pathway in greater detail.
Pathway Summary
Expert-curated descriptive text explains:
- What the pathway does and why it’s important
- Biological context and cellular roles
- Connections to other metabolic processes
- Key regulatory mechanisms
For example, the glyoxylate cycle page explains how this essential pathway allows yeast to grow on two-carbon compounds and its role in providing precursors for biosynthesis.
Genes Involved
A comprehensive table of genes participating in the pathway includes:
- Gene names (standard and systematic)
- EC numbers for enzymatic activities
- Functional descriptions
- Direct links to gene pages for detailed information
This makes it easy to see all the players in a pathway at a glance and dive deeper into any gene of interest.
Functional Networks
Pathway pages now include the same Functional Networks features available on gene pages:
Shared Annotations Network: Visualizes how genes in the pathway share phenotype and GO annotations, helping you identify:
- Functional relationships between pathway genes
- Connections to genes in related pathways
- Potential regulatory relationships
You can filter the network by the number of shared pathway genes to focus on the most relevant connections.
GO-CAMs: When available, Gene Ontology Causal Activity Model pathway models are displayed, showing:
- Causal relationships between molecular activities
- How gene products work together mechanistically
- Regulatory interactions and dependencies
If multiple GO-CAM models involve genes from the pathway, you can switch between them using a dropdown menu.
GO Enrichment Analysis
The GO Enrichment section shows which biological processes are statistically overrepresented among pathway genes. This helps you:
- Understand the broader biological context
- See connections to related processes
- Identify key functional themes
Each enriched term links to the genes involved and shows the statistical significance (p-value).
Browse All Pathways
Explore all 220 curated pathways:
- Browse pathways: Search for pathways
- Example: Glyoxylate cycle
- YeastPathways: All metabolic pathways
We Want Your Feedback!
Pathway pages are a new addition to SGD, and we want to make them as useful as possible. Have suggestions? Questions about specific pathways? Let us know at sgd-helpdesk@lists.stanford.edu.
Categories: Announcements, Website changes
Tags: biochemical pathways, GO enrichment, GO-CAM, metabolic pathways, pathway diagrams, YeastPathways