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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:

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

Redesigned Protein Complex Pages: Enhanced Data Access and Improved User Experience

August 04, 2026

We’re excited to announce a comprehensive redesign of SGD’s macromolecular complex pages! We’ve overhauled these pages to make complex information more accessible, comprehensive, and easier to navigate.

Why Protein Complexes Matter

Protein complexes are fundamental functional units in cells that operate as groups of proteins that work together to carry out specific biological processes. Since 2019, SGD has provided detailed information about yeast protein complexes, including subunit composition, functions, interactions, and references. With this major redesign, we’ve made this critical information even more accessible and useful for researchers.

What’s New?

All Gene Ontology Information on One Page

One of the most significant improvements is the reorganization of Gene Ontology (GO) annotations. Previously, GO information was tucked away on a separate tab, requiring you to navigate away from the main view. Now, all GO annotations are prominently displayed right on the Summary page.

What you can see at a glance:

  • Molecular Function: What the complex does
  • Biological Process: What pathways or processes it participates in
  • Cellular Component: Where in the cell it’s located

No more tab-switching—everything you need is in one place!

GO-CAM Pathway Models for Complexes

We’ve also integrated GO-CAM (Gene Ontology Causal Activity Models) pathway models directly into complex pages. When available, these models appear below the GO annotations, showing how entire protein complexes fit into larger biological pathways and regulatory networks. This provides a systems-level view that complements the detailed subunit information available on individual gene pages.

Enhanced Composition Section

The new Composition section is packed with detailed subunit information:

Stoichiometry Data: For complexes where the subunit ratios have been experimentally determined, you’ll now see the exact stoichiometry. This quantitative information is crucial for understanding complex architecture.

Structural Information:

  • Expert-curated notes about complex assembly and structural features
  • Direct links to Protein Data Bank (PDB) entries for complexes with experimentally determined 3D structures
  • Protein-protein binding regions and interaction interfaces (when characterized)

Organized Display: Subunits are now grouped by their roles or relationships within the complex, making it easier to understand how the complex is organized.

Easy Navigation: Each subunit links directly to its SGD gene page, so you can quickly dive deeper into individual components.

Shared Biology Networks

Complex pages now include a Shared Biology section that shows:

  • GO annotations shared with other complexes
  • Subunits shared between complexes
  • Ranked lists that prioritize the most functionally related complexes

The ranking system helps you quickly identify the most relevant relationships and potential functional connections, making it easier to understand how different complexes relate to each other.

Improved User Experience Throughout

Beyond these major features, we’ve focused on overall usability:

  • Clearer section headers make information easy to find
  • Better spacing and organization improve readability
  • Consistent styling with other SGD page types provides a unified experience
  • Logical information hierarchy puts the most commonly accessed data front and center

Try It Out!

Explore the new complex pages:

We Want Your Feedback!

These improvements are based on feedback from the yeast research community, and we want to keep making SGD better. Have suggestions? Questions? Let us know at sgd-helpdesk@lists.stanford.edu.

Categories: Announcements, Website changes

Tags: Gene Ontology, GO annotations, GO-CAM, protein complexes, redesign, stoichiometry, UI, user experience, UX

Functional Networks: A New Way to Explore Gene Relationships at SGD

August 03, 2026

We’re excited to announce new Functional Networks sections on gene and complex pages! This powerful addition helps researchers understand how genes and proteins work together in biological systems.

What Are Functional Networks?

The new Functional Networks section appears on most gene page, positioned just below the Gene Ontology section. It provides two complementary views of how gene products interact and function together:

1. Shared Annotations Networks

Ever wondered which other genes might have similar functions to your gene of interest? The Shared Annotations network visualizes genes that share similar Gene Ontology (GO) annotations with your query gene. These networks are generated based on overlapping GO terms across Molecular Function, Biological Process, and Cellular Component.

Why is this useful?

  • Identify potential interaction partners
  • Find paralogs with related functions
  • Discover genes that may participate in similar biological processes
  • Generate hypotheses for experimental design

Most genes in the S. cerevisiae genome have sufficient GO annotations to generate these networks, providing broad coverage across the yeast proteome.

2. GO-CAM Pathway Models

GO-CAMs (Gene Ontology Causal Activity Models) represent an exciting advancement in pathway representation. Unlike traditional GO annotations that link individual genes to single terms, GO-CAMs show how multiple gene products work together in integrated pathway models.

What makes GO-CAMs special?

  • Causal relationships: See how one molecular activity leads to another, including activation, inhibition, and regulatory interactions
  • Integrated view: Combines Molecular Function, Biological Process, and Cellular Component information in one unified model
  • Evidence-based: All models are manually curated by expert biologists and supported by published experimental data

Currently, 470 yeast genes are associated with GO-CAM models, and this number continues to grow as additional pathways are curated.

When multiple GO-CAM models are available for a gene, you can easily switch between them using a pull-down menu. Each model includes a “View GO-CAM at Gene Ontology” link that opens the interactive pathway in AmiGO, where you can explore detailed evidence codes, supporting references, and connections to other pathways.

Functional Networks on Complex Pages

We’ve also added a Shared Biology section to macromolecular complex pages. This section shows:

  • GO annotations shared with other complexes
  • Subunits shared between complexes
  • A ranked list summarizing these relationships

This helps researchers understand how protein complexes relate to each other and identify functionally similar complexes.

How to Access

Simply navigate to any gene page at SGD and scroll to the Functional Networks section (located beneath Gene Ontology). For complex pages, look for the Shared Biology section.

Try it out:

Part of a Bigger Picture

The GO-CAM display on SGD gene pages replicates the implementation from the Alliance of Genome Resources, providing a consistent user experience across model organism databases. This integration reflects our commitment to making yeast data accessible and interoperable with other genomic resources.

We Want Your Feedback!

This new feature is designed to help you explore gene relationships and generate hypotheses more effectively. We’d love to hear what you think! Contact us at sgd-helpdesk@lists.stanford.edu with your feedback or questions.

Categories: Announcements, Website changes

Tags: functional networks, gene annotation, GO-CAM, protein complexes, shared annotations

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