New & Noteworthy

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:

Example: Sulfite reductase complex (NADPH)
Browse all complexes: Search for complexes

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:

Example gene page: https://www.yeastgenome.org/locus/MET2
Example complex page: https://www.yeastgenome.org/complex/CPX-3163

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