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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 Chemical Pages: Comprehensive Small Molecule Information in One Place

August 07, 2026

We’re pleased to announce the redesign of SGD’s chemical pages! These updated pages provide comprehensive information about small molecules relevant to yeast biology such as metabolites, drugs, and experimental compounds, all in a more accessible, more user-friendly format.

Why Chemical Information Matters

Small molecules play crucial roles in yeast biology, from essential metabolites that keep cells functioning to experimental compounds that reveal how cellular processes work. SGD chemical pages bring together curated information about how these chemicals affect yeast, connecting chemical entities to genes, phenotypes, and biological pathways.

What’s New?

Chemical Structures Front and Center

The redesigned pages now display interactive 2D chemical structures prominently at the top of each page. These structures clearly show molecular connectivity and functional groups, providing immediate visual recognition of the compound. No more hunting for the structure because it’s the first thing you see!

All Information on One Page

No need to navigate between multiple tabs! Everything you need to know about a chemical is now presented on a single, unified page:

Comprehensive Identifiers and Database Links:

This integration makes it easy to explore the chemical across multiple resources and access broader chemical and metabolic information.

Curated Experimental Data

Each chemical page now includes rich experimental data curated from the yeast literature:

Phenotype Annotations
See the effects of the chemical on yeast:

  • Growth effects
  • Metabolic changes
  • Other cellular processes

This section includes annotation statistics, top genes and phenotypes involving each chemical. Every phenotype annotation is linked to supporting experimental evidence and literature references, so you can trace findings back to the original research.

Gene Ontology Annotations and Enrichment

The GO Annotations section shows how the chemical is annotated within the Gene Ontology framework, connecting it to specific biological processes, molecular functions, and cellular components.

For metabolites, you’ll also find links to relevant metabolic pathways in YeastPathways throughout the GO annotation tables, connecting chemical entities to their biological context in small molecule metabolism.

The GO Enrichment section takes this further with statistical analysis showing which biological processes and molecular functions are significantly associated with genes affected by the chemical. This enrichment analysis helps you:

  • Understand the broader biological context of chemical-gene interactions
  • Identify patterns in how chemicals influence cellular systems
  • Generate hypotheses about mechanism of action

Shared Chemicals Network

Discover related compounds! The Shared Chemicals section displays other chemical entities that share similar properties, annotations, or biological roles. This network view makes it easy to:

  • Explore chemical families
  • Find compounds with similar effects
  • Identify potential alternative compounds for experiments

Complete Literature Coverage

The References section compiles all publications from which data about the chemical has been curated. This provides direct access to the primary literature and shows you the full scope of research on each compound.

Try It Out!

Explore the new chemical pages:

We Want Your Feedback!

These improvements are part of our ongoing commitment to making SGD more comprehensive and user-friendly. Have thoughts on the new chemical pages? Contact us at sgd-helpdesk@lists.stanford.edu.

Categories: Website changes

Tags: ChEBI, chemicals, GO enrichment, metabolites, phenotypes, redesign, user experience

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