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:
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ChEBI ID (we use the Chemical Entities of Biological Interest ontology maintained by EMBL-EBI)
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IUPAC name
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PubChem CID
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Common names and synonyms
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Molecular formula and weight
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:
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Growth effects
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Metabolic changes
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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:
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Understand the broader biological context of chemical-gene interactions
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Identify patterns in how chemicals influence cellular systems
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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:
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Explore chemical families
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Find compounds with similar effects
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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:
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Example: Cisplatin
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Example: Caffeine
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Browse all chemicals: Search for chemicals
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.