annotation
Definition
Annotation in bioinformatics refers to the process of identifying and labeling biological features in sequence data, assigning functional information to genes, proteins, or other molecular entities. This includes determining gene locations, predicting protein functions, identifying regulatory elements, and linking sequences to biological pathways, diseases, and phenotypes. Annotations draw from curated databases like GO (Gene Ontology), KEGG, UniProt, and others to provide context and meaning to raw sequence data. High-quality annotation is essential for interpreting omics data, as it transforms lists of genes or proteins into biologically meaningful insights about cellular processes, molecular functions, and disease mechanisms.
Visualize annotation in Nodes Bio
Researchers can visualize annotated biological entities as networks where nodes represent genes or proteins colored or sized by annotation categories (GO terms, pathways, disease associations). Network clustering can reveal functional modules sharing similar annotations, while pathway enrichment results can be mapped onto interaction networks to identify key regulatory hubs and their annotated roles in specific biological processes.
Visualization Ideas:
- Gene networks colored by GO term annotations showing functional clustering
- Pathway annotation networks linking genes to KEGG or Reactome pathways
- Disease-gene association networks with phenotype annotations from databases like OMIM or DisGeNET
Example Use Case
A cancer researcher identifies 500 differentially expressed genes from RNA-seq data. Using annotation databases, they assign GO terms and KEGG pathways to each gene. By visualizing these annotated genes as a protein-protein interaction network in Nodes Bio, they discover that upregulated genes cluster into modules enriched for cell cycle regulation and DNA repair annotations, while downregulated genes are annotated with immune response functions, revealing potential therapeutic targets and mechanisms of immune evasion.