proteome
Definition
The proteome is the complete set of proteins expressed by a genome, cell, tissue, or organism at a specific time under defined conditions. Unlike the static genome, the proteome is highly dynamic, varying with developmental stage, environmental conditions, and disease states. Proteomics, the study of proteomes, encompasses protein identification, quantification, localization, modifications (such as phosphorylation), and interactions. The proteome provides functional insights beyond genomic data, as protein abundance doesn't always correlate with mRNA levels due to post-transcriptional regulation, protein stability, and degradation. Understanding proteome composition and dynamics is crucial for identifying disease biomarkers, drug targets, and elucidating cellular mechanisms underlying biological processes.
Visualize proteome in Nodes Bio
Researchers can visualize proteome data as protein-protein interaction networks, mapping how proteins physically interact or functionally associate within cellular pathways. Nodes Bio enables integration of quantitative proteomics data with interaction networks, allowing visualization of differentially expressed proteins across conditions, identification of protein complexes, and analysis of signaling cascades. Users can overlay post-translational modification data onto networks to understand regulatory mechanisms and identify key hub proteins.
Visualization Ideas:
- Protein-protein interaction networks colored by expression fold-change
- Pathway enrichment maps showing dysregulated proteome subsets
- Time-course proteome dynamics networks tracking protein abundance changes
Example Use Case
A cancer research team performs quantitative proteomics on tumor samples versus healthy tissue to identify therapeutic targets. They detect 500 differentially expressed proteins and want to understand which signaling pathways are dysregulated. By mapping these proteins onto interaction networks in Nodes Bio, they identify a cluster of upregulated kinases centered around a hub protein. Further analysis reveals this hub is a known oncogenic driver, and several connected proteins are druggable targets, providing multiple intervention points for combination therapy development.