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Updated: Dec 17, 2025
16:41
A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
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Predicting Functions of Uncharacterized Human Proteins: From Canonical to Proteoforms
Ekaterina Poverennaya1,2, Olga Kiseleva1, Anastasia Romanova1,3
1Institute of Biomedical Chemistry, 119121 Moscow, Russia.
Genes
|June 25, 2020
Summary
Researchers analyzed protein interactions to uncover functions for unannotated proteins (uPE1). This study predicts functions for 387 uPE1 genes and reveals functional differences in splice forms, highlighting the interactome
Area of Science:
- Proteomics and Systems Biology
- Gene Expression and Regulation
Background:
- Comprehensive functional annotation of protein-coding genes and proteoforms remains incomplete.
- A significant number of genes (1193) with confirmed protein expression lack functional annotation (uPE1 proteins).
Purpose of the Study:
- To predict the functions of unannotated proteins (uPE1) and their splice variants.
- To investigate the functional impact of alternative splicing on proteoform diversity.
Main Methods:
- Re-analysis of affinity purification-mass spectrometry (AP-MS) data from the BioPlex 2.0 database.
- Construction of a protein-protein interaction network for thousands of identified proteins.
- Prediction of Gene Ontology categories for unannotated genes.
Main Results:
- Functional annotations were predicted for 387 unannotated genes (uPE1).
- Distinct functions were identified for canonical and alternatively spliced forms of four uPE1 genes.
- Functional differences were revealed for 62 proteoforms across 31 genes, suggesting splice form dynamics contribute to interactome versatility.
Conclusions:
- Alternative splicing plays a crucial role in the functional diversity of the proteome.
- Large-scale AP-MS data analysis across diverse conditions is essential for understanding gene function and cellular processes.
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