Related Experiment Video
Updated: Dec 14, 2025
07:28
JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
Published on: October 19, 2021
3.5K
Using phosphoproteomics data to understand cellular signaling: a comprehensive guide to bioinformatics resources.
Sara R Savage1,2, Bing Zhang2,3
1Department of Biomedical Informatics, Vanderbilt University, Nashville, TN USA.
Clinical Proteomics
|July 18, 2020
Summary
Bioinformatics tools aid phosphoproteomics data analysis, but current resources are fragmented. This study compares existing tools to improve their usability for biological and clinical insights.
Area of Science:
- Biochemistry
- Bioinformatics
- Cellular Signaling
Background:
- Mass spectrometry-based phosphoproteomics is crucial for studying cellular signaling.
- Bioinformatics resources are vital for interpreting phosphoproteomics data into biological insights.
Purpose of the Study:
- To compile and compare existing bioinformatics resources for phosphoproteomics data interpretation.
- To assess the usability of these tools for biologists and clinicians.
Main Methods:
- Comprehensive collection of phosphoproteomics interpretation resources.
- Comparative analysis of tools with similar functions.
- Usability assessment from a biologist/clinician perspective.
Main Results:
- Existing resources are often siloed, making tool selection difficult.
- Identified areas for improvement in current bioinformatics tools.
- Assessed usability challenges for end-users.
Conclusions:
- Standardization of enzyme nomenclature, data formats, and consistent maintenance are needed.
- Improved documentation and usability are essential for broader adoption.
- Enhanced bioinformatics tools will accelerate phosphoproteomics research and clinical applications.
More Related Videos
Related Concept Videos
01:33Proteomics
9.1K
A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
9.1K
02:54Protein Kinases and Phosphatases
14.5K
Proteins undergo chemical modifications that trigger changes in the charge, structure, and conformation of the proteins. Phosphorylation, acetylation, glycosylation, nitrosylation, ubiquitination, lipidation, methylation, and proteolysis are various protein modifications that regulate protein activity. Such modifications are usually enzyme-driven.
Protein kinases
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...
Protein kinases
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...
14.5K
02:26Protein Networks
4.4K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.4K
01:30Assembly of Signaling Complexes
6.4K
Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
6.4K
01:22Amplifying Signals via Enzymatic Cascade
16.6K
When a ligand binds to a cell-surface receptor, the receptor's intracellular domain changes shape, which may either activate its enzyme function or allow its binding to other molecules. The initial signal is amplified by most signal transduction pathways. This means that a single ligand molecule can activate multiple molecules of a downstream target. Proteins that relay a signal are most commonly phosphorylated at one or more sites, activating or inactivating the protein. Kinases catalyze...
16.6K