Related Experiment Video
Updated: Jul 4, 2026
07:28
JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
Published on: October 19, 2021
Identification of dominant signaling pathways from proteomics expression data
Roman A Zubarev1, Michael L Nielsen, Eva M Fung
1Division of Molecular Biometry, Institute for Cell and Molecular Biology, Uppsala University, SE-75 124 Uppsala, Sweden. Roman.Zubarev@icm.uu.se
Journal of Proteomics
|June 11, 2008
Summary
This study introduces a pathway search engine for analyzing
Area of Science:
- Pathway biology
- Proteomics
- Computational biology
Background:
- High-throughput 'omic' technologies drive pathway biology.
- Analytical pathway biology aims to identify dominant pathways from 'omic' data.
- Existing computational tools are primarily for mRNA analysis.
Purpose of the Study:
- To design and validate the first pathway search engine for expression proteomics data.
- To adapt existing computational workflows for proteomics data analysis.
Main Methods:
- Developed a pathway search engine workflow for proteomics data.
- Utilized computational tools originally designed for mRNA analysis.
- Validated the engine using in-house and published proteomics datasets.
Main Results:
- The pathway search engine successfully identified dominant pathways (EGF, TGF(beta), stress, Fas) from proteomics data.
- Correct pathway identification was achieved even with limited datasets.
- Demonstrated the engine's capability using diverse datasets.
Conclusions:
- Pathway search engines are feasible for expression proteomics data.
- This approach enables the identification of key biological pathways from proteomics studies.
- Potential applications include fundamental molecular biology and disease biomarker discovery.
Related Concept Videos
01:33Proteomics
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...
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...
02:26Protein Networks
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,...
01:19Interactions Between Signaling Pathways
Signaling cascades usually lack linearity. Multiple pathways interact and regulate one another, allowing cells to integrate and respond to diverse environmental stimuli.
Convergence and divergence, and cross-talk between signaling pathways
Two distinct signaling pathways can converge on a single functional unit, which may either be a single protein or a complex of proteins. The response is either functionally distinct or synergistic between the two pathways but different from the response...
Convergence and divergence, and cross-talk between signaling pathways
Two distinct signaling pathways can converge on a single functional unit, which may either be a single protein or a complex of proteins. The response is either functionally distinct or synergistic between the two pathways but different from the response...
01:22Diversity in Cell Signaling Responses
The physiological function of a cell and cellular communication are outcomes of a range of extrinsic signals, intracellular signaling pathways, and cellular responses. No two cell types express the same repertoire of signaling components. Receptors are highly selective for their cognate ligands, but once activated, they can alter multiple cellular processes such as DNA transcription, protein synthesis, and metabolic activity.
Graded and Abrupt Responses
Some signaling systems generate...
Graded and Abrupt Responses
Some signaling systems generate...