Related Experiment Video
Updated: Jul 17, 2026
07:59
Temporal Quantification of MAPK Induced Expression in Single Yeast Cells
Published on: October 4, 2013
Understanding signaling in yeast: Insights from network analysis.
K Yalçin Arga1, Z Ilsen Onsan, Betül Kirdar
1Department of Chemical Engineering, Boğaziçi University, 34342 Istanbul, Turkey.
Biotechnology and Bioengineering
|January 26, 2007
Summary
This study introduces a new method to build protein interaction networks for understanding cell signaling. The approach successfully identifies known and new proteins in yeast signaling pathways.
Area of Science:
- Systems Biology
- Computational Biology
- Molecular Biology
Background:
- Protein interaction networks are crucial for understanding cellular functions and signal transduction.
- Quantitative studies of signaling pathways require accurate network reconstruction.
Purpose of the Study:
- To develop a novel approach for reconstructing highly correlated protein interaction networks.
- To identify unknown components within signaling pathways by integrating diverse biological data.
- To reconstruct specific signaling sub-networks in yeast Saccharomyces cerevisiae.
Main Methods:
- Integration of protein-protein interaction data, gene expression data, and Gene Ontology annotations.
- Development of a novel algorithm for reconstructing highly correlated protein interaction networks.
- Application of Receiver Operating Characteristic (ROC) curve analysis to assess reconstruction efficiency.
- Identification and scoring of linear pathways to reconstruct specific sub-networks.
Main Results:
- Successfully reconstructed protein interaction networks in yeast Saccharomyces cerevisiae.
- Identified known components and novel candidate proteins for glucose-induction and high osmolarity MAPK signaling pathways.
- Demonstrated high efficiency and accuracy of the reconstruction algorithm via ROC analysis.
- Reconstructed two model pathways, highlighting the utility of the integrated approach.
Conclusions:
- The integrated approach is effective for predicting new signaling pathways.
- The method successfully identifies unknown members of documented signaling pathways.
- The approach aids in identifying functional network modules and their components.
Related Concept Videos
01:28Yeast Signaling
Yeasts are single-celled organisms, but unlike bacteria, they are eukaryotes (cells with a nucleus). Cell signaling in yeast is similar to signaling in other eukaryotic cells. A ligand, such as a protein or a small molecule released from a yeast cell, attaches to a receptor on the cell surface. The binding stimulates second-messenger kinases to activate or inactivate transcription factors that further regulate gene expression. Many of the yeast intracellular signaling cascades have similar...
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...
01:23Overview of Cell Signaling
Despite the protective membrane that separates a cell from the environment, cells need the ability to detect and respond to environmental changes. Additionally, cells often need to communicate with one another. Unicellular and multicellular organisms use a variety of cell signaling mechanisms to communicate with the environment.
Cells respond to many types of information, often through receptor proteins positioned on the membrane. For example, skin cells respond to and transmit touch...
Cells respond to many types of information, often through receptor proteins positioned on the membrane. For example, skin cells respond to and transmit touch...
01:23Overview of Cell Signaling
Despite the protective membrane that separates a cell from the environment, cells need the ability to detect and respond to environmental changes. Additionally, cells often need to communicate with one another. Unicellular and multicellular organisms use a variety of cell signaling mechanisms to communicate with the environment.
Cells respond to many types of information, often through receptor proteins positioned on the membrane. For example, skin cells respond to and transmit touch...
Cells respond to many types of information, often through receptor proteins positioned on the membrane. For example, skin cells respond to and transmit touch...
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...
01:26Signal Transduction: Overview
Cells respond to many types of information, often through receptor proteins positioned on the membrane. They respond to chemical signals, such as hormones, neurotransmitters, and other signaling molecules, initiating a series of molecular reactions to produce an appropriate response. This is called signal transduction. Cells also coordinate different responses elicited by the same signaling molecule via mediators, allowing molecular cross-talk.
Typically, signal transduction involves three...
Typically, signal transduction involves three...