Related Experiment Video
Updated: Jul 24, 2025

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
Published on: October 19, 2021
Bayesian Network Structure Learning Method Based on Causal Direction Graph for Protein Signaling Networks
Xiaohan Wei1, Yulai Zhang1, Cheng Wang1
1School of Information and Electronic Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, China.
Abstract:
Constructing the structure of protein signaling networks by Bayesian network technology is a key issue in the field of bioinformatics. The primitive structure learning algorithms of the Bayesian network take no account of the causal relationships between variables, which is unfortunately important in the application of protein signaling networks. In addition, as a combinatorial optimization problem with a large searching space, the computational complexities of the structure learning algorithms are unsurprisingly high. Therefore, in this paper, the causal directions between any two variables are calculated first and stored in a graph matrix as one of the constraints of structure learning. A continuous optimization problem is constructed next by using the fitting losses of the corresponding structure equations as the target, and the directed acyclic prior is used as another constraint at the same time. Finally, a pruning procedure is developed to keep the result of the continuous optimization problem sparse. Experiments show that the proposed method improves the structure of the Bayesian network compared with the existing methods on both the artificial data and the real data, meanwhile, the computational burdens are also reduced significantly.
Related Concept Videos
Protein Networks
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,...
Interactions Between Signaling Pathways
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...
G Protein-coupled Receptors
GPCRs are also called heptahelical, 7TM, or serpentine receptors, and consist of seven (H1-H7) transmembrane alpha-helices that span the bilayer to form a cylindrical core. The transmembrane helices are connected by three extracellular loops and three...
Protein Organization
The primary structure of a protein is its amino acid sequence....
Directing Proteins to the Rough Endoplasmic Reticulum
Assembly of Signaling Complexes
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...

