ProteinNetworkSight: a user-friendly platform for transforming co-expression patterns into actionable therapeutic insights through interactive network visualization.
| Title: | ProteinNetworkSight: a user-friendly platform for transforming co-expression patterns into actionable therapeutic insights through interactive network visualization. |
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| Authors: | Nahor O; Software Engineering Department, School of Software and Electrical Engineering, Azrieli College of Engineering, Jerusalem 9103501, Israel.; Migdal N; Software Engineering Department, School of Software and Electrical Engineering, Azrieli College of Engineering, Jerusalem 9103501, Israel.; Gibli A; Software Engineering Department, School of Software and Electrical Engineering, Azrieli College of Engineering, Jerusalem 9103501, Israel.; Tsvitman T; Software Engineering Department, School of Software and Electrical Engineering, Azrieli College of Engineering, Jerusalem 9103501, Israel.; Eldad A; Software Engineering Department, School of Software and Electrical Engineering, Azrieli College of Engineering, Jerusalem 9103501, Israel.; Raveh S; The Institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, Jerusalem 9103401, Israel.; Polinovski G; The Institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, Jerusalem 9103401, Israel.; Zaid D; The Institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, Jerusalem 9103401, Israel.; Kravchenko-Balasha N; The Institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, Jerusalem 9103401, Israel.; Cohen NE; Software Engineering Department, School of Software and Electrical Engineering, Azrieli College of Engineering, Jerusalem 9103501, Israel. |
| Source: | Nucleic acids research [Nucleic Acids Res] 2026 May 14. Date of Electronic Publication: 2026 May 14. |
| Publication Model: | Ahead of Print |
| Publication Type: | Journal Article |
| Language: | English |
| Journal Info: | Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE |
| Imprint Name(s): | Publication: 1992- : Oxford : Oxford University Press; Original Publication: London, Information Retrieval ltd. |
| Abstract: | ProteinNetworkSight (https://proteinnetworksight.jce.ac) addresses a pervasive bottleneck in modern systems biology: the inability to simultaneously analyze multiple feature vectors generated by quantitative techniques-such as machine learning, deep learning, or statistical modeling-that provide series of patterns in a dataset. Modern computational pipelines, ranging from PCA to deep autoencoders, rarely identify a single gene list; instead, they extract a series of distinct patterns representing diverse patient subgroups or independent components. Current web servers are ill-equipped for this high-dimensional reality, forcing researchers to analyze vectors one-by-one or merge them into a static consensus, obliterating unique topological signatures. ProteinNetworkSight introduces a novel web server architecture for simultaneous multi-pattern analysis. Unlike standard tools, our server accepts multi-column tables and transforms every input vector into a discrete, interactive protein-protein interaction network in a single run. This batch vector architecture allows side-by-side visualization of distinct topologies, preserving disease heterogeneity. Furthermore, the server enables prescriptive intervention by calculating a composite perturbation score to identify key protein nodes specific to each pattern. By mapping FDA-approved anti-cancer drugs to these targets, it facilitates the rapid design of personalized combinatorial therapies.; (© The Author(s) 2026. Published by Oxford University Press.) |
| Grant Information: | 1961/19 Deutsches Krebsforschungszentrum; 1961/19 Ministry of Science and Technology; 1961/19 Israel Science Foundation; Azrieli College of Engineering Research Fund |
| Entry Date(s): | Date Created: 20260514 Latest Revision: 20260514 |
| Update Code: | 20260514 |
| DOI: | 10.1093/nar/gkag477 |
| PMID: | 42130472 |
| Database: | MEDLINE |
Journal Article