ArticleBMC bioinformatics2015
Integrated web visualizations for protein-protein interaction databases.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
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- Overview of methods for characterization and visualization of a protein-protein interaction network in a multi-omics integration context.Frontiers in molecular biosciences · 2022Review
- SISTEMA: A large and standardized collection of transcriptome data sets for human pluripotent stem cell research.iScience · 2021Article
- Bioinformatic profiling identifies prognosis-related genes in the immune microenvironment of endometrial carcinoma.Scientific reports · 2021Article
- Exploring the differentially expressed genes in human lymphocytes upon response to ionizing radiation: a network biology approach.Radiation oncology journal · 2021Article
- Bioinformatics Analysis Reveals Crosstalk Among Platelets, Immune Cells, and the Glomerulus That May Play an Important Role in the Development of Diabetic Nephropathy.Frontiers in medicine · 2021Article
- Identifying essential proteins in dynamic protein networks based on an improved h-index algorithm.BMC medical informatics and decision making · 2020Article
- Classification of Cancer Types Using Graph Convolutional Neural Networks.Frontiers in physics · 2020Article
- GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns.BMC bioinformatics · 2020Article
- Open Data for Differential Network Analysis in Glioma.International journal of molecular sciences · 2020Article
- Cellular Processes Involved in Jurkat Cells Exposed to Nanosecond Pulsed Electric Field.International journal of molecular sciences · 2019Article
- HMNPPID-human malignant neoplasm protein-protein interaction database.Human genomics · 2019Article
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- Computer aided analysis of disease linked protein networks.Bioinformation · 2019Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundUnderstanding living systems is crucial for curing diseases. To achieve this task we have to understand biological networks based on protein-protein interactions. Bioinformatics has come up with a great amount of databases and tools that support analysts in exploring protein-protein interactions on an integrated level for knowledge discovery. They provide predictions and correlations, indicate possibilities for future experimental research and fill the gaps to complete the picture of biochemical processes. There are numerous and huge databases of protein-protein interactions used to gain insights into answering some of the many questions of systems biology. Many computational resources integrate interaction data with additional information on molecular background. However, the vast number of diverse Bioinformatics resources poses an obstacle to the goal of understanding. We present a survey of databases that enable the visual analysis of protein networks.
resultsWe selected M=10 out of N=53 resources supporting visualization, and we tested against the following set of criteria: interoperability, data integration, quantity of possible interactions, data visualization quality and data coverage. The study reveals differences in usability, visualization features and quality as well as the quantity of interactions. StringDB is the recommended first choice. CPDB presents a comprehensive dataset and IntAct lets the user change the network layout. A comprehensive comparison table is available via web. The supplementary table can be accessed on http://tinyurl.com/PPI-DB-Comparison-2015.
conclusionsOnly some web resources featuring graph visualization can be successfully applied to interactive visual analysis of protein-protein interaction. Study results underline the necessity for further enhancements of visualization integration in biochemical analysis tools. Identified challenges are data comprehensiveness, confidence, interactive feature and visualization maturing.
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