ArticleBMC bioinformatics2006
An evaluation of human protein-protein interaction data in the public domain.
Article in BMC bioinformatics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 85 papers.
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Who cites it
85 citing papers in PubMed, 233 citations in OpenAlex.
- Pathogen-driven cancers from a structural perspective: Targeting host-pathogen protein-protein interactions.Frontiers in oncology · 2023Review
- Graph Neural Network for Protein-Protein Interaction Prediction: A Comparative Study.Molecules (Basel, Switzerland) · 2022Article
- Identifying intracellular signaling modules and exploring pathways associated with breast cancer recurrence.Scientific reports · 2021Article
- Getting to know each other: PPIMem, a novel approach for predicting transmembrane protein-protein complexes.Computational and structural biotechnology journal · 2021Article
- Article
- Identification of pharmacodynamic biomarker hypotheses through literature analysis with IBM Watson.PloS one · 2019Article
- Automatic extraction of protein-protein interactions using grammatical relationship graph.BMC medical informatics and decision making · 2018Article
- Identify Down syndrome transcriptome associations using integrative analysis of microarray database and correlation-interaction network.Human genomics · 2018Article
- A bioinformatics potpourri.BMC genomics · 2018Article
- Profiling of Human Molecular Pathways Affected by Retrotransposons at the Level of Regulation by Transcription Factor Proteins.Frontiers in immunology · 2018Article
- Interplay Between Amphetamine and Activity Level in Gene Networks of the Mouse Striatum.Bioinformatics and biology insights · 2018Article
- The use of gene interaction networks to improve the identification of cancer driver genes.PeerJ · 2017Article
- Epigenetic profiling of human brain differential DNA methylation networks in schizophrenia.BMC medical genomics · 2016Article
- Using contrast patterns between true complexes and random subgraphs in PPI networks to predict unknown protein complexes.Scientific reports · 2016Article
- Exploring novel mechanistic insights in Alzheimer's disease by assessing reliability of protein interactions.Scientific reports · 2015Article
- Integrated web visualizations for protein-protein interaction databases.BMC bioinformatics · 2015Article
- Non-thermal plasma treatment altered gene expression profiling in non-small-cell lung cancer A549 cells.BMC genomics · 2015Article
- Computational prediction of protein-protein interactions.Methods in molecular biology (Clifton, N.J.) · 2015Article
- PathwayMatrix: visualizing binary relationships between proteins in biological pathways.BMC proceedings · 2015Article
- Signaling pathways activation profiles make better markers of cancer than expression of individual genes.Oncotarget · 2014Article
25 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 2 countries.
Funding
Abstract
backgroundProtein-protein interaction (PPI) databases have become a major resource for investigating biological networks and pathways in cells. A number of publicly available repositories for human PPIs are currently available. Each of these databases has their own unique features with a large variation in the type and depth of their annotations.
resultsWe analyzed the major publicly available primary databases that contain literature curated PPI information for human proteins. This included BIND, DIP, HPRD, IntAct, MINT, MIPS, PDZBase and Reactome databases. The number of binary non-redundant human PPIs ranged from 101 in PDZBase and 346 in MIPS to 11,367 in MINT and 36,617 in HPRD. The number of genes annotated with at least one interactor was 9,427 in HPRD, 4,975 in MINT, 4,614 in IntAct, 3,887 in BIND and <1,000 in the remaining databases. The number of literature citations for the PPIs included in the databases was 43,634 in HPRD, 11,480 in MINT, 10,331 in IntAct, 8,020 in BIND and <2,100 in the remaining databases.
conclusionGiven the importance of PPIs, we suggest that submission of PPIs to repositories be made mandatory by scientific journals at the time of manuscript submission as this will minimize annotation errors, promote standardization and help keep the information up to date. We hope that our analysis will help guide biomedical scientists in selecting the most appropriate database for their needs especially in light of the dramatic differences in their content.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.