ArticleBioinformatics (Oxford, England)2012
Multifunctional proteins revealed by overlapping clustering in protein interaction network.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
55 citing papers in PubMed.
- De novo variants in HK1 associated with neurodevelopmental abnormalities and visual impairment.European journal of human genetics : EJHG · 2019Trial
- A multi-objective evolutionary algorithm for detecting protein complexes in PPI networks using gene ontology.Scientific reports · 2025Article
- Protein covariation networks for elucidating ferroptosis inducer mechanisms and potential synergistic drug targets.Communications biology · 2025Article
- Integrated network pharmacology andFrontiers in molecular biosciences · 2025Article
- Peptide mimetic NC114 induces growth arrest by preventing PKCδ activation and FOXM1 nuclear translocation in colorectal cancer cells.FEBS open bio · 2024Article
- Predictive modeling of moonlighting DNA-binding proteins.NAR genomics and bioinformatics · 2022Article
- Entropy-Based Graph Clustering of PPI Networks for Predicting Overlapping Functional Modules of Proteins.Entropy (Basel, Switzerland) · 2021Article
- Microscopic image-based covariation network analysis for actin scaffold-modified insulin signaling.iScience · 2021Article
- Approaches to Integrating Metabolomics and Multi-Omics Data: A Primer.Metabolites · 2021Review
- The role of 3'UTR-protein complexes in the regulation of protein multifunctionality and subcellular localization.Nucleic acids research · 2020Article
- Effects of IL-1β and TNF-α on the Expression of P311 in Vascular Endothelial Cells and Wound Healing in Mice.Frontiers in physiology · 2020Article
- Multiple Forms of Multifunctional Proteins in Health and Disease.Frontiers in cell and developmental biology · 2020Review
- Understanding protein multifunctionality: from short linear motifs to cellular functions.Cellular and molecular life sciences : CMLS · 2019Review
- Post-transcriptional regulatory patterns revealed by protein-RNA interactions.Scientific reports · 2019Article
- MoonDB 2.0: an updated database of extreme multifunctional and moonlighting proteins.Nucleic acids research · 2019Article
- Reconstruction and Functional Annotation of P311 Protein-Protein Interaction Network Reveals Its New Functions.Frontiers in genetics · 2019Article
- Discovery of two-level modular organization from matched genomic data via joint matrix tri-factorization.Nucleic acids research · 2018Article
- Detecting protein complexes based on a combination of topological and biological properties in protein-protein interaction network.Journal, genetic engineering & biotechnology · 2018Article
- The utility of a network-based clustering method for dimension reduction of imaging and non-imaging biomarkers predictive of Alzheimer's disease.Scientific reports · 2018Article
- Protein complex scaffolding predicted as a prevalent function of long non-coding RNAs.Nucleic acids research · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationMultifunctional proteins perform several functions. They are expected to interact specifically with distinct sets of partners, simultaneously or not, depending on the function performed. Current graph clustering methods usually allow a protein to belong to only one cluster, therefore impeding a realistic assignment of multifunctional proteins to clusters.
resultsHere, we present Overlapping Cluster Generator (OCG), a novel clustering method which decomposes a network into overlapping clusters and which is, therefore, capable of correct assignment of multifunctional proteins. The principle of OCG is to cover the graph with initial overlapping classes that are iteratively fused into a hierarchy according to an extension of Newman's modularity function. By applying OCG to a human protein-protein interaction network, we show that multifunctional proteins are revealed at the intersection of clusters and demonstrate that the method outperforms other existing methods on simulated graphs and PPI networks. AVAILABILITY: This software can be downloaded from http://tagc.univ-mrs.fr/welcome/spip.php?rubrique197 CONTACT: brun@tagc.univ-mrs.fr SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Indexed as
Identifiers
What OpenQuestion holds
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.