ArticlePLoS computational biology2009
The Modular Organization of Protein Interactions in Escherichia coli.
Article in PLoS computational biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- ToxoNet: A high confidence map of protein-protein interactions in Toxoplasma gondii.PLoS computational biology · 2024Article
- Commensal protist Tritrichomonas musculus exhibits a dynamic life cycle that induces extensive remodeling of the gut microbiota.The ISME journal · 2024Article
- Article
- Auxotrophic and prototrophic conditional genetic networks reveal the rewiring of transcription factors in Escherichia coli.Nature communications · 2022Article
- Computationally Reconstructed Interactome ofInternational journal of molecular sciences · 2021Article
- Identification of protein complexes and functional modules in E. coli PPI networks.BMC microbiology · 2020Article
- Grasping frequent subgraph mining for bioinformatics applications.BioData mining · 2018Review
- Vicus: Exploiting local structures to improve network-based analysis of biological data.PLoS computational biology · 2017Article
- Improving protein complex prediction by reconstructing a high-confidence protein-protein interaction network of Escherichia coli from different physical interaction data sources.BMC bioinformatics · 2017Article
- Cell-free Determination of Binary Complexes That Comprise Extended Protein-Protein Interaction Networks of Yersinia pestis.Molecular & cellular proteomics : MCP · 2016Article
- Article
- Prediction and characterization of protein-protein interaction network in Bacillus licheniformis WX-02.Scientific reports · 2016Article
- Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality.Microbiome · 2016Article
- Article
- Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis.PloS one · 2015Article
- HubAlign: an accurate and efficient method for global alignment of protein-protein interaction networks.Bioinformatics (Oxford, England) · 2014Article
- A network-based approach to identify substrate classes of bacterial glycosyltransferases.BMC genomics · 2014Article
- Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli.PLoS genetics · 2014Article
- Corbi: a new R package for biological network alignment and querying.BMC systems biology · 2013Article
- Genome-scale co-evolutionary inference identifies functions and clients of bacterial Hsp90.PLoS genetics · 2013Article
Corrections and comments
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Authors and funding
4 authors.
Funding
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Abstract
Escherichia coli serves as an excellent model for the study of fundamental cellular processes such as metabolism, signalling and gene expression. Understanding the function and organization of proteins within these processes is an important step towards a 'systems' view of E. coli. Integrating experimental and computational interaction data, we present a reliable network of 3,989 functional interactions between 1,941 E. coli proteins ( approximately 45% of its proteome). These were combined with a recently generated set of 3,888 high-quality physical interactions between 918 proteins and clustered to reveal 316 discrete modules. In addition to known protein complexes (e.g., RNA and DNA polymerases), we identified modules that represent biochemical pathways (e.g., nitrate regulation and cell wall biosynthesis) as well as batteries of functionally and evolutionarily related processes. To aid the interpretation of modular relationships, several case examples are presented, including both well characterized and novel biochemical systems. Together these data provide a global view of the modular organization of the E. coli proteome and yield unique insights into structural and evolutionary relationships in bacterial networks.
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