ArticleBMC genomics2007
Comprehensive analysis of co-occurring domain sets in yeast proteins.
Article in BMC genomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 17 citations in OpenAlex.
- Unbiased Protein Association Study on the Public Human Proteome Reveals Biological Connections between Co-Occurring Protein Pairs.Journal of proteome research · 2017Article
- SpidermiR: An R/Bioconductor Package for Integrative Analysis with miRNA Data.International journal of molecular sciences · 2017Article
- Predicting the function of 4-coumarate:CoA ligase (LJ4CL1) in Lonicera japonica.International journal of molecular sciences · 2014Article
- Identification of divergent protein domains by combining HMM-HMM comparisons and co-occurrence detection.PloS one · 2014Article
- A novel function prediction approach using protein overlap networks.BMC systems biology · 2013Article
- Evolutionary dynamics of protein domain architecture in plants.BMC evolutionary biology · 2012Article
- Heat shock partially dissociates the overlapping modules of the yeast protein-protein interaction network: a systems level model of adaptation.PLoS computational biology · 2011Article
- Processes of fungal proteome evolution and gain of function: gene duplication and domain rearrangement.Physical biology · 2011Article
- Evolution of domain promiscuity in eukaryotic genomes--a perspective from the inferred ancestral domain architectures.Molecular bioSystems · 2011Article
- Triangle network motifs predict complexes by complementing high-error interactomes with structural information.BMC bioinformatics · 2009Article
- Protein domain organisation: adding order.BMC bioinformatics · 2009Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 2 countries.
Funding
Abstract
backgroundProtein domains are fundamental evolutionary units of protein architecture, composing proteins in a modular manner. Combinations of two or more, possibly non-adjacent, domains are thought to play specific functional roles within proteins. Indeed, while the number of potential co-occurring domain sets (CDSs) is very large, only a few of these occur in nature. Here we study the principles governing domain content of proteins, using yeast as a model species.
resultsWe design a novel representation of proteins and their constituent domains as a protein-domain network. An analysis of this network reveals 99 CDSs that occur in proteins more than expected by chance. The identified CDSs are shown to preferentially include ancient domains that are conserved from bacteria or archaea. Moreover, the protein sets spanned by these combinations were found to be highly functionally coherent, significantly match known protein complexes, and enriched with protein-protein interactions. These observations serve to validate the biological significance of the identified CDSs.
conclusionOur work provides a comprehensive list of co-occurring domain sets in yeast, and sheds light on their function and evolution.
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Registered trials
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