ArticleNucleic acids research2009
Patterns of co-expression for protein complexes by size in Saccharomyces cerevisiae.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 34 citations in OpenAlex.
- Strategies for constructing context-specific protein-protein interaction networks.Briefings in bioinformatics · 2026Review
- A method for benchmarking genetic screens reveals a predominant mitochondrial bias.Molecular systems biology · 2021Article
- Precise Post-translational Tuning Occurs for Most Protein Complex Components during Meiosis.Cell reports · 2018Article
- Genome-wide trait-trait dynamics correlation study dissects the gene regulation pattern in maize kernels.BMC plant biology · 2017Article
- Gene coexpression network forPlant biotechnology (Tokyo, Japan) · 2017Article
- Time dynamics of protein complexes in the AD11 transgenic mouse model for Alzheimer's disease like pathology.BMC neuroscience · 2015Article
- Mutation bias, rather than binding preference, underlies the nucleosome-associated G+C% variation in eukaryotes.Genome biology and evolution · 2015Article
- Identification of under-detected periodicity in time-series microarray data by using empirical mode decomposition.PloS one · 2014Article
- PCDq: human protein complex database with quality index which summarizes different levels of evidences of protein complexes predicted from h-invitational protein-protein interactions integrative dataset.BMC systems biology · 2012Article
- Assessing the utility of gene co-expression stability in combination with correlation in the analysis of protein-protein interaction networks.BMC genomics · 2011Article
- Improving gene expression data interpretation by finding latent factors that co-regulate gene modules with clinical factors.BMC genomics · 2011Article
- Genome-wide expression links the electron transfer pathway of Shewanella oneidensis to chemotaxis.BMC genomics · 2010Article
- Dynamically weighted clustering with noise set.Bioinformatics (Oxford, England) · 2010Article
- The Negatome database: a reference set of non-interacting protein pairs.Nucleic acids research · 2010Article
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Many successful functional studies by gene expression profiling in the literature have led to the perception that profile similarity is likely to imply functional association. But how true is the converse of the above statement? Do functionally associated genes tend to be co-regulated at the transcription level? In this paper, we focus on a set of well-validated yeast protein complexes provided by Munich Information Center for Protein Sequences (MIPS). Using four well-known large-scale microarray expression data sets, we computed the correlations between genes from the same complex. We then analyzed the relationship between the distribution of correlations and the complex size (the number of genes in a protein complex). We found that except for a few large protein complexes, such as mitochondrial ribosomal and cytoplasmic ribosomal proteins, the correlations are on the average not much higher than that from a pair of randomly selected genes. The global impact of large complexes on the expression of other genes in the genome is also studied. Our result also showed that the expression of over 85% of the genes are affected by six large complexes: the cytoplasmic ribosomal complex, mitochondrial ribosomal complex, proteasome complex, F0/F1 ATP synthase (complex V) (size 18), rRNA splicing (size 24) and H+- transporting ATPase, vacular (size 15).
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