ArticleGenome research2002
Relating whole-genome expression data with protein-protein interactions.
Article in Genome research, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 274 papers, 1 of them a synthesis that pooled it.
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Who cites it
274 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Systems-level transcriptional regulation of Caenorhabditis elegans metabolism.Molecular systems biology · 2023Article
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- Computational Methods and Deep Learning for Elucidating Protein Interaction Networks.Methods in molecular biology (Clifton, N.J.) · 2023Article
- An Integrated Approach of Learning Genetic Networks From Genome-Wide Gene Expression Data Using Gaussian Graphical Model and Monte Carlo Method.Bioinformatics and biology insights · 2023Article
- A Comprehensive Weighted Gene Co-expression Network Analysis Uncovers Potential Targets in Diabetic Kidney Disease.Journal of translational internal medicine · 2022Article
- Computational Network Inference for Bacterial Interactomics.mSystems · 2022Review
- Are transient protein-protein interactions more dispensable?PLoS computational biology · 2022Article
- A microRNA-microRNA crosstalk network inferred from genome-wide single nucleotide polymorphism variants in natural populations ofFrontiers in plant science · 2022Article
- Bacterial genome reductions: Tools, applications, and challenges.Frontiers in genome editing · 2022Review
- Finding Correlations Between mRNA and Protein Levels inFrontiers in cellular and infection microbiology · 2022Review
- Computationally Reconstructed Interactome ofInternational journal of molecular sciences · 2021Article
214 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We investigate the relationship of protein-protein interactions with mRNA expression levels, by integrating a variety of data sources for yeast. We focus on known protein complexes that have clearly defined interactions between their subunits. We find that subunits of the same protein complex show significant coexpression, both in terms of similarities of absolute mRNA levels and expression profiles, e.g., we can often see subunits of a complex having correlated patterns of expression over a time course. We classify the yeast protein complexes as either permanent or transient, with permanent ones being maintained through most cellular conditions. We find that, generally, permanent complexes, such as the ribosome and proteasome, have a particularly strong relationship with expression, while transient ones do not. However, we note that several transient complexes, such as the RNA polymerase II holoenzyme and the replication complex, can be subdivided into smaller permanent ones, which do have a strong relationship to gene expression. We also investigated the interactions in aggregated, genome-wide data sets, such as the comprehensive yeast two-hybrid experiments, and found them to have only a weak relationship with gene expression, similar to that of transient complexes. (Further details on genecensus.org/expression/interactions and bioinfo.mbb.yale.edu/expression/interactions.)
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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.