ArticleBMC bioinformatics2011
Inferring functional modules of protein families with probabilistic topic models.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 13 citations in OpenAlex.
- SEEK-VEC: Robust Latent Structure Discovery via Ensemble Topic Modeling.bioRxiv : the preprint server for biology · 2025Article
- Understanding Genotype-Phenotype Effects in Cancer via Network Approaches.PLoS computational biology · 2016Review
- Review
- Inference of phenotype-defining functional modules of protein families for microbial plant biomass degraders.Biotechnology for biofuels · 2014Article
- A Module Analysis Approach to Investigate Molecular Mechanism of TCM Formula: A Trial on Shu-feng-jie-du Formula.Evidence-based complementary and alternative medicine : eCAM · 2013Article
- Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
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Abstract
backgroundGenome and metagenome studies have identified thousands of protein families whose functions are poorly understood and for which techniques for functional characterization provide only partial information. For such proteins, the genome context can give further information about their functional context.
resultsWe describe a Bayesian method, based on a probabilistic topic model, which directly identifies functional modules of protein families. The method explores the co-occurrence patterns of protein families across a collection of sequence samples to infer a probabilistic model of arbitrarily-sized functional modules.
conclusionsWe show that our method identifies protein modules - some of which correspond to well-known biological processes - that are tightly interconnected with known functional interactions and are different from the interactions identified by pairwise co-occurrence. The modules are not specific to any given organism and may combine different realizations of a protein complex or pathway within different taxa.
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