ArticlePLoS computational biology2011
Accurate quantification of functional analogy among close homologs.
Article in PLoS computational biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed.
- Computational strategies for cross-species knowledge transfer and translational biomedicine.ArXiv · 2024Article
- Comparative single-cell transcriptomic analysis of primate brains highlights human-specific regulatory evolution.Nature ecology & evolution · 2023Article
- Interspecific comparison of gene expression profiles using machine learning.PLoS computational biology · 2023Article
- Article
- Decoding disease: from genomes to networks to phenotypes.Nature reviews. Genetics · 2021Review
- Cancer systems immunology.eLife · 2020Review
- A Literature Review of Gene Function Prediction by Modeling Gene Ontology.Frontiers in genetics · 2020Review
- NewG3 (Bethesda, Md.) · 2019Article
- Enabling Precision Medicine through Integrative Network Models.Journal of molecular biology · 2018Review
- Machine Learning Analysis IdentifiesG3 (Bethesda, Md.) · 2017Article
- Meta-analysis of Liver and Heart Transcriptomic Data for Functional Annotation Transfer in Mammalian Orthologs.Computational and structural biotechnology journal · 2017Article
- Implications of Big Data for cell biology.Molecular biology of the cell · 2015Article
- IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.Nucleic acids research · 2015Article
- Article
- Current challenges and future potential of tomato breeding using omics approaches.Breeding science · 2013Article
- Functional knowledge transfer for high-accuracy prediction of under-studied biological processes.PLoS computational biology · 2013Article
- IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks.Nucleic acids research · 2012Article
- Comparative microbial modules resource: generation and visualization of multi-species biclusters.PLoS computational biology · 2011Article
- Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in Arabidopsis and rice.Plant physiology · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Correctly evaluating functional similarities among homologous proteins is necessary for accurate transfer of experimental knowledge from one organism to another, and is of particular importance for the development of animal models of human disease. While the fact that sequence similarity implies functional similarity is a fundamental paradigm of molecular biology, sequence comparison does not directly assess the extent to which two proteins participate in the same biological processes, and has limited utility for analyzing families with several parologous members. Nevertheless, we show that it is possible to provide a cross-organism functional similarity measure in an unbiased way through the exclusive use of high-throughput gene-expression data. Our methodology is based on probabilistic cross-species mapping of functionally analogous proteins based on Bayesian integrative analysis of gene expression compendia. We demonstrate that even among closely related genes, our method is able to predict functionally analogous homolog pairs better than relying on sequence comparison alone. We also demonstrate that the landscape of functional similarity is often complex and that definitive "functional orthologs" do not always exist. Even in these cases, our method and the online interface we provide are designed to allow detailed exploration of sources of inferred functional similarity that can be evaluated by the user.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.