ArticleBMC bioinformatics2019
A likelihood ratio test for changes in homeolog expression bias.
Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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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.
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Who cites it
7 citing papers in PubMed, 13 citations in OpenAlex.
- Remodeling of homoeolog expression bias buffers stress response in allotetraploid cotton.BMC plant biology · 2026Article
- Genomic Patterns of Loss of Distyly and Polyploidization in Primroses.Molecular biology and evolution · 2025Article
- Genetic Architecture and Functional Implications of the CSF-Contacting Nucleus.Neuroscience bulletin · 2023Article
- Global transcriptome analysis of allopolyploidization reveals large-scale repression of the D-subgenome in synthetic hexaploid wheat.Communications biology · 2023Article
- Expression Level Dominance and Homeolog Expression Bias Upon Cold Stress in the F1 Hybrid Between the InvasiveFrontiers in genetics · 2022Article
- Comparison of Brassica Genomes reveals asymmetrical gene retention between functional groups of genes in recurrent polyploidizations.Plant molecular biology · 2021Article
- Subgenome Dominance in an Interspecific Hybrid, Synthetic Allopolyploid, and a 140-Year-Old Naturally Established Neo-Allopolyploid Monkeyflower.The Plant cell · 2017Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
backgroundGene duplications are a major source of raw material for evolution and a likely contributor to the diversity of life on earth. Duplicate genes (i.e., homeologs, in the case of a whole genome duplication) may retain their ancestral function, sub- or neofunctionalize, or be lost entirely. A primary way that duplicate genes evolve new functions is by altering their expression patterns. Comparing the expression patterns of duplicate genes gives clues as to whether any of these evolutionary processes have occurred.
resultsWe develop a likelihood ratio test for the analysis of the expression ratios of duplicate genes across two conditions (e.g., tissues). We demonstrate an application of this test by comparing homeolog expression patterns of 1448 homeologous gene pairs using RNA-seq data generated from leaves and petals of an allotetraploid monkeyflower (Mimulus luteus). We assess the sensitivity of this test to different levels of homeolog expression bias and compare the method to several alternatives.
conclusionsThe likelihood ratio test derived here is a direct, transparent, and easily implemented method for detecting changes in homeolog expression bias that outperforms alternative approaches. While our method was derived with homeolog analysis in mind, this method can be used to analyze changes in the ratio of expression levels between any two genes in any two conditions.
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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.