ReviewF1000Research2019
Recent advances in gene function prediction using context-specific coexpression networks in plants.
Review in F1000Research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Constructing gene co-functional and co-regulatory networks from public transcriptomes using condition-specific ensemble co-expression.Nature communications · 2026Article
- Comprehensive characterization of safflower cytochrome P450 family and the role of CtCYP41 in flavonoid biosynthesis and drought response.BMC plant biology · 2026Article
- Characterization and Transcriptomic Analysis of Sorghum EIN/EIL Family and Identification of Their Roles in Internode Maturation.Plants (Basel, Switzerland) · 2024Article
- Potential Roles of the GRF Transcription Factors in Sorghum Internodes during Post-Reproductive Stages.Plants (Basel, Switzerland) · 2024Article
- Interplay of EXO70 and MLO proteins modulates trichome cell wall composition and susceptibility to powdery mildew.The Plant cell · 2024Article
- Co-Expression Networks in Sunflower: Harnessing the Power of Multi-Study Transcriptomic Public Data to Identify and Categorize Candidate Genes for Fungal Resistance.Plants (Basel, Switzerland) · 2023Article
- Comparative Coexpression Analysis of Indole Synthase and Tryptophan Synthase A Reveals the Independent Production of Auxin via the Cytosolic Free Indole.Plants (Basel, Switzerland) · 2023Article
- Transcriptomic analysis reveals the gene regulatory networks involved in leaf and root response to osmotic stress in tomato.Frontiers in plant science · 2023Article
- Interspecific comparison of gene expression profiles using machine learning.PLoS computational biology · 2023Article
- A globalBMC bioinformatics · 2022Article
- Unleashing the power within short-read RNA-seq for plant research: Beyond differential expression analysis and toward regulomics.Frontiers in plant science · 2022Review
- Hormonal Regulation and Crosstalk of Auxin/Cytokinin Signaling Pathways in Potatoes In Vitro and in Relation to Vegetation or Tuberization Stages.International journal of molecular sciences · 2021Article
- Using Network-Based Machine Learning to Predict Transcription Factors Involved in Drought Resistance.Frontiers in genetics · 2021Article
- Transcriptional analyses of two soybean cultivars under salt stress.Molecular biology reports · 2020Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Predicting gene functions from genome sequence alone has been difficult, and the functions of a large fraction of plant genes remain unknown. However, leveraging the vast amount of currently available gene expression data has the potential to facilitate our understanding of plant gene functions, especially in determining complex traits. Gene coexpression networks-created by integrating multiple expression datasets-connect genes with similar patterns of expression across multiple conditions. Dense gene communities in such networks, commonly referred to as modules, often indicate that the member genes are functionally related. As such, these modules serve as tools for generating new testable hypotheses, including the prediction of gene function and importance. Recently, we have seen a paradigm shift from the traditional "global" to more defined, context-specific coexpression networks. Such coexpression networks imply genetic correlations in specific biological contexts such as during development or in response to a stress. In this short review, we highlight a few recent studies that attempt to fill the large gaps in our knowledge about cellular functions of plant genes using context-specific coexpression networks.
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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.