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Multi‐omics network‐based functional annotation of unknown Arabidopsis genes

Thomas Depuydt (UGent) and Klaas Vandepoele (UGent)
(2021) PLANT JOURNAL. 108. p.1193-1212
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Abstract
Unraveling gene function is pivotal to understanding the signaling cascades that control plant development and stress responses. Since experimental profiling is costly and labor intensive, there is a clear need for high-confidence computational annotation. In contrast to detailed gene-specific functional information, transcriptomics data is widely available for both model and crop species. Here, we describe a novel automated function prediction (AFP) method, which leverages complementary information from multiple expression datasets by analyzing study-specific gene co-expression networks. First, we benchmarked the prediction performance on recently characterized Arabidopsis thaliana genes, and showed that our method outperforms state-of-the-art expression-based approaches. Next, we predicted biological process annotations for known (n=15,790) and unknown (n=11,865) genes in A. thaliana and validated our predictions using experimental protein-DNA and protein-protein interaction data (covering >220 thousand interactions in total), obtaining a set of high-confidence functional annotations. Our method assigned at least one validated annotation to 5,054 (42.6%) unknown genes, and at least one novel validated function to 3,408 (53.0%) genes with computational annotations only. These omics-supported functional annotations shed light on a variety of developmental processes and molecular responses, such as flower and root development, defense responses to fungi and bacteria, and phytohormone signaling, and help fill the information gap on biological process annotations in Arabidopsis. An in-depth analysis of two context-specific networks, modeling seed development and response to water deprivation, shows how previously uncharacterized genes function within the respective networks. Moreover, our AFP approach can be applied in future studies to facilitate gene discovery for crop improvement.
Keywords
Arabidopsis thaliana, Co-expression, Gene function, Networks, Regulation of gene expression, GENOME-WIDE BINDING, TRANSCRIPTIONAL CONTROL, FUNCTION PREDICTION, REGULATORY NETWORK, REVEALS DISTINCT, PLANT-RESPONSES, CELL-WALL, DATA SETS, EXPRESSION, THALIANA

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Citation

Please use this url to cite or link to this publication:

MLA
Depuydt, Thomas, and Klaas Vandepoele. “Multi‐omics Network‐based Functional Annotation of Unknown Arabidopsis Genes.” PLANT JOURNAL, vol. 108, 2021, pp. 1193–212, doi:10.1111/tpj.15507.
APA
Depuydt, T., & Vandepoele, K. (2021). Multi‐omics network‐based functional annotation of unknown Arabidopsis genes. PLANT JOURNAL, 108, 1193–1212. https://doi.org/10.1111/tpj.15507
Chicago author-date
Depuydt, Thomas, and Klaas Vandepoele. 2021. “Multi‐omics Network‐based Functional Annotation of Unknown Arabidopsis Genes.” PLANT JOURNAL 108: 1193–1212. https://doi.org/10.1111/tpj.15507.
Chicago author-date (all authors)
Depuydt, Thomas, and Klaas Vandepoele. 2021. “Multi‐omics Network‐based Functional Annotation of Unknown Arabidopsis Genes.” PLANT JOURNAL 108: 1193–1212. doi:10.1111/tpj.15507.
Vancouver
1.
Depuydt T, Vandepoele K. Multi‐omics network‐based functional annotation of unknown Arabidopsis genes. PLANT JOURNAL. 2021;108:1193–212.
IEEE
[1]
T. Depuydt and K. Vandepoele, “Multi‐omics network‐based functional annotation of unknown Arabidopsis genes,” PLANT JOURNAL, vol. 108, pp. 1193–1212, 2021.
@article{8721875,
  abstract     = {{Unraveling gene function is pivotal to understanding the signaling cascades that control plant development and stress responses. Since experimental profiling is costly and labor intensive, there is a clear need for high-confidence computational annotation. In contrast to detailed gene-specific functional information, transcriptomics data is widely available for both model and crop species. Here, we describe a novel automated function prediction (AFP) method, which leverages complementary information from multiple expression datasets by analyzing study-specific gene co-expression networks. First, we benchmarked the prediction performance on recently characterized Arabidopsis thaliana genes, and showed that our method outperforms state-of-the-art expression-based approaches. Next, we predicted biological process annotations for known (n=15,790) and unknown (n=11,865) genes in A. thaliana and validated our predictions using experimental protein-DNA and protein-protein interaction data (covering >220 thousand interactions in total), obtaining a set of high-confidence functional annotations. Our method assigned at least one validated annotation to 5,054 (42.6%) unknown genes, and at least one novel validated function to 3,408 (53.0%) genes with computational annotations only. These omics-supported functional annotations shed light on a variety of developmental processes and molecular responses, such as flower and root development, defense responses to fungi and bacteria, and phytohormone signaling, and help fill the information gap on biological process annotations in Arabidopsis. An in-depth analysis of two context-specific networks, modeling seed development and response to water deprivation, shows how previously uncharacterized genes function within the respective networks. Moreover, our AFP approach can be applied in future studies to facilitate gene discovery for crop improvement.}},
  author       = {{Depuydt, Thomas and Vandepoele, Klaas}},
  issn         = {{0960-7412}},
  journal      = {{PLANT JOURNAL}},
  keywords     = {{Arabidopsis thaliana,Co-expression,Gene function,Networks,Regulation of gene expression,GENOME-WIDE BINDING,TRANSCRIPTIONAL CONTROL,FUNCTION PREDICTION,REGULATORY NETWORK,REVEALS DISTINCT,PLANT-RESPONSES,CELL-WALL,DATA SETS,EXPRESSION,THALIANA}},
  language     = {{eng}},
  pages        = {{1193--1212}},
  title        = {{Multi‐omics network‐based functional annotation of unknown Arabidopsis genes}},
  url          = {{http://dx.doi.org/10.1111/tpj.15507}},
  volume       = {{108}},
  year         = {{2021}},
}

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