ReviewFrontiers in plant science2014
Elucidating gene function and function evolution through comparison of co-expression networks of plants.
Review in Frontiers in plant science, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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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
42 citing papers in PubMed, 92 citations in OpenAlex.
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- Transcriptome-Based Screening of Candidate Low-Temperature-Associated Genes and Analysis of theInternational journal of molecular sciences · 2024Article
- Multi-Omics Approaches and Resources for Systems-Level Gene Function Prediction in the Plant Kingdom.Plants (Basel, Switzerland) · 2022Review
- Integrative omics approaches for biosynthetic pathway discovery in plants.Natural product reports · 2022Review
- Exploiting plant transcriptomic databases: Resources, tools, and approaches.Plant communications · 2022Review
- Characterization and evolutionary diversification of the phospholipase D gene family in mosses.Frontiers in genetics · 2022Article
- TopoFun: a machine learning method to improve the functional similarity of gene co-expression modules.NAR genomics and bioinformatics · 2021Article
- A novel estimator of the interaction matrix in Graphical Gaussian Model of omics data using the entropy of non-equilibrium systems.Bioinformatics (Oxford, England) · 2021Article
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- LSTrAP-Crowd: prediction of novel components of bacterial ribosomes with crowd-sourced analysis of RNA sequencing data.BMC biology · 2020Article
- Differential Evolution of α-Glucan Water Dikinase (GWD) in Plants.Plants (Basel, Switzerland) · 2020Article
- TeaCoN: a database of gene co-expression network for tea plant (Camellia sinensis).BMC genomics · 2020Article
- Convergent Loss of an EDS1/PAD4 Signaling Pathway in Several Plant Lineages Reveals Coevolved Components of Plant Immunity and Drought Response.The Plant cell · 2020Article
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- Expression Atlas ofThe Plant cell · 2020Article
- Malaria.tools-comparative genomic and transcriptomic database for Plasmodium species.Nucleic acids research · 2020Article
- Peroxiredoxins and Immune Infiltrations in Colon Adenocarcinoma: Their Negative Correlations and Clinical Significances, an In Silico Analysis.Journal of Cancer · 2020Article
- Fungi.guru: Comparative genomic and transcriptomic resource for the fungi kingdom.Computational and structural biotechnology journal · 2020Article
- Phylostratigraphic Analysis Shows the Earliest Origination of the Abiotic Stress Associated Genes inGenes · 2019Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The analysis of gene expression data has shown that transcriptionally coordinated (co-expressed) genes are often functionally related, enabling scientists to use expression data in gene function prediction. This Focused Review discusses our original paper (Large-scale co-expression approach to dissect secondary cell wall formation across plant species, Frontiers in Plant Science 2:23). In this paper we applied cross-species analysis to co-expression networks of genes involved in cellulose biosynthesis. We showed that the co-expression networks from different species are highly similar, indicating that whole biological pathways are conserved across species. This finding has two important implications. First, the analysis can transfer gene function annotation from well-studied plants, such as Arabidopsis, to other, uncharacterized plant species. As the analysis finds genes that have similar sequence and similar expression pattern across different organisms, functionally equivalent genes can be identified. Second, since co-expression analyses are often noisy, a comparative analysis should have higher performance, as parts of co-expression networks that are conserved are more likely to be functionally relevant. In this Focused Review, we outline the comparative analysis done in the original paper and comment on the recent advances and approaches that allow comparative analyses of co-function networks. We hypothesize that in comparison to simple co-expression analysis, comparative analysis would yield more accurate gene function predictions. Finally, by combining comparative analysis with genomic information of green plants, we propose a possible composition of cellulose biosynthesis machinery during earlier stages of plant evolution.
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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.