ArticlePloS one2017
Identifying novel fruit-related genes in Arabidopsis thaliana based on the random walk with restart algorithm.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed, 19 citations in OpenAlex.
- Prediction of drug's anatomical therapeutic chemical (ATC) code by constructing biological profiles of ATC codes.BMC bioinformatics · 2025Article
- Genome-Wide Characterization and Gene Expression Analyses of Malate Dehydrogenase (International journal of molecular sciences · 2023Article
- Genetic control of the operculum and capsule morphology of Eucalyptus globulus.Annals of botany · 2022Article
- Linkage and association study discovered loci and candidate genes for glycinin and β-conglycinin in soybean (Glycine max L. Merr.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- A Random Walk-Based Method to Identify Candidate Genes Associated With Lymphoma.Frontiers in genetics · 2021Article
- Fruit ripening in Lycium barbarum and Lycium ruthenicum is associated with distinct gene expression patterns.FEBS open bio · 2020Article
- Identification of COVID-19 Infection-Related Human Genes Based on a Random Walk Model in a Virus-Human Protein Interaction Network.BioMed research international · 2020Article
- Prediction of Drug Side Effects with a Refined Negative Sample Selection Strategy.Computational and mathematical methods in medicine · 2020Article
- Inferring novel genes related to colorectal cancer via random walk with restart algorithm.Gene therapy · 2019Article
- Large Scale Proteomic Data and Network-Based Systems Biology Approaches to Explore the Plant World.Proteomes · 2018Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Fruit is essential for plant reproduction and is responsible for protection and dispersal of seeds. The development and maturation of fruit is tightly regulated by numerous genetic factors that respond to environmental and internal stimulation. In this study, we attempted to identify novel fruit-related genes in a model organism, Arabidopsis thaliana, using a computational method. Based on validated fruit-related genes, the random walk with restart (RWR) algorithm was applied on a protein-protein interaction (PPI) network using these genes as seeds. The identified genes with high probabilities were filtered by the permutation test and linkage tests. In the permutation test, the genes that were selected due to the structure of the PPI network were discarded. In the linkage tests, the importance of each candidate gene was measured from two aspects: (1) its functional associations with validated genes and (2) its similarity with validated genes on gene ontology (GO) terms and KEGG pathways. Finally, 255 inferred genes were obtained, subsequent extensive analysis of important genes revealed that they mainly contribute to ubiquitination (UBQ9, UBQ8, UBQ11, UBQ10), serine hydroxymethyl transfer (SHM7, SHM5, SHM6) or glycol-metabolism (HXKL2_ARATH, CSY5, GAPCP1), suggesting essential roles during the development and maturation of fruit in Arabidopsis thaliana.
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