Identifying novel fruit-related genes in Arabidopsis thaliana based on the random walk with restart algorithm

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.

Prediction of Drug Side Effects with a Refined Negative Sample Selection Strategy

“…where λ was set to 0.8, as used in other studies [27,[32][33][34], in this study and A represents the columnwise normalized adjacency matrix of the network. When kp t+1 − p t k L 1 < θ, the update procedure stops, and p t+1 is picked up as the output of the RWR algorithm.…”

Identification of COVID-19 Infection-Related Human Genes Based on a Random Walk Model in a Virus–Human Protein Interaction Network

“…Initialization vector P 0 was constructed. It consisted of 19,247 elements, wherein the elements corresponding to the seed genes were set to 1/11419, the other elements were set to zero, and the probability of returning to seed node λ was set to 0.8 as suggested in some studies [25][26][27][28][29]. The algorithm termination rule was kP i+1 − P i k 1 < 10 −6 .…”

Fruit ripening in Lycium barbarum and Lycium ruthenicum is associated with distinct gene expression patterns

“…This gene plays a major role in glycolytic energy production in nongreen plastids and chloroplasts, and it is essential for breakdown of starch to form sucrose for export to nonphotosynthetic tissues and to generate primary metabolites for anabolic pathways such as fatty acid and amino acid synthesis [39][40][41]. As such, it has an important developmental role, for example in pollen development [39], and in the production of glycolytic energy in fruits [41]. We hypothesise that its high expression in the S2 may be associated with its role in maintaining the sugar and amino acid balance, especially the serine biosynthesis [39,40].…”