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Xie M, Xie R, Wang H. LPI-IBWA: Predicting lncRNA-protein interactions based on an improved Bi-Random walk algorithm. Methods 2023; 220:98-105. [PMID: 37972912 DOI: 10.1016/j.ymeth.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/14/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
Many studies have shown that long-chain noncoding RNAs (lncRNAs) are involved in a variety of biological processes such as post-transcriptional gene regulation, splicing, and translation by combining with corresponding proteins. Predicting lncRNA-protein interactions is an effective approach to infer the functions of lncRNAs. The paper proposes a new computational model named LPI-IBWA. At first, LPI-IBWA uses similarity kernel fusion (SKF) to integrate various types of biological information to construct lncRNA and protein similarity networks. Then, a bounded matrix completion model and a weighted k-nearest known neighbors algorithm are utilized to update the initial sparse lncRNA-protein interaction matrix. Based on the updated lncRNA-protein interaction matrix, the lncRNA similarity network and the protein similarity network are integrated into a heterogeneous network. Finally, an improved Bi-Random walk algorithm is used to predict novel latent lncRNA-protein interactions. 5-fold cross-validation experiments on a benchmark dataset showed that the AUC and AUPR of LPI-IBWA reach 0.920 and 0.736, respectively, which are higher than those of other state-of-the-art methods. Furthermore, the experimental results of case studies on a novel dataset also illustrated that LPI-IBWA could efficiently predict potential lncRNA-protein interactions.
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Affiliation(s)
- Minzhu Xie
- College of Information Science and Engineering, Hunan Normal University, China.
| | - Ruijie Xie
- College of Information Science and Engineering, Hunan Normal University, China.
| | - Hao Wang
- College of Information Science and Engineering, Hunan Normal University, China.
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Shokrollahi N, Ho CL, Mohd Zainudin NAI, Abdul Wahab MAB, Wong MY. Plant Defense Inducers and Antioxidant Metabolites Produced During Oil Palm-Ganoderma boninense Interaction In Vitro. CHEMISTRY AFRICA 2022. [DOI: 10.1007/s42250-022-00501-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Liu M, Overy DP, Cayouette J, Shoukouhi P, Hicks C, Bisson K, Sproule A, Wyka SA, Broders K, Popovic Z, Menzies JG. Four phylogenetic species of ergot from Canada and their characteristics in morphology, alkaloid production, and pathogenicity. Mycologia 2020; 112:974-988. [PMID: 32936061 DOI: 10.1080/00275514.2020.1797372] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Four ergot species (Claviceps ripicola, C. quebecensis, C. perihumidiphila, and C. occidentalis) were recognized based on analyses of DNA sequences from multiple loci, including two housekeeping genes, RNA polymerase II second largest subunit (RPB2), and translation elongation factor 1-α (TEF1-α), and a single-copy ergot alkaloid synthesis gene (easE) encoding chanoclavine I synthase oxidoreductase. Morphological features, ergot alkaloid production, and pathogenicity on five common cereal crops of each species were evaluated and presented in taxonomic descriptions. A synoptic key was also provided for identification.
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Affiliation(s)
- Miao Liu
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada , Ottawa, K1A 0C6, Canada
| | - David P Overy
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada , Ottawa, K1A 0C6, Canada
| | - Jacques Cayouette
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada , Ottawa, K1A 0C6, Canada
| | - Parivash Shoukouhi
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada , Ottawa, K1A 0C6, Canada
| | - Carmen Hicks
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada , Ottawa, K1A 0C6, Canada
| | - Kassandra Bisson
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada , Ottawa, K1A 0C6, Canada
| | - Amanda Sproule
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada , Ottawa, K1A 0C6, Canada
| | - Stephen A Wyka
- Colorado State University , Fort Collins, Colorado 80523
| | - Kirk Broders
- Colorado State University , Fort Collins, Colorado 80523
| | - Zlatko Popovic
- Morden Research and Development Centre, Agriculture and Agri-Food Canada , 101 Route 100, Morden, Manitoba R6M 1Y5, Canada
| | - Jim G Menzies
- Morden Research and Development Centre, Agriculture and Agri-Food Canada , 101 Route 100, Morden, Manitoba R6M 1Y5, Canada
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Zavadil Kokáš F, Bergougnoux V, Majeská Čudejková M. SATrans: New Free Available Software for Annotation of Transcriptome and Functional Analysis of Differentially Expressed Genes. J Comput Biol 2018; 26:117-123. [PMID: 30328709 DOI: 10.1089/cmb.2018.0149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recent technological advances have made next-generation sequencing (NGS) a popular and financially accessible technique allowing a broad range of analyses to be done simultaneously. A huge amount of newly generated NGS data, however, require advanced software support to help both in analyzing the data and biologically interpreting the results. In this article, we describe SATrans (Software for Annotation of Transcriptome), a software package providing fast and robust functional annotation of novel sequences obtained from transcriptome sequencing. Moreover, it performs advanced gene ontology analysis of differentially expressed genes, thereby helping to interpret biologically-and in a user-friendly form-the quantitative changes in gene expression. The software is freely available and provides the possibility to work with thousands of sequences using a standard personal computer or notebook running on the Linux operating system.
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Affiliation(s)
- Filip Zavadil Kokáš
- Department of Molecular Biology, Centre of Region Haná for Biotechnological and Agricultural Research, Palacký University in Olomouc, Olomouc, Czech Republic
| | - Véronique Bergougnoux
- Department of Molecular Biology, Centre of Region Haná for Biotechnological and Agricultural Research, Palacký University in Olomouc, Olomouc, Czech Republic
| | - Mária Majeská Čudejková
- Department of Molecular Biology, Centre of Region Haná for Biotechnological and Agricultural Research, Palacký University in Olomouc, Olomouc, Czech Republic
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Dopstadt J, Vens-Cappell S, Neubauer L, Tudzynski P, Cramer B, Dreisewerd K, Humpf HU. Localization of ergot alkaloids in sclerotia of Claviceps purpurea by matrix-assisted laser desorption/ionization mass spectrometry imaging. Anal Bioanal Chem 2016; 409:1221-1230. [DOI: 10.1007/s00216-016-0047-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 10/04/2016] [Accepted: 10/21/2016] [Indexed: 12/11/2022]
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