Protein–protein interactions (PPIs) are of great importance to understand genetic mechanisms, delineate disease pathogenesis, and guide drug design. With the increase of PPI data and development of machine learning technologies, prediction and identification of PPIs have become a research hotspot in proteomics. In this study, we propose a new prediction pipeline for PPIs based on gradient tree boosting (GTB). First, the initial feature vector is extracted by fusing pseudo amino acid composition (PseAAC), pseudo position-specific scoring matrix (PsePSSM), reduced sequence and index-vectors (RSIV), and autocorrelation descriptor (AD). Second, to remove redundancy and noise, we employ L1-regularized logistic regression (L1-RLR) to select an optimal feature subset. Finally, GTB-PPI model is constructed. Five-fold cross-validation showed that GTB-PPI achieved the accuracies of 95.15% and 90.47% on Saccharomyces cerevisiae and Helicobacter pylori datasets, respectively. In addition, GTB-PPI could be applied to predict the independent test datasets for Caenorhabditis elegans, Escherichia coli, Homo sapiens, and Mus musculus, the one-core PPI network for CD9, and the crossover PPI network for the Wnt-related signaling pathways. The results show that GTB-PPI can significantly improve accuracy of PPI prediction. The code and datasets of GTB-PPI can be downloaded from https://github.com/QUST-AIBBDRC/GTB-PPI/.
PDF全文下载地址:
http://gpb.big.ac.cn/articles/download/814
删除或更新信息,请邮件至freekaoyan#163.com(#换成@)
GTB-PPI: Predict Protein–protein Interactions Based on L1-regularized Logistic Regression and Gradie
本站小编 Free考研考试/2022-01-03
相关话题/gen
SeSaMe PS Function: Functional Analysis of the Whole Metagenome Sequencing Data of the Arbuscular My
Inthisstudy,weintroduceanovelbioinformaticsprogram,Spore-associatedSymbioticMicrobesPosition-specificFunction(SeSaMePSFunction),forposition-specificfu ...中科院北京基因组研究所 本站小编 Free考研考试 2022-01-03SeSaMe: Metagenome Sequence Classification of Arbuscular Mycorrhizal Fungi-associated Microorganisms
Arbuscularmycorrhizalfungi(AMF)areplantrootsymbiontsthatplaykeyrolesinplantgrowthandsoilfertility.Theyareobligatebiotrophicfungithatformcoenocyticmult ...中科院北京基因组研究所 本站小编 Free考研考试 2022-01-03m6A Regulates Liver Metabolic Disorders and Hepatogenous Diabetes
N6-methyladenosine(m6A)isoneofthemostabundantmodificationsonmRNAsandplaysimportantrolesinvariousbiologicalprocesses.Theformationofm6Aiscatalyzedbyamet ...中科院北京基因组研究所 本站小编 Free考研考试 2022-01-03Corrigendum to “Antibiotic Treatment Drives the Diversification of the Human Gut Resistome” [Genomic
PDF全文下载地址:/articles/download/818 ...中科院北京基因组研究所 本站小编 Free考研考试 2022-01-03Tissue-specific Gene Expression Changes Are Associated with Aging in Mice
Agingisacomplexprocessthatcanbecharacterizedbyfunctionalandcognitivedeclineinanindividual.Agingcanbeassessedbasedonthefunctionalcapacityofvitalorgansa ...中科院北京基因组研究所 本站小编 Free考研考试 2022-01-03Transcriptomic and Proteomic Analysis of Mannitol-metabolism-associated Genes in Saccharina japonica
Asacarbon-storagecompoundandosmoprotectantinbrownalgae,mannitolissynthesizedandthenaccumulatedathighlevelsinSaccharinajaponica(Sja);however,theunderly ...中科院北京基因组研究所 本站小编 Free考研考试 2022-01-03The Wolfiporia cocos Genome and Transcriptome Shed Light on the Formation of Its Edible and Medicina
Wolfiporiacocos(F.A.Wolf)hasbeenpraisedasafooddelicacyandmedicineforcenturiesinChina.Here,wepresentthegenomeandtranscriptomeoftheChinesestrainCGMCC5.7 ...中科院北京基因组研究所 本站小编 Free考研考试 2022-01-03Global Analysis of Gene Expression Profiles Provides Novel Insights into the Development and Evoluti
Chinesemittencrab(Eriocheirsinensis)isanimportantaquaculturespeciesinCrustacea.Functionalanalysis,althoughessential,hasbeenhinderedduetothelackofsuffi ...中科院北京基因组研究所 本站小编 Free考研考试 2022-01-03mrMLM v4.0.2: An R Platform for Multi-locus Genome-wide Association Studies
Previousstudieshavereportedthatsomeimportantlociaremissedinsingle-locusgenome-wideassociationstudies(GWAS),especiallybecauseofthelargephenotypicerrori ...中科院北京基因组研究所 本站小编 Free考研考试 2022-01-03Corrigendum to “Large-scale Identification and Time-course Quantification of Ubiquitylation Events D
PDF全文下载地址:/articles/download/800 ...中科院北京基因组研究所 本站小编 Free考研考试 2022-01-03