ArticleBMC bioinformatics2009
TransportTP: a two-phase classification approach for membrane transporter prediction and characterization.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed, 65 citations in OpenAlex.
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- Bodo saltans (Kinetoplastida) is dependent on a novel Paracaedibacter-like endosymbiont that possesses multiple putative toxin-antitoxin systems.The ISME journal · 2021Article
- Transportome-wide engineering of Saccharomyces cerevisiae.Metabolic engineering · 2021Article
- Addressing uncertainty in genome-scale metabolic model reconstruction and analysis.Genome biology · 2021Review
- Utilizing Plant Synthetic Biology to Improve Human Health and Wellness.Frontiers in plant science · 2021Review
- Deciphering the Infectious Process ofMicroorganisms · 2020Article
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- Genome-Wide Identification and Comparative Analysis for OPT Family Genes inMolecules (Basel, Switzerland) · 2018Article
- The genome sequence of the soft-rot fungusMycology · 2018Article
- Comparative Genome Analysis Reveals Adaptation to the Ectophytic Lifestyle of Sooty Blotch and Flyspeck Fungi.Genome biology and evolution · 2017Article
- Global analysis of the MATE gene family of metabolite transporters in tomato.BMC plant biology · 2017Article
- TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life.Nucleic acids research · 2017Article
- Comprehensive Genomic Analyses of the OM43 Clade, Including a Novel Species from the Red Sea, Indicate Ecotype Differentiation among Marine Methylotrophs.Applied and environmental microbiology · 2016Article
- HRGRN: A Graph Search-Empowered Integrative Database of Arabidopsis Signaling Transduction, Metabolism and Gene Regulation Networks.Plant & cell physiology · 2016Article
- Adaptive Evolution of Thermotoga maritima Reveals Plasticity of the ABC Transporter Network.Applied and environmental microbiology · 2015Article
- SCMMTP: identifying and characterizing membrane transport proteins using propensity scores of dipeptides.BMC genomics · 2015Article
- The genome of the myxosporean Thelohanellus kitauei shows adaptations to nutrient acquisition within its fish host.Genome biology and evolution · 2014Article
- Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine.BMC genomics · 2014Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMembrane transporters play crucial roles in living cells. Experimental characterization of transporters is costly and time-consuming. Current computational methods for transporter characterization still require extensive curation efforts, especially for eukaryotic organisms. We developed a novel genome-scale transporter prediction and characterization system called TransportTP that combined homology-based and machine learning methods in a two-phase classification approach. First, traditional homology methods were employed to predict novel transporters based on sequence similarity to known classified proteins in the Transporter Classification Database (TCDB). Second, machine learning methods were used to integrate a variety of features to refine the initial predictions. A set of rules based on transporter features was developed by machine learning using well-curated proteomes as guides.
resultsIn a cross-validation using the yeast proteome for training and the proteomes of ten other organisms for testing, TransportTP achieved an equivalent recall and precision of 81.8%, based on TransportDB, a manually annotated transporter database. In an independent test using the Arabidopsis proteome for training and four recently sequenced plant proteomes for testing, it achieved a recall of 74.6% and a precision of 73.4%, according to our manual curation.
conclusionsTransportTP is the most effective tool for eukaryotic transporter characterization up to date.
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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.