Predicting Human Protein Subcellular Localization by Heterogeneous and Comprehensive Approaches

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2017 Jun 29

PMID 28658305

Citations 3

Authors

Chi-Hua Tung

Chi-Wei Chen

Han-Hao Sun

Yen-Wei Chu

Affiliations

Soon will be listed here.

Abstract

Drug development and investigation of protein function both require an understanding of protein subcellular localization. We developed a system, REALoc, that can predict the subcellular localization of singleplex and multiplex proteins in humans. This system, based on comprehensive strategy, consists of two heterogeneous systematic frameworks that integrate one-to-one and many-to-many machine learning methods and use sequence-based features, including amino acid composition, surface accessibility, weighted sign aa index, and sequence similarity profile, as well as gene ontology function-based features. REALoc can be used to predict localization to six subcellular compartments (cell membrane, cytoplasm, endoplasmic reticulum/Golgi, mitochondrion, nucleus, and extracellular). REALoc yielded a 75.3% absolute true success rate during five-fold cross-validation and a 57.1% absolute true success rate in an independent database test, which was >10% higher than six other prediction systems. Lastly, we analyzed the effects of Vote and GANN models on singleplex and multiplex localization prediction efficacy. REALoc is freely available at http://predictor.nchu.edu.tw/REALoc.

Citing Articles

Ensemble of Multiple Classifiers for Multilabel Classification of Plant Protein Subcellular Localization.

Wattanapornprom W, Thammarongtham C, Hongsthong A, Lertampaiporn S Life (Basel). 2021; 11(4).

PMID: 33808227 PMC: 8066735. DOI: 10.3390/life11040293.

Plant-mSubP: a computational framework for the prediction of single- and multi-target protein subcellular localization using integrated machine-learning approaches.

Sahu S, Loaiza C, Kaundal R AoB Plants. 2020; 12(3):plz068.

PMID: 32528639 PMC: 7274489. DOI: 10.1093/aobpla/plz068.

Prediction of bacterial E3 ubiquitin ligase effectors using reduced amino acid peptide fingerprinting.

McDermott J, Cort J, Nakayasu E, Pruneda J, Overall C, Adkins J PeerJ. 2019; 7:e7055.

PMID: 31211016 PMC: 6557245. DOI: 10.7717/peerj.7055.

References

Yu C, Chen Y, Lu C, Hwang J . Prediction of protein subcellular localization. Proteins. 2006; 64(3):643-51. DOI: 10.1002/prot.21018. View

Shen H, Chou K . A top-down approach to enhance the power of predicting human protein subcellular localization: Hum-mPLoc 2.0. Anal Biochem. 2009; 394(2):269-74. DOI: 10.1016/j.ab.2009.07.046. View

Kawashima S, Ogata H, Kanehisa M . AAindex: Amino Acid Index Database. Nucleic Acids Res. 1998; 27(1):368-9. PMC: 148186. DOI: 10.1093/nar/27.1.368. View

Blum T, Briesemeister S, Kohlbacher O . MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction. BMC Bioinformatics. 2009; 10:274. PMC: 2745392. DOI: 10.1186/1471-2105-10-274. View

Guo X, Liu F, Ju Y, Wang Z, Wang C . Human Protein Subcellular Localization with Integrated Source and Multi-label Ensemble Classifier. Sci Rep. 2016; 6:28087. PMC: 4914962. DOI: 10.1038/srep28087. View

Mei S . Multi-label multi-kernel transfer learning for human protein subcellular localization. PLoS One. 2012; 7(6):e37716. PMC: 3374840. DOI: 10.1371/journal.pone.0037716. View

Chou K, Shen H . A new method for predicting the subcellular localization of eukaryotic proteins with both single and multiple sites: Euk-mPLoc 2.0. PLoS One. 2010; 5(4):e9931. PMC: 2848569. DOI: 10.1371/journal.pone.0009931. View

Chen J, Guo M, Wang X, Liu B . A comprehensive review and comparison of different computational methods for protein remote homology detection. Brief Bioinform. 2016; 19(2):231-244. DOI: 10.1093/bib/bbw108. View

Fu L, Niu B, Zhu Z, Wu S, Li W . CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012; 28(23):3150-2. PMC: 3516142. DOI: 10.1093/bioinformatics/bts565. View

10.

Nair R, Rost B . Mimicking cellular sorting improves prediction of subcellular localization. J Mol Biol. 2005; 348(1):85-100. DOI: 10.1016/j.jmb.2005.02.025. View

11.

Liu B, Fang L, Liu F, Wang X, Chou K . iMiRNA-PseDPC: microRNA precursor identification with a pseudo distance-pair composition approach. J Biomol Struct Dyn. 2015; 34(1):223-35. DOI: 10.1080/07391102.2015.1014422. View

12.

Briesemeister S, Rahnenfuhrer J, Kohlbacher O . Going from where to why--interpretable prediction of protein subcellular localization. Bioinformatics. 2010; 26(9):1232-8. PMC: 2859129. DOI: 10.1093/bioinformatics/btq115. View

13.

Chi S, Nam D . WegoLoc: accurate prediction of protein subcellular localization using weighted Gene Ontology terms. Bioinformatics. 2012; 28(7):1028-30. DOI: 10.1093/bioinformatics/bts062. View

14.

von Heijne G . Signal sequences. The limits of variation. J Mol Biol. 1985; 184(1):99-105. DOI: 10.1016/0022-2836(85)90046-4. View

15.

Emanuelsson O, Nielsen H, Brunak S, von Heijne G . Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol. 2000; 300(4):1005-16. DOI: 10.1006/jmbi.2000.3903. View

16.

Bairoch A, Apweiler R, Wu C, Barker W, Boeckmann B, Ferro S . The Universal Protein Resource (UniProt). Nucleic Acids Res. 2004; 33(Database issue):D154-9. PMC: 540024. DOI: 10.1093/nar/gki070. View

17.

Walter P, Ibrahimi I, Blobel G . Translocation of proteins across the endoplasmic reticulum. I. Signal recognition protein (SRP) binds to in-vitro-assembled polysomes synthesizing secretory protein. J Cell Biol. 1981; 91(2 Pt 1):545-50. PMC: 2111968. DOI: 10.1083/jcb.91.2.545. View

18.

Petersen T, Brunak S, von Heijne G, Nielsen H . SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods. 2011; 8(10):785-6. DOI: 10.1038/nmeth.1701. View

19.

Peng H, Long F, Ding C . Feature selection based on mutual information: criteria of max-dependency, max-relevance, and min-redundancy. IEEE Trans Pattern Anal Mach Intell. 2005; 27(8):1226-38. DOI: 10.1109/TPAMI.2005.159. View

20.

Goldberg T, Hamp T, Rost B . LocTree2 predicts localization for all domains of life. Bioinformatics. 2012; 28(18):i458-i465. PMC: 3436817. DOI: 10.1093/bioinformatics/bts390. View