A multi-label predictor for identifying the subcellular locations of singleplex and multiplex eukaryotic proteins

• Published in: PloS one 2012-05, Vol.7 (5), p.e36317-e36317
• Main Authors: Wang, Xiao, Li, Guo-Zheng
• Format: Article
• Language: English
• Subjects: Animals; Annotations; Artificial intelligence; Bioinformatics; Biology; Breakdowns; Cell walls; Classification; Computational Biology; Cytoplasm; Cytoskeleton; Data mining; Databases, Protein; Datasets; Embedded systems; Endoplasmic reticulum; Genomes; Golgi apparatus; Hybridization; Knowledge discovery; Localization; Localization method; Multiplexing; Nuclei; Ontology; Proteins; Proteins - analysis; Proteins - metabolism; Subcellular Fractions - metabolism; Synapses
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0036317

Subcellular locations of proteins are important functional attributes. An effective and efficient subcellular localization predictor is necessary for rapidly and reliably annotating subcellular locations of proteins. Most of existing subcellular localization methods are only used to deal with single-location proteins. Actually, proteins may simultaneously exist at, or move between, two or more different subcellular locations. To better reflect characteristics of multiplex proteins, it is highly desired to develop new methods for dealing with them. In this paper, a new predictor, called Euk-ECC-mPLoc, by introducing a powerful multi-label learning approach which exploits correlations between subcellular locations and hybridizing gene ontology with dipeptide composition information, has been developed that can be used to deal with systems containing both singleplex and multiplex eukaryotic proteins. It can be utilized to identify eukaryotic proteins among the following 22 locations: (1) acrosome, (2) cell membrane, (3) cell wall, (4) centrosome, (5) chloroplast, (6) cyanelle, (7) cytoplasm, (8) cytoskeleton, (9) endoplasmic reticulum, (10) endosome, (11) extracellular, (12) Golgi apparatus, (13) hydrogenosome, (14) lysosome, (15) melanosome, (16) microsome, (17) mitochondrion, (18) nucleus, (19) peroxisome, (20) spindle pole body, (21) synapse, and (22) vacuole. Experimental results on a stringent benchmark dataset of eukaryotic proteins by jackknife cross validation test show that the average success rate and overall success rate obtained by Euk-ECC-mPLoc were 69.70% and 81.54%, respectively, indicating that our approach is quite promising. Particularly, the success rates achieved by Euk-ECC-mPLoc for small subsets were remarkably improved, indicating that it holds a high potential for simulating the development of the area. As a user-friendly web-server, Euk-ECC-mPLoc is freely accessible to the public at the website http://levis.tongji.edu.cn:8080/bioinfo/Euk-ECC-mPLoc/. We believe that Euk-ECC-mPLoc may become a useful high-throughput tool, or at least play a complementary role to the existing predictors in identifying subcellular locations of eukaryotic proteins.