Dataset Information

PRED_PPI: a server for predicting protein-protein interactions based on sequence data with probability assignment.

ABSTRACT:

Background

Protein-protein interactions (PPIs) are crucial for almost all cellular processes, including metabolic cycles, DNA transcription and replication, and signaling cascades. Given the importance of PPIs, several methods have been developed to detect them. Since the experimental methods are time-consuming and expensive, developing computational methods for effectively identifying PPIs is of great practical significance.

Findings

Most previous methods were developed for predicting PPIs in only one species, and do not account for probability estimations. In this work, a relatively comprehensive prediction system was developed, based on a support vector machine (SVM), for predicting PPIs in five organisms, specifically humans, yeast, Drosophila, Escherichia coli, and Caenorhabditis elegans. This PPI predictor includes the probability of its prediction in the output, so it can be used to assess the confidence of each SVM prediction by the probability assignment. Using a probability of 0.5 as the threshold for assigning class labels, the method had an average accuracy for detecting protein interactions of 90.67% for humans, 88.99% for yeast, 90.09% for Drosophila, 92.73% for E. coli, and 97.51% for C. elegans. Moreover, among the correctly predicted pairs, more than 80% were predicted with a high probability of >/=0.8, indicating that this tool could predict novel PPIs with high confidence.

Conclusions

Based on this work, a web-based system, Pred_PPI, was constructed for predicting PPIs from the five organisms. Users can predict novel PPIs and obtain a probability value about the prediction using this tool. Pred_PPI is freely available at http://cic.scu.edu.cn/bioinformatics/predict_ppi/default.html.

SUBMITTER: Guo Y

PROVIDER: S-EPMC2883990 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundRNA-protein interactions (RPIs) play important roles in a wide variety of cellular processes, ranging from transcriptional and post-transcriptional regulation of gene expression to host defense against pathogens. High throughput experiments to identify RNA-protein interactions are beginning to provide valuable information about the complexity of RNA-protein interaction networks, but are expensive and time consuming. Hence, there is a need for reliable computational methods for predicting RNA-protein interactions.ResultsWe propose RPISeq, a family of classifiers for predicting RNA-protein interactions using only sequence information. Given the sequences of an RNA and a protein as input, RPIseq predicts whether or not the RNA-protein pair interact. The RNA sequence is encoded as a normalized vector of its ribonucleotide 4-mer composition, and the protein sequence is encoded as a normalized vector of its 3-mer composition, based on a 7-letter reduced alphabet representation. Two variants of RPISeq are presented: RPISeq-SVM, which uses a Support Vector Machine (SVM) classifier and RPISeq-RF, which uses a Random Forest classifier. On two non-redundant benchmark datasets extracted from the Protein-RNA Interface Database (PRIDB), RPISeq achieved an AUC (Area Under the Receiver Operating Characteristic (ROC) curve) of 0.96 and 0.92. On a third dataset containing only mRNA-protein interactions, the performance of RPISeq was competitive with that of a published method that requires information regarding many different features (e.g., mRNA half-life, GO annotations) of the putative RNA and protein partners. In addition, RPISeq classifiers trained using the PRIDB data correctly predicted the majority (57-99%) of non-coding RNA-protein interactions in NPInter-derived networks from E. coli, S. cerevisiae, D. melanogaster, M. musculus, and H. sapiens.ConclusionsOur experiments with RPISeq demonstrate that RNA-protein interactions can be reliably predicted using only sequence-derived information. RPISeq offers an inexpensive method for computational construction of RNA-protein interaction networks, and should provide useful insights into the function of non-coding RNAs. RPISeq is freely available as a web-based server at http://pridb.gdcb.iastate.edu/RPISeq/.