GOPET: A tool for automated predictions of Gene Ontology terms

The expanding amount of sequence data generated from genome and cDNA sequencing projects creates an ever extending demand for automated annotation. The annotation represented in standardised formats like the ones designed by ontologies benefits from its straightforward operability across different analysis platforms. The Gene Ontology (GO) project is a collaborative initiative and provides consistent descriptions of gene products across different species [1, 2]. This gives Gene Ontology the potential of becoming a major basis for automatic annotation.

Gene product prediction is confronted with a variety of challenges coming from ambiguities concerning the underlying input databases, e.g. sequence errors, erroneous and incomplete annotation, and inconsistent annotation across databases or consistent but erroneous annotation across databases. A broad variety of excellent annotation systems have been developed to tackle these problems, e.g. RiceGAAS [3], GAIA [4], Genotator [5], Magpie [6], GeneQuiz [7], GeneAtlas [8], PEDANT [9], cDNA2Genome [10], GenDB [11], GOFigure [12] and GOtcha [13]. However, little has been done to quantify the annotation accuracy by defined benchmarks and establishing a method to provide a confidence value for each annotation. We developed an automated system for large-scale cDNA function assignment, designed and optimised to achieve a high-level of prediction accuracy without any manual refinement. With our system, Gene Ontology molecular function terms are predicted for uncharacterised cDNA sequences and a defined confidence value is calculated for each prediction. The performance of the system was benchmarked with 36,771 GO annotated cDNA sequences derived from 13 organisms [14].

We have now extended our approach to predict biological process terms and implemented our method as an online sequence annotation tool (GOPET, Gene Ontology term Prediction and Evaluation Tool). From a user-friendly front-end, the user can upload query protein- and nucleotide-sequences for which the tool assigns Gene Ontology molecular function and biological process terms. It is implemented under the W3H-Task-System which provides a flexible way to configure program and data flow between different biocomputational methods [15]. The W3H-Task-System uses the Heidelberg Unix Sequence Analysis Resources (HUSAR [16]) which is a sequence analysis software package operating at the German Cancer Research Center.

Nucleotide or protein query sequences are blasted [17] against GO-mapped protein databases. Currently, we apply 16 GO-annotated protein databases from the following model organisms (downloaded from the data sources given in brackets): Saccharomyces cerevisiae (Stanford University), Drosophila melanogaster (Berkeley Drosophila Genome Project), Mus musculus (Ensembl), Arabidopsis thaliana (MIPS), Caenorhabditis elegans (Sanger Center), Rattus norvegicus (NCBI), Danio rerio (SwissProt), Leishmania major (Sanger Center), Bacillus anthracis Ame (TIGR), Coxiella burnetii RSA 493 (NCBI), Shewanella oneidensis MR-1 (TIGR), Vibrio cholerae (TIGR), Plasmodium falciparum (Plasmodium Genome Research), Oryza sativa (SwissProt, Trembl), Trypanosoma brucei (Sanger Center), Homo sapiens (GOA annotated sequences of SwissProt, Trembl and Enseml), as well as the protein database SwissProt (the SwissProt part of the UniProt family of databases). These databases are constantly updated to keep track of the latest information. The corresponding GO annotations were taken from Gene Ontology [18]. The Sequence Retrieval System SRS [19] is used to retrieve GO annotation from GO-mapping relations. Blast hits with a relaxed e-value threshold (e-value < 0.01) are considered and all GO-terms are extracted from these hits. Each extracted GO-term is attached to a broad variety of elaborated attributes, including sequence similarity measures, such as e-value, bitscore, identity, coverage score and alignment length. Further attributes use GO-term frequency, GO-term relationships between homologues, the level of annotation within the GO hierarchy and annotation quality of the homologues which are calculated using the evidence codes provided by the gene association tables of the GO mapped sequence databases. Nine commonly used evidence codes are taken into acoount: TAS, NAS, ISS, IPI, IMP, IGI, IEP, IEA, IDA. The entries of theses attributes for each GO term are calculated by summing over the occurrences of the corresponding evidence codes of all blast hits (for more details, see [14]). In the following, the term "instance" is used for a GO-term together with its corresponding attribute values.

Furthermore, we compared GOPET and GOTCHA in more detail. We selected manually 100 random sequences (excluding IEA annotated ones) from DictyBase (Version 1.68, DictyBase, database for Dictyostelium discoideum[25]). This database was used for the comparison as it was not used for the training of both systems. From GOPET and GOTcha, we selected again only annotations with ≥ 80% confidence. Of the 100 sequences, 72 and 77 were annotated with 332 (true positive: 296) and 535 (true positive: 430) terms by GOPET and GOTcha, respectively. Hence, GOPET showed a better precision (89%) compared to GOTcha (80%) (p-value of a two-sided Fisher exact test: 0.0006) and GOTcha showed a better recall. Note that, in the most cases, GOPET provided more specific annotation terms (all data is provided in supplementary Tables S1 and S2, see Additional file 1 and Additional file 2, respectively).

The GOPET web-server is accessible via the web-page [32]. The starting page shows the user interface to upload query sequences. More than one sequence can be queried if uploaded in FastA format. GOPET accepts nucleotide and protein sequences as input. The running time of the task depends on the size and complexity of the input sequences and varies between 2 to 4 minutes per sequence on our Sun Multiprocessor machine (Sun E4500). For example, annotating a cDNA sequence with 1173 base pairs (TC291942 from TIGR XGI, [33]) takes about 2 min 30 seconds. Figure 2 shows the prediction results for this sequence. The output displays every predicted GO-term having at least one vote. The results are sorted by their confidence values. By default, only the top 20 predictions are displayed if more hits have been found.

Confidence values may serve in several ways. Predictions with confidence values ≥ 80% can be used straight away for annotation. In contrast, predictions with low confidence values may serve as a basis for new hypotheses and research, e.g. to infer further relationships to the original function. Automated annotation fails for sequences without any annotated and known homologues and the only alternative remains to analyse the sequence manually and in depth. We included IEA annotated sequences (automated annotated sequences) to improve the annotation coverage. To compare the performance with and without IEA annotated sequences, we calculated the respective prediction accuracies for yeast (non-IEA) based on the worm data-set (IEA) and fly data-set (non-IEA). The results were quite similar (test yeast and training worm: 82%, test yeast and training fly: 81% accuracy, see [14] for details). However, restricting to non-IEA terms may improve the precision. We consider to provide an option for the user to exclude IEA annotations based predictions for the next release of GOPET.

GOPET serves as a valuable tool for experimental researchers as well as for the bioinformatics community. The underlying methodology shows numerous advantages. The prediction performance is organism-independent, since the applied annotation databases cover a broad variety of different organisms and the attributes selected for classification are by definition not specific to any organism. The prediction quality can be assessed by assigned confidence values. It could be shown recently, that the prediction quality for confidence values ≥ 80% is comparable to high-quality manual annotation [14]. Our confidence values give the user a concrete evaluation of the results and a distinct further processing capability when inspecting the annotation at different levels of certainty. The GOPET server predicts both molecular function and biological GO-terms. In future, we plan to predict cellular component terms and to improve the quality of biological process predictions by including protein-protein interaction data.

GOPET is available via Open-HUSAR, (Heidelberg Unix Sequence Analysis Resources) [32].

Contact: genome@dkfz.de