Limits...
In-depth performance evaluation of PFP and ESG sequence-based function prediction methods in CAFA 2011 experiment.

Chitale M, Khan IK, Kihara D - BMC Bioinformatics (2013)

Bottom Line: The meeting of CAFA was held as a Special Interest Group (SIG) meeting at the Intelligent Systems in Molecular Biology (ISMB) conference in 2011.Successful and unsuccessful predictions by PFP and ESG are also discussed in comparison with BLAST.Since PFP and ESG are based on sequence database search results, our analyses are not only useful for PFP and ESG users but will also shed light on the relationship of the sequence similarity space and functions that can be inferred from the sequences.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science, Purdue University, 305 N, University Street, West Lafayette, Indiana 47907, USA.

ABSTRACT

Background: Many Automatic Function Prediction (AFP) methods were developed to cope with an increasing growth of the number of gene sequences that are available from high throughput sequencing experiments. To support the development of AFP methods, it is essential to have community wide experiments for evaluating performance of existing AFP methods. Critical Assessment of Function Annotation (CAFA) is one such community experiment. The meeting of CAFA was held as a Special Interest Group (SIG) meeting at the Intelligent Systems in Molecular Biology (ISMB) conference in 2011. Here, we perform a detailed analysis of two sequence-based function prediction methods, PFP and ESG, which were developed in our lab, using the predictions submitted to CAFA.

Results: We evaluate PFP and ESG using four different measures in comparison with BLAST, Prior, and GOtcha. In addition to the predictions submitted to CAFA, we further investigate performance of a different scoring function to rank order predictions by PFP as well as PFP/ESG predictions enriched with Priors that simply adds frequently occurring Gene Ontology terms as a part of predictions. Prediction accuracies of each method were also evaluated separately for different functional categories. Successful and unsuccessful predictions by PFP and ESG are also discussed in comparison with BLAST.

Conclusion: The in-depth analysis discussed here will complement the overall assessment by the CAFA organizers. Since PFP and ESG are based on sequence database search results, our analyses are not only useful for PFP and ESG users but will also shed light on the relationship of the sequence similarity space and functions that can be inferred from the sequences.

Show MeSH

Related in: MedlinePlus

Performance of PFP and ESG as compared with Prior, BLAST, and GOtcha using semantic similarity method. A, Semantic similarity relative to the score threshold. Predictions in the BP domain are evaluated; B, semantic precision vs semantic recall for the BP domain; C, Semantic similarity relative to the score threshold in the MF domain; D, semantic precision vs semantic recall for the MF domain.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3584938&req=5

Figure 3: Performance of PFP and ESG as compared with Prior, BLAST, and GOtcha using semantic similarity method. A, Semantic similarity relative to the score threshold. Predictions in the BP domain are evaluated; B, semantic precision vs semantic recall for the BP domain; C, Semantic similarity relative to the score threshold in the MF domain; D, semantic precision vs semantic recall for the MF domain.

Mentions: In Figure 3 the performance of the methods are evaluated in terms of the semantic similarity. The average of the semantic similarity between all pairs of true and predicted GO terms for each method is plotted relative to thresholds in Figure 3A and 3C for the BP and MF domain, respectively. It is shown that ESG's performance is significantly better than the other methods for both BP and MF targets. PFP performance is average among all the teams in this measure. On the other hand, PFP stands out in the semantic precision and recall plots (Figures 3B &3D). ESG comes second in the BP domain (Figure 3B) but shows worst performance among all in the prediction of MF terms (Figure 3D).


In-depth performance evaluation of PFP and ESG sequence-based function prediction methods in CAFA 2011 experiment.

Chitale M, Khan IK, Kihara D - BMC Bioinformatics (2013)

Performance of PFP and ESG as compared with Prior, BLAST, and GOtcha using semantic similarity method. A, Semantic similarity relative to the score threshold. Predictions in the BP domain are evaluated; B, semantic precision vs semantic recall for the BP domain; C, Semantic similarity relative to the score threshold in the MF domain; D, semantic precision vs semantic recall for the MF domain.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3584938&req=5

Figure 3: Performance of PFP and ESG as compared with Prior, BLAST, and GOtcha using semantic similarity method. A, Semantic similarity relative to the score threshold. Predictions in the BP domain are evaluated; B, semantic precision vs semantic recall for the BP domain; C, Semantic similarity relative to the score threshold in the MF domain; D, semantic precision vs semantic recall for the MF domain.
Mentions: In Figure 3 the performance of the methods are evaluated in terms of the semantic similarity. The average of the semantic similarity between all pairs of true and predicted GO terms for each method is plotted relative to thresholds in Figure 3A and 3C for the BP and MF domain, respectively. It is shown that ESG's performance is significantly better than the other methods for both BP and MF targets. PFP performance is average among all the teams in this measure. On the other hand, PFP stands out in the semantic precision and recall plots (Figures 3B &3D). ESG comes second in the BP domain (Figure 3B) but shows worst performance among all in the prediction of MF terms (Figure 3D).

Bottom Line: The meeting of CAFA was held as a Special Interest Group (SIG) meeting at the Intelligent Systems in Molecular Biology (ISMB) conference in 2011.Successful and unsuccessful predictions by PFP and ESG are also discussed in comparison with BLAST.Since PFP and ESG are based on sequence database search results, our analyses are not only useful for PFP and ESG users but will also shed light on the relationship of the sequence similarity space and functions that can be inferred from the sequences.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Computer Science, Purdue University, 305 N, University Street, West Lafayette, Indiana 47907, USA.

ABSTRACT

Background: Many Automatic Function Prediction (AFP) methods were developed to cope with an increasing growth of the number of gene sequences that are available from high throughput sequencing experiments. To support the development of AFP methods, it is essential to have community wide experiments for evaluating performance of existing AFP methods. Critical Assessment of Function Annotation (CAFA) is one such community experiment. The meeting of CAFA was held as a Special Interest Group (SIG) meeting at the Intelligent Systems in Molecular Biology (ISMB) conference in 2011. Here, we perform a detailed analysis of two sequence-based function prediction methods, PFP and ESG, which were developed in our lab, using the predictions submitted to CAFA.

Results: We evaluate PFP and ESG using four different measures in comparison with BLAST, Prior, and GOtcha. In addition to the predictions submitted to CAFA, we further investigate performance of a different scoring function to rank order predictions by PFP as well as PFP/ESG predictions enriched with Priors that simply adds frequently occurring Gene Ontology terms as a part of predictions. Prediction accuracies of each method were also evaluated separately for different functional categories. Successful and unsuccessful predictions by PFP and ESG are also discussed in comparison with BLAST.

Conclusion: The in-depth analysis discussed here will complement the overall assessment by the CAFA organizers. Since PFP and ESG are based on sequence database search results, our analyses are not only useful for PFP and ESG users but will also shed light on the relationship of the sequence similarity space and functions that can be inferred from the sequences.

Show MeSH
Related in: MedlinePlus