An empirical analysis based on a carefully curated dataset would thus be a great complement to this study.
The hand curated dataset was constructed using two parallel approaches: The entire PDB was searched using Dockground server [23] in order to collect protein-protein complexes.
The GEO curated dataset (GSE9476, of type HG-U133A) contained 64 samples, 38 from healthy donors and 26 from AML patients.
Further, statistical analysis is performed using GO curated dataset as ground truth.
This curated dataset allowed biomedical researchers to rapidly query, visualize, and analyze the entirety of the yeast literature for biological interactions.
The YGOB curated dataset for 11 yeast species is a reliable way to obtain orthologs, but this kind of database is not available for most species.
Our software achieved a high classification performance when used to evaluate a curated dataset of Trypanosoma brucei paralogs previously surveyed for positive selection.
We hope that the new figures, the added results and new organization of the manuscript helped to bring out how valuable VirSorter curated dataset is, and what insights into virus-host interactions were obtained.
We also performed an RRT on a carefully curated dataset consisting of 623 orthologous genes, in which caecilian, frog and human were used as the ingroups and coelacanth was used as the outgroup.
Our results provide a summary of specific, consistent differences in particular proteins, which may be valuable for internal review to improve the manually curated dataset and to identify targets for improvement of NCBI's genome annotation pipeline.
The full data set can be viewed as supplementary materials in both PSI-MI 2.5 XML or MITAB2.5 formats or can be viewed as a fully curated dataset in the IntAct database (EBI-914159, EBI-914232, EBI-914360).
