Bioinformatic Prediction of Gene Ontology Terms of Uncharacterized Proteins from Chromosome 11

In chromosome 11, 71 out of its 1254
proteins remain functionally
uncharacterized on the basis of their existence evidence (uPE1s) following
the latest version of neXtProt (release 2020-01-17). Because in vivo and in vitro experimental strategies are often time-consuming
and labor-intensive, there is a need for a bioinformatics tool to
predict the function annotation. Here, we used I-TASSER/COFACTOR provided
on the neXtProt web site, which predicts gene ontology (GO) terms
based on the 3D structure of the protein. I-TASSER/COFACTOR predicted
2413 GO terms with a benchmark dataset of the 22 proteins belonging
to PE1 of chromosome 11. In this study, we developed a filtering algorithm
in order to select specific GO terms using the GO map generated by
I-TASSER/COFACTOR. As a result, 187 specific GO terms showed a higher
average precision-recall score at the least cellular component term
compared to 2413 predicted GO terms. Next, we applied 65 proteins
belonging to uPE1s of chromosome 11, and then 409 out of 6684 GO terms
survived, where 103 and 142 GO terms of molecular function and biological
process, respectively, were included. Representatively, the cellular
component GO terms of CCDC90B, C11orf52, and the SMAP were predicted
and validated using the overexpression system into 293T cells and
immunofluorescence staining. We will further study their biological
and molecular functions toward the goal of the neXt-CP50 project as
a part of C-HPP. We shared all results and programs in Github (https://github.com/heeyounh/I-TASSER-COFACTOR-filtering.git).