We considered the top 950 most-populated EC numbers in terms of available structures, with at least 9 representatives per class, in a total of 55,474 chains, which covered 95% of the reviewed enzymes from Uniprot [ 1], i.e., the experimentally validated annotations from that database.
The genes, transcripts, and variants that were selected for qPCR validation (Table 6) include a range of expression levels and targeted functional annotations (from Blast2GO) that indicate potential roles in xenobiotic metabolism.
The initial build was further subjected to (1) mapping annotations against the Uniprot features and annotations, (2) picking up annotations from KEGG that were missed by our pipeline, (3) second-level pruning for species filters, (4) manual quality control and (5) manual curation of new and existing pathways to integrate rice specific data,and literature citations.
For this, we extracted annotations from entries that appeared for the first time in a given database version.
We then tested all the keyword annotations (from UniProt) that are most statistically significant according to their P-value (P-value is calculated according to the hypergeometric distribution and corrected by Bonferroni correction for multiple hypothesis testing).
Importantly, the YGOB database contains accurate ortholog annotations from species that predate and postdate the WGD event, as well as an accurate annotation of hundreds of such 'trap groups', allowing us to compare algorithm performance against orthogroup sets that are much more challenging to decipher.
Persistence is used to prevent a phylotype from having a direct root descendant with annotation different from that of the root.
However, they were sensitive to the reference transcriptome, with the regulated genes found based on the Ensembl annotation differing from that obtained from RefSeq or UCSC.
One example of how our manual annotation differed from that of the automated pipeline used by Brown et al. can be found in the case of CLAU_3519 CAETHG_36099).
EC numbers for proteins of known function were those from the proteins' PDB files, except for proteins from the Toronto functional annotation pipeline, whose annotations were taken from that publication [12].
In a study of several functionally diverse superfamilies, Schnoes, Babbitt, and co-workers concluded that 85% of misannotations resulted from annotations that are more detailed than justified.
