We stress that our results do not depend on whether one believes that multifunctionality is a true property of genes reflected in the patterns of annotation, or some kind of artifact of how genes are studied and annotated.
After the map's arrival at the Bodleian Library, it was studied and annotated in Latin in 1687 by the librarian Thomas Hyde with the help of a Chinese Jesuit convert Michael Shen Fuzong who had arrived at the court of James II from China.
Typically, all genes associated with the function being studied and annotated as such in the GO database, are included in the training set as positive samples.
As a result, it is well studied and annotated datasets are readily available.
Most identified hub genes, however, haven't been studied or annotated, albeit their potential important roles in embryo development.
These results are clearly biased towards organisms whose genome has been largely and deeply studied and annotated, mainly because of the higher quality of genome assemblies, of the more accurate gene predictions and of the higher number of protein sequences deposited in public sequence databases.
Of these, the largest proportion (43%) were in S. bayanus, which is still relatively poorly studied and annotated [ 13, 20].
While several genes have been studied previously and have been annotated in depth, including introns, exons and flanking regions, the vast majority of gene annotations do not have such a well defined structure and therefore we employed the following convention to annotate the genome.
Wrapper induction specifically has been studied extensively, where users annotate a couple of data sources with examples of the data they want, after which a procedure (wrapper) is constructed that can optimally extract similar data as well.
We have assessed the quality of the predicted modules that contain the known CESA genes responsible for secondary wall cellulose, namely CESA4, CESA7 and CESA8, which have been widely studied and well annotated [ 12, 13, 23].
