The observed median AUC is 56% averaged across all species and functional classes, and is higher for some important functional classes such as intermediary metabolism, DNA metabolism, and transport and binding proteins.
The set of median-ranked genes has good coverage of all important functional classes compared to the top and bottom-ranked genes, so using their concatenation for phylogenetic inference potentially avoids systematic biases that can be caused by having a concentration of genes in the ranked list for some particular functional class.
The larger comparative data set, used to define important functional classes for viruses, includes protein sequences from completely sequenced plasmids (all available at NCBI) and a phylogenetically balanced selection of cellular organisms from all of life, resulting in a total of 740,842 sequences.
We predicted 106 aligned nonidentical residues to be in the same functional class (38 were functionally important).
The classification of genes into gene families by Human Gene Nomenclature Committee (HGNC) on the basis of sequence similarity of the encoded proteins [ 4] and the availability of human genome sequence [ 5] allow us to carry out a comprehensive survey of a class of important functional element, namely the (TG/CA)n repeats.
In the enriched functions of slow-evolving genes, we found a number of important house-keeping functional classes, including transcription, mRNA processing/splicing, translation, protein modification, metabolism, protein traffic, cell cycle, development and endocytosis (Table 1).
Including regulators of GTPases or MHC class proteins has important functional significance and should be included in gene set analysis and functional cohesion determinations.
Maternal functional class is an important predictor of outcome; a high index of suspicion for cardiac diseases is essential to identify risk [ 1], once these patients are referred for a cardiologic opinion there is a needed for cardiologist to develop a systematic approach to their evaluation.
Fructooligosaccharides (FOS) represent a major class of prebiotics and have been classified as important functional food ingredients due to their well-recognized nutritional and health benefits (Vancova et al. 2008; Wang 2015).
We have noticed that most of the genes included in this functional class can also drive neural connectivity remodelling in larvae, a process particularly important during metamorphosis.
It is also important to note that we do not merely give annotations but also provide a measure for each functional class that states how probable it is that the query protein is a member of that class.
