Indeed, 33% of all identified metabolic enzymes are inferred to function in carbohydrate biosynthesis, and the majority are predicted to be localized to the plastid (table 2, supplementary table S1, Supplementary Material online).
If a domain currently classified as non-CM has a higher affinity for CM domains than for other domains, this domain is inferred to have CM function.
As a result, the expression of genes where CISs are inferred to cause loss of function was positively correlated with metagene score (e.g. MYT1L), whereas the expression of genes where CISs are inferred to cause gain of function (e.g. TGIF2, Additional file 2: Figure S1) was negatively correlated.
For example, a novel protein isoform possessing a new domain known to facilitate interactions with signaling proteins of known function can be inferred to potentially interact with these other proteins and function in those signal transduction pathways.
This is recorded as an annotation of a gene at an internal node in the phylogenetic tree and means that the function is inferred to have evolved along the branch leading to that gene.
The amino acid residues directly altering protein functions were inferred according to the locations of substitutions on the functional sites of protein structures.
Sequence information alone may be sufficient to consider a gene to be of interest, because sequence comparison tools that detect protein sequence similarity to previously studied genes often allow a related function to be inferred.
Nonetheless, results on P. falciparum show that the approach has high accuracy and potentially allows a function to be inferred for several unknown genes.
The aim of the present study was to infer functions of previously uncharacterized lineage-specific genes (LSGs) using co-expression, promoter, pathway and network analysis.
For survivorship trials, insects were exposed to x-rays on the head, thorax, or abdomen until they clearly showed a respiratory signature that we infer to be respiratory function damage; otherwise, trials were ended after 2 hrs.
