Dissection of Genetic Pathways in C. elegans - Caenorhabditis Elegans: Molecular Genetics and Development - page 143

Fig. 9 Consideration regarding alleles used for epistatic analysis (i) Normally, gene B negatively
regulates a functional state (illustrated as a bulb with light), causing the inactivation of this state
(illustrated as a bulb without light). Gene A, however, acts upstream of gene B in this pathway and
negatively regulates it, thereby maintaining the functional state. (ii) Complete loss of gene B activity
abolishes its negative regulatory effects on the functional state (''light on''). In contrast, complete loss of
gene A activity removes its negative regulation on gene B, releasing gene B inhibitory effects on the
functional state, therefore inactivating the functional state (''no light''). The single mutants of gene B
and A display the opposite phenotypes, which makes epistasis analysis applicable for organizing genes
B and A. (iii) When one performs epistasis analysis using the null allele of gene A and the hypomorphic
allele for gene B, the constructed double mutant might inactivate the functional state as the hypomorphic
allele of gene B preserves some residual inhibitory activity. Thus, the possible phenotype of this double
mutant (''no light'') would be similar to that of the single null of gene A (''no light''), leading to a
misinterpretation that gene A is epistatic to (downstream of) gene B. Using null alleles of both genes A and
B, however, reveals the correct epistatic relationship of gene B downstream of gene A. (For color version
of this figure, the reader is referred to the web version of this topic.)
C. Properties of Gene Products for Gene Ordering
The properties of proteins, including conserved function of their homologs/ortho-
logs, site of action, and cellular/subcellular localization, are also useful for ordering
genes into pathways. Comparative genomic analysis based on sequence homology and
conservation across species can be used to deduce the potential functions of genes
identified from screens. This information can provide clues for gene ordering. For
example, in the case of two genes with the same phenotype when mutated, if a gene A
is predicted to encode a potential transmembrane receptor and gene B encodes a
potential cytoplasmic signaling transducer, this suggests that gene A likely acts
upstream of gene B in a pathway, a hypothesis that can be further tested with cell
biological analysis. If this hierarchical relationship between genes A and B is also
conserved in other species, it would make this conclusion more solid. A good example