Patterns

GenePath is a program that may assist in the construction of genetic pathways from genetic data. In this, it mimics the geneticist by applying a set of patterns that search for specific gene-to-gene or gene-to-biological process relations. The relations include:

• epistasis (two genes act in a linear pathway and one follows the other)
• parallel (two genes act in parallel pathways)
• influences (a gene influences the biological process)
• non-influences (a gene does not influence the biological process)

Patterns are expressed as rules. For instance, the simplest pattern is "IF a mutation in a gene changes the phenotype relative to an otherwise identical strain THEN the gene influences the biological process" which, when applied to genetic data, may find influences relations.

Relations found by GenePath are then used as constraints over the possible genetic networks that can explain the data. While a number of such networks may exist, GenePath proposes a single pathway that accounts for all the epistatic and influences relations.

Here is a list of patterns that are implemented in the current version of GenePath:

Relation Epistasis

Pattern epMut: Assuming a linear pathway, IF two different mutations (of genes A and B) result in two different phenotypes AND the phenotype of the double gene mutation is the same as one of the single gene mutations (B), THEN that single gene mutation (B) is epistatic AND gene B is considered to act after gene A.

Pattern epEss: Assuming a linear pathway, IF two different mutations (of genes A and B) result in two different expression levels of another gene AND the expression of that gene in a strain with a double gene mutation is the same as one of the single gene mutations (B), THEN that single gene mutation (B) is epistatic AND gene B is considered to act after gene A.

Pattern epTC: IF gene A precedes gene B AND gene B precedes gene C THEN gene A precedes gene C. Note: this relation can be applied recursively (Transitive Closure).

Relation Parallel

Pattern parDiff: Two genes are in parallel pathways IF mutations in either gene have an effect on the biological process AND the phenotype of the double mutant is different from the phenotype of either mutation alone.

Pattern parEss: Two genes are in parallel pathways IF mutations in either gene have an effect on some other gene AND the expression of that other gene in the double-mutant is different from either mutation alone.

Pattern parTC: IF genes A and B act in parallel pathways AND genes B and C act in parallel pathways THEN genes A and C also act in parallel pathways. Note: this relation can be applied recursively (Transitive Closure).

Relation Influences

Pattern inf: IF a mutation in a gene changes the phenotype relative to an otherwise identical strain THEN the gene influences the biological process.

Pattern infEss: IF a mutation in a gene A changes the expression of gene B relative to an otherwise identical strain THEN gene A influences gene B.

Pattern infTC: IF gene A precedes gene B AND gene B influences the biological process THEN gene A influences the biological process. Note: this relation can be applied recursively (Transitive Closure).

Relation Non-Influences

Pattern notInf: IF a mutation in a gene does not change the phenotype THEN the gene does not influence the biological process.