fix: existing geneRules based on latest gene annotation

[hongzhonglu]

Compared with the latest genome annotation, it can be found that there existed obvious errors in some gene-relations . It is essential to correct them in this round of update.

[hongzhonglu]

@BenjaSanchez one comment: this issue will focus on the gene relation check in present model based on the latest genome annotation.

[hongzhonglu]

@edkerk @BenjaSanchez @feiranl
In BioGRID database, we can find the different interaction between two genes for the yeast, which could help to check the gene relation in our model, however there are so many kinds of relations between two genes:
Dosage Growth Defect - A genetic interaction is inferred when over expression or increased dosage of one gene causes a growth defect in a strain that is mutated or deleted for another gene.
Dosage Lethality - A genetic interaction is inferred when over expression or increased dosage of one gene causes lethality in a strain that is mutated or deleted for another gene.
Dosage Rescue - A genetic interaction is inferred when over expression or increased dosage of one gene rescues the lethality or growth defect of a strain that is mutated or deleted for another gene.
Negative Genetic - Mutations/deletions in separate genes, each of which alone causes a minimal phenotype, but when combined in the same cell results in a more severe fitness defect or lethality under a given condition. This term is reserved for high or low throughput studies with scores.
Phenotypic Enhancement - A genetic interaction is inferred when mutation or overexpression of one gene results in enhancement of any phenotype (other than lethality/growth defect) associated with mutation or over expression of another gene.
Phenotypic Suppression - A genetic interaction is inferred when mutation or over expression of one gene results in suppression of any phenotype (other than lethality/growth defect) associated with mutation or over expression of another gene.
Positive Genetic - Mutations/deletions in separate genes, each of which alone causes a minimal phenotype, but when combined in the same cell results in a less severe fitness defect than expected under a given condition. This term is reserved for high or low throughput studies with scores.
Synthetic Growth Defect - A genetic interaction is inferred when mutations in separate genes, each of which alone causes a minimal phenotype, result in a significant growth defect under a given condition when combined in the same cell.
Synthetic Haploinsufficiency - A genetic interaction is inferred when mutations or deletions in separate genes, at least one of which is hemizygous, cause a minimal phenotype alone but result in lethality when combined in the same cell under a given condition.
Synthetic Lethality - A genetic interaction is inferred when mutations or deletions in separate genes, each of which alone causes a minimal phenotype, result in lethality when combined in the same cell under a given condition.
Synthetic Rescue - A genetic interaction is inferred when mutations or deletions of one gene rescues the lethality or growth defect of a strain mutated or deleted for another gene.

Do you have any idea about how to establish these gene interaction with "or" ,"and" relation of gene in our model?