Skip to main content

Table 1 Parameters of the Hypergeometic test for the seven constructed biological annotations.

From: YAGM: a web tool for mining associated genes in yeast based on diverse biological associations

Biological Association

Parameters of the Hypergeometric Test

TF Regulation/TF Binding

N: # of TFs collected from YEASTRACT

n: # of TFs that regulate/bind to gene a

m: # of TFs that regulate/bind to gene b

k: # of TFs that regulate/bind to both gene a and gene b

Mutant Phenotype/Literature Evidence

N: # of mutant phenotypes/literature evidences collected from SGD

n: # of mutant phenotypes/literature evidences of gene a

m: # of mutant phenotypes/literature evidences of gene b

k: # of mutant phenotypes/literature evidences of both gene a and gene b

Functional Annotation

N: # of functional annotations collected from MIPS

n: # of functional annotations of gene a

m: # of functional annotations of gene b

k: # of functional annotations of both gene a and gene b

Physical Interaction/Genetic Interaction

N: # of genes in the yeast genome

n: # of genes that have physical/genetic interactions with gene a

m: # of genes that have physical/genetic interactions with gene b

k: # of genes that have physical/genetic interactions with both gene a and gene b