Table 1.

Gene Categories Overrepresented in the Set of Genes Detected as Differentially Expressed in TMZ-LTT Compared with TMZ-S Hs683 Cells.

System	Gene Category	List		Population		Ease Score	Bootstrap Score
		Hits	Total	Hits	Total
Biologic process	Amine metabolism	36	588	328	10,937	0.00008	0.006
Biologic process	Amino acid and derivative metabolism	32	588	290	10,937	0.0002	0.01
Biologic process	Amine biosynthesis	14	588	80	10,937	0.0003	0.02
Biologic process	Amino acid metabolism	27	588	252	10,937	0.001	0.07

System refers to the system of categorizing genes (e.g., “Biologic process”) in the databases provided by the Ease software package.

Gene Category refers to the specific category of genes within the System (e.g., “Amine metabolism”).

List Hits refers to the number of genes in the list of differentially expressed genes (list_diff resulting from the microarray data analysis) that belong to the Gene Category. List Total refers to the number of genes in list_diff that belong to any Gene Category within the System.

Population Hits is the number of genes in the total group of genes assayed (list_tot) that belong to the specific Gene Category.

Population Total refers to the number of genes in list_tot that belong to any Gene Category within the System.

The EASE score is the probability value characterizing the change of proportion between the two ratios: population hits/population total and list hits/list total. It constitutes the upper band of the distribution of leave-one-out Fisher exact probabilities computed on these two ratios.

The Bootstrap method is an iteratively running overrepresentation analysis on random gene lists to determine true probability more accurately.