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SPM is a statistical parameter introduced as a sensitive indicator in quantitative estimation of gene expression patterns.Each gene expression profile of gene x is transformed into a vector X_p
where n is the number of samples in the profile and x_iis the gene expression level in sample i. For each element in the profile X, the expression x_ican also be represented by a vector X_i in high dimension feature space:

The SPM of a gene in a sample was then determined by calculating the cosine value of intersection angle Θ between vector X_i and X_p in high dimension feature space:

Theoretically, the SPM ranges from 0 to 1.0. A value close to 1.0 indicates that element xi is the major contributor to the length of profile Xp in high dimension feature space; in biological term, high sample specificity.

r_i is a parameter to measure fractional gene expression in a definite sample i against the whole gene expression profile. The ri was calculated by:

SUM is the sum of fractional expressions in selective samples. The SUM was calculated by:

The Contribution Measure (CTM) is a parameter developed to help identification of selective genes. The CTM was calculated by:
where k is the number of selective samples.
Theoretically, the CTM ranges from 0 to 1.0. In biology, a CTM value close to 1.0 suggests gene expressions are enriched in selective samples (normally 2 < SampleNum(k) < 4) comparing to that in other samples.

The DPM, in principle, is to map the standard deviation of a gene expression profile into a region of 0 to 1.0. The gene expression profile (Xp) is first converted to its corresponding SPM profile (X_SPM):

Then, the DPM is determined by:

Theoretically, the DPM ranges from 0 to 1.0. In biology, a DPM value close to 0 suggests that gene evenly expresses in all samples of a gene expression profile.

The Repression Measure (RPM) is a parameter for identification of repressed genes.The gene expression profile in multiple samples were roughly divided into two groups according to their expression levels: the putative repressed expressions and the expressions. Then the RPM was calculated by:

where the "SPMrep_max" stands for the maximum SPM value in the putative repressed expression group and "SPMexp_min" stands for minimun SPM value in the expression group, and k is the number of repressed samples.
Theoretically, the RPM ranges from 0 to 1.0. A RPM value close to 0 indicates high degree of difference between repression group and expression group.

Genes that specifically express in only one sample. Noramlly, specific gene has a high SPM value, e.g. SPM > 0.9.

The selective genes are a group of genes whose expressions are enriched in only several conditions (samples). Normally, gene expressions are enriched in limited (e.g. 2 < SampleNum(k) < 4) samples (e.g. CTM > 0.9), and expressions in each of the selective samples are comparatively high (e.g. SPMi > 0.3).

Housekeeping genes are generally defined as genes that express ubiquitously in all conditions. In strict sense, housekeeping genes evenly express in all samples (e.g. DPM < 0.3).

Genes are expressed in almost all conditions except in one or several conditions. Normally, gene expressions are repressed in limited (e.g. 1 < SampleNum(k) < 4) samples (e.g. SPM < 0.1 and RPM< 0.2).