Computer systems and methods for identifying surrogate markers

A computer program product for use in conjunction with a computer system, the computer program product comprising a computer readable storage medium and a computer program mechanism embedded therein, the computer program mechanism comprising:

• a classification module for identifying a set of cellular constituents in a secondary tissue of a species that serves as a surrogate marker for an activity of a target gene expressed in a primary tissue of said species;
• the classification module comprising:
• (a) instructions for constructing a classifier using a cellular constituent level of each cellular constituent in a first plurality of cellular constituents measured in said secondary tissue in each member of a population of said species, wherein said population comprises a first subgroup and a second subgroup, wherein
• said classifier is based on a second plurality of cellular constituents that comprises all or a portion of said first plurality of cellular constituents, and
• respective abundance levels of each cellular constituent in said second plurality of cellular constituents varies between said first subgroup and said second subgroup;
• (b) instructions for classifying all or a portion of said population of said species into a plurality of subtypes using said classifier;
• and
• (c) instructions for identifying one or more cellular constituents that can discriminate members of said population between a first subtype in said plurality of subtypes and a second subtype in said plurality of subtypes.

A computer system for identifying a set of cellular constituents in a secondary tissue of a species that serves as a surrogate marker for an activity of a target gene expressed in a primary tissue of said species, the computer system comprising:

• a central processing unit;
• a memory, coupled to the central processing unit, the memory storing a classification module, the classification module comprising:
• (a) instructions for constructing a classifier using a cellular constituent level of each cellular constituent in a first plurality of cellular constituents measured in said secondary tissue in each member of a population of said species, wherein said population comprises a first subgroup and a second subgroup, wherein
• said classifier is based on a second plurality of cellular constituents that comprises all or a portion of said first plurality of cellular constituents, and
• respective abundance levels of each cellular constituent in said second plurality of cellular constituents varies between said first subgroup and said second subgroup;
• (b) instructions for classifying all or a portion of said population of said species into a plurality of subtypes using said classifier;
• and
• (c) instructions for identifying one or more cellular constituents that can discriminate members of said population between a first subtype in said plurality of subtypes and a second subtype in said plurality of subtypes.