Computer systems and methods for identifying genes and determining pathways associated with traits

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:

• an identification module for identifying members of a biological pathway in a species, comprising:
• (a) instructions for clustering quantitative trait locus data from a plurality of quantitative trait locus analyses to form a quantitative trait locus interaction map, wherein
• each quantitative trait locus analysis in said plurality of quantitative trait locus analyses is performed for a gene in a plurality of genes in the genome of said species using a genetic marker map and a quantitative trait in order to produce said quantitative trait locus data, wherein, for each quantitative trait locus analysis, said quantitative trait comprises an expression statistic for the gene for which the quantitative trait locus analysis has been performed, for each organism in a plurality of organisms that are members of said species;
• and wherein
• said genetic marker map is constructed from a set of genetic markers associated with said species;
• and
• (b) instructions for identifying a cluster of genes in said quantitative trait locus interaction map, thereby identifying members of said biological pathway.

A computer system for associating a gene with a trait exhibited by one or more organisms in a plurality of organisms, the computer system comprising:

• a central processing unit;
• a memory, coupled to the central processing unit, the memory storing an identification module, the identification module for identifying members of a biological pathway in a species, the identification module comprising:
• the clustering module for clustering quantitative trait locus data from a plurality of quantitative trait locus analyses to form a quantitative trait locus interaction map;
• wherein
• (a) instructions for clustering quantitative trait locus data from a plurality of quantitative trait locus analyses to form a quantitative trait locus interaction map, wherein
• each quantitative trait locus analysis in said plurality of quantitative trait locus analyses is performed for a gene in a plurality of genes in the genome of said species using a genetic marker map and a quantitative trait in order to produce said quantitative trait locus data, wherein, for each quantitative trait locus analysis, said quantitative trait comprises an expression statistic for the gene for which the quantitative trait locus analysis has been performed, for each organism in a plurality of organisms that are members of said species;
• and wherein
• said genetic marker map is constructed from a set of genetic markers associated with said species;
• and
• (b) instructions for identifying a cluster of genes in said quantitative trait locus interaction map, thereby identifying members of said biological pathway.

A computer system for identifying members of a biological pathway in a species, the computer system comprising:

• a central processing unit;
• a memory, coupled to the central processing unit, the memory storing an identification module and a database;
• the database for storing quantitative trait locus data from a plurality of quantitative trait locus analyses;
• each quantitative trait locus analysis in said plurality of quantitative trait locus analyses is performed for a gene in a plurality of genes in the genome of said species using a genetic marker map and a quantitative trait in order to produce said quantitative trait locus data, wherein, for each quantitative trait locus analysis, said quantitative trait comprises an expression statistic for the gene, for which the quantitative trait locus analysis is performed, from each organism in a plurality of organisms that are members of said speices;
• and wherein said genetic marker map is constructed from a set of genetic markers associated with said species;
• and
• the identification module for clustering said quantitative trait locus data stored in said database to form a quantitative trait locus interaction map;
• wherein a cluster of genes in said quantitative trait locus interaction map is identified, thereby identifying members of said biological pathway.