System and method for analyzing gene expression data

A method for determining sequence variations using gene expression arrays wherein the gene expression arrays comprise a plurality of oligonucleotide fragments of one or more expressed genes, the method comprising:

• analyzing a first nucleotide population using a first expression array to produce a first binding pattern;
• analyzing a second nucleotide population using a second expression array to produce a second binding pattern;
• and
• identifying differences between the first binding pattern and the second binding pattern to determine binding differences between the first nucleotide population and second nucleotide population.

A method for identifying sequence variations between a first and second nucleotide population using gene expression arrays, the method comprising:

• interacting the first nucleotide population with a first expression array to generate a first binding pattern;
• interacting the second nucleotide population with a second expression array to generate a second binding pattern;
• scaling the first and second binding patterns with respect to one another to create a first and second normalized binding pattern;
• and
• identifying differences between the first and the second normalized binding patterns indicative of sequence variations between the first and the second nucleotide populations.

A method for identifying sequence variations between a first and second nucleotide sequence using binding information obtained from oligonucleotide array analysis, the method comprising:

• obtaining binding information from oligonucleotide array analysis using at least two nucleotides wherein a first nucleotide contains a first expressed nucleotide sequence having a first binding pattern and a second nucleotide contains a second expressed nucleotide sequence having a second binding pattern;
• normalizing the binding patterns to produce a first scaled binding pattern and a second scaled binding pattern;
• comparing the first scaled binding pattern and the second scaled binding pattern to identify differences between the scaled binding patterns;
• and
• associating the differences with sequence variations between the first and the second expressed nucleotide sequence.

A method for identifying sequence variations using expression pattern differences, the method comprising:

• identifying a first expression pattern for a first nucleotide strand and a second expression pattern for a second nucleotide strand wherein the first and second expression patterns are obtained by annealing the first and second nucleotide strands with a complimentary probe set;
• comparing the first expression pattern and the second expression pattern and identifying differences between the binding of the first nucleotide strand with the complimentary probe set and the binding of the second nucleotide strand with the complimentary probe set;
• and
• identifying sequence variations between the first nucleotide strand and the second nucleotide strand based upon the binding differences.