Patent ID: 7807447

Claim:
A method for analyzing expression levels of different exon variants of a plurality of different genes in the genome of an organism in a cell sample derived from said organism, said method comprising measuring, in vitro, the expression levels of said different exon variants, each of said different exon variants being a different splicing variant of each of said plurality of different genes generated using a different 3′ or 5′ splicing site located in each of said plurality of different genes; and wherein said measuring step is performed by a method comprising: (a) contacting a positionally-addressable array of polynucleotide probes with a nucleic acid sample comprising RNAs from said cell sample or cDNAs transcripted from said RNAs under conditions conducive to hybridizations between said probes and said RNAs or said cDNAs, wherein said array comprises a plurality of polynucleotide probes comprising different nucleotide sequences, wherein said plurality of polynucleotide probes are bound to different regions of said array and comprises variant junction probes that specifically hybridize to said different exon variants and each of said variant junction probes is complementary and hybridizes to a junction region of two adjacent exons of one of said variants from said cDNAs; and (b) measuring levels of hybridizations between said variant junction probes and said RNAs or said cDNAs and analyzing the expression levels of said exon variants based on said levels of hybridizations.