Methods for monitoring the expression of alternatively spliced genes

Abstract

Methods, probe arrays and computer software products are provided for determining the arrangement of sequence elements. In one embodiment, methods for making and using exon chips are provided. The exon chips may be used to identify and quantify splice variants.

1 . A computerized method for analyzing the expression of splice variants comprising: 
 Obtaining probe intensities, wherein the probe intensities reflect the hybridization of nucleic acid probes with various gene structures;    Modeling probe intensities across multiple experiments using gene structures as constraints;    Estimating the levels of the splice variants based upon model parameters.    
   
   
       2 . The method of  claim 1  wherein the model parameters are obtained through maximum likelihood estimation process.  
   
   
       3 . The method of  claim 1  wherein the nucleic acid probes are oligonucleotide probes.  
   
   
       4 . The method of  claim 3  wherein the the oligonucleotide probes are immobilized on a substrate.