This invention relates generally to analysis of gene expression profiles. In particular, the present invention provides a method for a method for analyzing gene expression profiles of a cell, which method comprises: a) providing for isolated mRNA or cDNA target sequences from a cell; b) sequentially hybridizing said isolated mRNA or cDNA target sequences with a plurality of nucleotide probes; and c) assessing the sequential hybridization between said isolated mRNA or cDNA target sequences and said plurality of nucleotide probes to analyze gene expression profiles of said cell. Systems for analyzing gene expression profiles are also provided. Optical devices for detecting hybridization signal are further provided.