display if the profile of its transcriptional effects is related to the profiles displayed by a group of previously studied compounds the assays of the invention are used to analyze and characterize candidate compounds which have been identified in a primary screen as modulators of the production or activity of a transcription regulatory protein as used herein the terms u201c transcription regulatory protein u201d u201c transcription regulator u201d and u201c transcription factor u201d are interchangeable all referring to a class of proteins whose function is to interact with transcriptional regulatory regions of genes and thus activate or repress or increase or decrease transcription of those genes once a candidate compound has been identified an assay of the invention is performed on a cell population or tissue known to contain the specified transcription regulatory protein the cells or tissues are maintained under conditions that allow for normal cellular processes specifically transcription gene expression to occur in the presence or absence of the candidate compound a gene expression profile is then generated by isolating mrna from the cells then identifying and quantitating each mrna produced by the cells this is typically done through the use of an addressable population of nucleic acids that represent part or all of the expressed gene.