Method for detecting transcription factor-protein interactions

Abstract

A method is provided for identifying complexes between a transcription factor and another protein, the method comprising: isolating from a biological sample transcription factor complexes based on whether the transcription factor complexes comprise a particular type of transcription factor; and identifying which of a plurality of different proteins are present in the isolated transcription factor complexes.

1 - 2 . (canceled) 
     
     
         3 . A method for identifying complexes between a transcription factor and another protein, the method comprising:
 isolating from a biological sample transcription factor complexes based on whether the transcription factor complexes comprise a particular type of transcription factor; and   identifying which of a plurality of different proteins are present in the isolated transcription factor complexes;   wherein identifying which of a plurality of different proteins are present in the isolated transcription factor complexes comprises identifying which of a plurality of different non-transcription factor proteins are present in the isolated transcription factor complexes.   
     
     
         4 . A method according to  claim 3  wherein identifying which of a plurality of different proteins are present in the isolated transcription factor complexes comprises detecting which of a plurality of different transcription factor and non-transcription factor proteins are present in the isolated transcription factor complexes. 
     
     
         5 . A method according to  claim 3  wherein isolating transcription factor complexes comprises
 contacting the biological sample with an agent that selectively binds to the particular type of transcription factor; and 
 isolating those transcription factor complexes to which the agent binds. 
 
     
     
         6 . A method according to  claim 3  wherein isolating transcription factor complexes comprises
 contacting the biological sample with an agent that selectively binds to the particular type of transcription factor; 
 precipitating those transcription factor complexes to which the agent binds; and 
 isolating the precipitate. 
 
     
     
         7 . A method according to  claim 3  wherein isolating transcription factor complexes comprises
 contacting the biological sample with an agent immobilized on a solid support that selectively binds to the particular type of transcription factor; and 
 isolating transcription factor complexes immobilized on the solid support through binding to the agent. 
 
     
     
         8 . A method according to  claim 3  wherein isolating transcription factor complexes comprises
 contacting the biological sample with an antibody that selectively binds to the particular type of transcription factor; and 
 isolating those transcription factor complexes to which the antibody binds. 
 
     
     
         9 . A method according to  claim 3  wherein identifying which of a plurality of different types of proteins are present in the isolated transcription factor complexes comprises simultaneously identifying multiple different types of proteins in a same assay. 
     
     
         10 . A method according to  claim 9 , wherein identifying which of a plurality of different proteins are present in the isolated transcription factor complexes comprises detecting which of a plurality of different transcription factor and non-transcription factor proteins are present in the isolated transcription factor complexes, and wherein simultaneously identifying multiple different types of proteins in a same assay is based on a characterization of which different types of transcription factors are present in the isolated transcription factor complexes. 
     
     
         11 . A method according to  claim 9 , wherein identifying which of a plurality of different proteins are present in the isolated transcription factor complexes comprises detecting which of a plurality of different transcription factor and non-transcription factor proteins are present in the isolated transcription factor complexes, and wherein simultaneously identifying multiple different types of proteins in a same assay is based on an identification of transcription factor probes isolated from the isolated transcription factor complexes. 
     
     
         12 . A method according to  claim 9  wherein simultaneously identifying multiple different types of proteins in a same assay comprises simultaneously identifying at least 5 different types of proteins in a same assay. 
     
     
         13 . (canceled) 
     
     
         14 . A method according to  claim 9  wherein simultaneously identifying multiple different types of proteins in a same assay comprises simultaneously identifying at least 20 different types of proteins in a same assay. 
     
     
         15 . (canceled) 
     
     
         16 . A method according to  claim 3  wherein identifying which of a plurality of different types of proteins are present in the isolated transcription factor complexes comprises simultaneously identifying multiple different types of non-transcription factor proteins in a same assay. 
     
     
         17 - 20 . (canceled) 
     
     
         21 . A method for identifying complexes between a transcription factor and another protein, the method comprising:
 isolating from a biological sample transcription factor complexes based on whether the transcription factor complexes comprise a particular type of transcription factor; and   identifying which of a plurality of different proteins are present in the isolated transcription factor complexes by taking an array of immobilized agents capable of binding to the different types of proteins to be identified and contacting the isolated transcription factor complexes with the array under conditions suitable for binding between proteins in the isolated transcription factor complexes and the agents in the array.   
     
     
         22 . A method for identifying complexes between a protein and a plurality of transcription factors, the method comprising:
 isolating from a biological sample transcription factor complexes based on whether the transcription factor complexes comprise a particular type of non-transcription factor protein; and   identifying which of a plurality of different transcription factors are present in the isolated transcription factor complexes.   
     
     
         23 . A method according to  claim 22  wherein isolating transcription factor complexes comprises
 contacting the biological sample with an agent that selectively binds to the particular type of non-transcription factor protein; and 
 isolating those transcription factor complexes to which the agent binds. 
 
     
     
         24 . A method according to  claim 22  wherein isolating transcription factor complexes comprises
 contacting the biological sample with an agent that selectively binds to the particular type of non-transcription factor protein; 
 precipitating those transcription factor complexes to which the agent binds; and 
 isolating the precipitate. 
 
     
     
         25 . A method according to  claim 22  wherein isolating transcription factor complexes comprises
 contacting the biological sample with an agent immobilized on a solid support that selectively binds to the particular type of non-transcription factor protein; and 
 isolating transcription factor complexes immobilized on the solid support through binding to the agent. 
 
     
     
         26 . A method according to  claim 22  wherein isolating transcription factor complexes comprises
 contacting the biological sample with an antibody that selectively binds to the particular type of non-transcription factor protein; and 
 isolating those transcription factor complexes to which the antibody binds. 
 
     
     
         27 . A method according to  claim 22  wherein identifying which of a plurality of different types of transcription factors are present in the isolated transcription factor complexes comprises simultaneously identifying multiple different types of transcription factors in a same assay. 
     
     
         28 . A method according to  claim 27  wherein simultaneously identifying multiple different types of transcription factors in a same assay comprises simultaneously identifying at least 5 different types of transcription factors in a same assay. 
     
     
         29 . (canceled) 
     
     
         30 . A method according to  claim 27  wherein simultaneously identifying multiple different types of transcription factors in a same assay comprises simultaneously identifying at least 20 different types of transcription factors in a same assay. 
     
     
         31 . (canceled)