Claims
- 1. 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.
- 2. A method according to claim 1 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 transcription factors are present in the isolated transcription factor complexes.
- 3. A method according to claim 1 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 1 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 1 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 1 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 1 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 1 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 1 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 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 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. A method according to claim 9 wherein simultaneously identifying multiple different types of proteins in a same assay comprises simultaneously identifying at least 10 different types of proteins in a same assay.
- 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. A method according to claim 9 wherein simultaneously identifying multiple different types of proteins in a same assay comprises simultaneously identifying at least 50 different types of proteins in a same assay.
- 16. A method according to claim 1 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. A method according to claim 2, wherein
prior to isolating transcription factor complexes, the method further comprises contacting the biological sample with a library of transcription factor probes under conditions where transcription factor probe—transcription factor complexes are formed between the transcription factor probes and activated transcription factors present in the biological sample; and identifying which of a plurality of different types of transcription factors are present in the isolated transcription factor complexes comprises identifying which transcription factor probes are present in the isolated transcription factor complexes.
- 18. A method according to claim 2,
wherein prior to isolating transcription factor complexes, the method further comprises
taking a library of transcription factor probes, the transcription factor probes each comprising a recognition sequence capable of binding to an activated transcription factor, the recognition sequence varying within the library for binding to different activated transcription factors, and contacting the biological sample with the library of transcription factor probes under conditions where transcription factor probe—transcription factor complexes are formed between the transcription factor probes and activated transcription factors present in the biological sample; and wherein identifying which of a plurality of different types of transcription factors are present in the isolated transcription factor complexes comprises identifying which transcription factor probes are present in the isolated transcription factor complexes.
- 19. A method according to claim 2wherein prior to selectively isolating transcription factor complexes, the method further comprises
taking a library of transcription factor probes, the transcription factor probes each comprising a recognition sequence capable of binding to an activated transcription factor, the recognition sequence varying within the library for binding to different activated transcription factors, and contacting a biological sample with the library of transcription factor probes under conditions where transcription factor probe—transcription factor complexes are formed between the transcription factor probes and activated transcription factors present in the biological sample; and wherein identifying which of a plurality of different types of transcription factors are present in the isolated transcription factor complexes comprises taking an array of immobilized hybridization probes capable of hybridizing to the transcription factor probes in the library and contacting the isolated transcription factor probes with the array under conditions suitable for hybridization of the different transcription factor probes to the hybridization probes in the array.
- 20. A method according to claim 2 wherein identifying which of a plurality of different types of transcription factors are present in the isolated transcription factor complexes comprises taking an array of immobilized transcription factor probes capable of binding to the different types of transcription factors to be identified and contacting the isolated transcription factor complexes with the array under conditions suitable for binding between the transcription factors in the isolated transcription factor complexes and the transcription factor probes in the array.
- 21. A method according to claim 1 wherein identifying which of a plurality of different types of proteins are present in the isolated transcription factor complexes comprises 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. A method according to claim 27 wherein simultaneously identifying multiple different types of transcription factors in a same assay comprises simultaneously identifying at least 10 different types of transcription factors in a same assay.
- 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. A method according to claim 27 wherein simultaneously identifying multiple different types of transcription factors in a same assay comprises simultaneously identifying at least 50 different types of transcription factors in a same assay.
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a continuation in part of application Ser. Nos. 09/877,738, 09/877,243, 09/877,403, and 09/877,705, each filed on Jun. 8, 2001, each of which are incorporated herein by reference.
Continuation in Parts (4)
|
Number |
Date |
Country |
Parent |
09877738 |
Jun 2001 |
US |
Child |
09947274 |
Sep 2001 |
US |
Parent |
09877243 |
Jun 2001 |
US |
Child |
09947274 |
Sep 2001 |
US |
Parent |
09877403 |
Jun 2001 |
US |
Child |
09947274 |
Sep 2001 |
US |
Parent |
09877705 |
Jun 2001 |
US |
Child |
09947274 |
Sep 2001 |
US |