Methods and systems for determining the biological function of cell constituents using response profiles

• US 7,657,379 B2
• Filed: 07/02/2001
• Issued: 02/02/2010
• Est. Priority Date: 07/05/2000
• Status: Active Grant

• Current Assignee: Microsoft Technology Licensing LLC (Microsoft Corporation)
• Original Assignee: Microsoft Corporation
• Inventors: Stoughton, Roland, Hughes, Timothy R.
• Primary Examiner(s): Clow; Lori A
• Application Number:
  US10/332,305
• Publication Number:
  US 20040048264A1
• Time in Patent Office: 3,137 Days
• Field of Search: None
• US Class Current: 702/19
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2521/107 RNA dependent DNA polymerase,(i.e. reverse transcriptase)
• CPC Class Codes: C12Q 2539/113 Differential Display Analysis [DDA]
• CPC Class Codes: C12Q 2545/114 involving a quantitation step
• CPC Class Codes: C40B 30/04 by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
• CPC Class Codes: G01N 2500/00 Screening for compounds of potential therapeutic value
• CPC Class Codes: G01N 33/5005 involving human or animal cells immunoassay G01N33/56966; immunoassays of protozoa G01N33/56905; protozoa in screening assays C12Q1/025
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/50 Mutagenesis
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/10 Gene or protein expression profiling; Expression-ratio estimation or normalisation
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• CPC Class Codes: G16B 40/30 Unsupervised data analysis

Abstract

The invention relates to methods and systems (e.g., computer systems and computer program products) for determining the biological function of uncharacterized cellular constituents, particularly genes and gene products, by using “response profiles,” i.e., measurements of pluralities of cellular constituents in cells having a modified gene or gene product, as phenotypic markers for the gene or gene product. Methods are provided for clustering such response profiles so that similar or correlated response profiles are organized into the same cluster. The invention also provides databases or “compendiums” of response profiles to which the response profile of an uncharacterized gene or gene product can be compared. In one embodiment, steps of the methods comprise comparing the measured response profiles to response profiles stored in the databases or compendiums, and determining the biological function of the response profiles in the databases that are most similar to the measured response profiles.

Claims

1. A method for determining a biological function of a cellular constituent that is perturbed in one or more landmark response profiles that are most similar to a first response profile, comprising:

(a) receiving a first response profile comprising measured amounts of a plurality of different cellular constituents in a first cell of a cell type or type of organism, said first cell having a first perturbation to said first cellular constituent;

(b) comparing said first response profile to a plurality of landmark response profiles stored in a database to determine a measure of similarity between said first response profile and each said landmark response profile in said plurality of landmark response profiles, each said landmark response profile comprising measured amounts of said plurality of different cellular constituents in a second cell of said cell type or type of organism, said second cell having a second perturbation to a second cellular constituent associated with a known biological function, wherein said plurality of landmark response profiles comprises landmark response profiles corresponding to respective perturbations to at least 118 different genes of a cell of said cell type or type of organism, and wherein said measured amounts in said first response profile and in said plurality of landmark response profiles are all measured amounts of transcripts or are all measured amounts of proteins;

(c) determining one or more landmark response profiles most similar to said first response profile based on the measures of similarity determined in step

(b); and

(d) identifying the known biological function associated with the one or more second cellular constituents that are perturbed in the one or more second cells corresponding to the respective one or more landmark response profiles determined to be most similar to said first response profile in step (c);

wherein steps (a), (b), (c), and (d) are implemented on a suitably programmed computer.

3. The method of claim 1 or 2, wherein the first cellular constituent is a first gene or first gene product.

4. The method of claim 3, wherein the first perturbation to the first cellular constituent comprises a mutation of said first gene.

5. The method of claim 3, wherein the first perturbation to the first cellular constituent comprises modification of abundance of an mRNA transcript of said first gene.

6. The method of claim 3, wherein the first perturbation to the first cellular constituent comprises modification of abundance or activity of said first gene product.

7. The method of claim 1 or 2, wherein said second cellular constituent is a second gene, and wherein the second perturbation to said second cellular constituent comprises a mutation of said second gene.

8. The method of claim 1 or 2, wherein said second cellular constituent is a second gene, and wherein the second perturbation to said second cellular constituent comprises modification of abundance of an mRNA transcript of said second gene.

9. The method of claim 1 or 2, wherein said second cellular constituent is a second gene, and wherein the second perturbation to said second cellular constituent comprises modification of abundance or activity of a gene product of said second gene.

10. The method of claim 1 or 2, wherein said plurality of different cellular constituents in said first response profile and said plurality of landmark response profiles comprises abundances of different mRNA species.

11. The method of claim 10, further comprising obtaining said abundances of different mRNA species by a method comprising measuring abundances of polynucleotide species on a microarray, said microarray comprising:

(a) a surface, and

(b) binding sites for a plurality of polynucleotide species attached to said surface wherein said binding sites are attached to said surface such that the identity of a binding site can be determined from its position on the surface.

12. The method of claim 1 or 2, wherein said plurality of different cellular constituents in said first response profile and said plurality landmark response profiles comprises abundances of different proteins.

13. The method of claim 1 or 2, further comprising identifying the one or more landmark response profiles most similar to the first response profile by a method comprising:

(a) clustering a plurality of response profiles comprising said first response profile and said plurality of landmark response profiles so that response profiles that are correlated are located within a particular cluster; and

(b) identifying landmark response profiles that cluster with the first response profile.

14. The method of claim 13, wherein said clustering is carried out by means of an agglomerative hierarchical clustering algorithm.

15. The method of claim 1 or 2, wherein the measured amounts of the plurality of different cellular constituents in said first response profile are values of measurements of amounts of said plurality of different cellular constituents in said first cell of said cell type or type of organism relative to measurements of amounts of respective cellular constituents in a wild-type cell of said cell type or type of organism, and wherein the measured amounts of the plurality of different cellular constituents in each said landmark response profile are values of measurements of amounts of said plurality of different cellular constituents in said second cell of said cell type or type of organism relative to measurements of amounts of respective cellular constituents in a wild-type cell of said cell type or type of organism.

16. The method of claim 1 or 2, wherein the measured amounts of the plurality of different cellular constituents in said first response profile and the measured amounts of the plurality of different cellular constituents in each said landmark response profile are measurements of absolute amounts of the respective cellular constituents.

17. The method of claim 1 or 2, wherein each of said one or more landmark response profiles determined to be most similar to said first response profile is a consensus profile for perturbation to a cellular constituent associated with said known biological function corresponding to said one or more landmark response profiles determined to be most similar to said first response profile.

18. The method of claim 1 or 2, wherein said comparing said first response profile to said plurality of landmark response profiles comprises clustering said first response profile and said plurality of landmark response profiles, and wherein said determining comprises identifying one or more landmark response profiles in said plurality of landmark response profiles that cluster with said first response profile.

2. A method for determining a biological function of a cellular constituent that is perturbed in one or more landmark response profiles that are most similar to a first response profile, comprising:

(a) comparing a first response profile to a plurality of landmark response profiles stored in a database to determine a measure of similarity between said first response profile and each said landmark response profile in said plurality of landmark response profiles;

wherein said first response profile comprises measured amounts of a plurality of different cellular constituents in a first cell of a cell type or type of organism, said first cell having a first perturbation to said first cellular constituent;

wherein each landmark response profile comprises measured amounts of said plurality of different cellular constituents in a second cell of said cell type or type of organism, said second cell having a second perturbation to a second cellular constituent associated with a known biological function, wherein said plurality of landmark response profiles comprises landmark response profiles corresponding to respective perturbations to at least 118 different genes of a cell of said cell type or type of organism, and wherein said measured amounts in said first response profile and in said plurality of landmark response profiles are all measured amounts of transcripts or are all measured amounts of proteins;

(b) determining one or more landmark response profiles most similar to said first response profile based on the measures of similarity determined in step

(a); and

(c) identifying the known biological function associated with the one or more second cellular constituents that are perturbed in the one or more second cells corresponding to the respective one or more landmark response profiles determined to be most similar to said first response profile in step (b);

wherein steps (a), (b), and (c) are implemented on a suitably programmed computer.

19. A method for characterizing a first cellular constituent as being associated with a particular biological function, comprising:

(a) measuring a first response profile comprising measured amounts of a plurality of different cellular constituents in a first cell of a cell type or type of organism, said first cell having a first perturbation to said first cellular constituent;

(b) clustering a plurality of response profiles, which plurality comprises said first response profile and a plurality of landmark response profiles, each landmark response profile comprising measured amounts of said plurality of different cellular constituents in a second cell of said cell type or type of organism, said second cell having a second perturbation to a second cellular constituent associated with a known biological function, wherein said plurality of landmark response profiles comprises landmark response profiles corresponding to respective perturbations to at least 118 different genes of a cell of said cell type or type of organism, and wherein said measured amounts in said first response profile and in said plurality of landmark response profiles are all measured amounts of transcripts or are all measured amounts of proteins;

(c) identifying one or more landmark response profiles in said plurality of landmark response profiles that cluster with the first response profile; and

(d) characterizing the first cellular constituent as being associated with said known biological function associated with the one or more second cellular constituents that are perturbed in the one or more second cells corresponding to said respective one or more landmark response profiles identified as clustered with said first response profile in step (c).

21. The method of claim 19 or 20, wherein the first cellular constituent is a first gene or first gene product.

22. The method of claim 21, wherein the first perturbation to the first cellular constituent comprises a mutation of said first gene.

23. The method of claim 21, wherein the first perturbation to the first cellular constituent comprises modification of abundance of an mRNA transcript of said first gene.

24. The method of claim 21, wherein the first perturbation to the first cellular constituent comprises modification of abundance or activity of said first gene product.

25. The method of claim 19 or 20, wherein said second cellular constituent is a second gene, and wherein the second perturbation to said second cellular constituent comprises a mutation of said second gene.

26. The method of claim 19 or 20, wherein said second cellular constituent is a second gene, and wherein the second perturbation to said second cellular constituent comprises modification of abundance of an mRNA transcript of said second gene.

27. The method of claim 19 or 20, wherein said second cellular constituent is a second gene, and wherein the second perturbation to the second cellular constituent comprises modification of abundance or activity of a gene product of said second gene.

28. The method of claim 19 or 20, wherein said plurality of different cellular constituents in said first response profile and said plurality of landmark response profiles comprise abundances of different mRNA species.

29. The method of claim 28, wherein said abundances of different mRNA species are obtained by a method comprising measuring abundances of polynucleotide species on a microarray, said microarray comprising:

(a) a surface; and

(b) binding sites for a plurality of polynucleotide species attached to said surface, wherein said binding sites are attached to said surface such that the identity of a binding site can be determined from its position on the surface.

30. The method of claim 19 or 20, wherein the measured amounts of the plurality of different cellular constituents in said first response profile are values of measurements of amounts of said plurality of different cellular constituents in said first cell of said cell type or type of organism relative to measurements of amounts of respective cellular constituents in a wild-type cell of said cell type or type of organism, and wherein the measured amounts of the plurality of different cellular constituents in each said landmark response profile are values of measurements of amounts of said plurality of different cellular constituents in said second cell of said cell type or type of organism relative to measurements of amounts of respective cellular constituents in a wild-type cell of said cell type or type of organism.

31. The method of claim 19 or 20, wherein the measured amounts of the plurality of different cellular constituents in said first response profile and the measured amounts of the plurality of different cellular constituents in each said landmark response profile are measurements of absolute amounts of the respective cellular constituents.

32. The method of claim 19 or 20, wherein said one or more landmark response profiles identified as clustering with said first response profile are one or more consensus profiles for perturbation to a cellular constituent associated with said known biological function corresponding to said one or more landmark response profiles determined to be most similar to said first response profile.

20. A method for characterizing a first cellular constituent as being associated with a particular biological function, comprising:

(a) clustering a plurality of response profiles, which plurality comprises;

(i) a first response profile comprising measured amounts of a plurality of different cellular constituents in a first cell of a cell type or type of organism, said first cell having a first perturbation to said first cellular constituent; and

(ii) a plurality of landmark response profiles, each landmark response profile comprising measured amounts of said plurality of different cellular constituents in a second cell of said cell type or type of organism, said second cell having a second perturbation to a second cellular constituent associated with a known biological function, wherein said plurality of landmark response profiles comprises landmark response profiles corresponding to respective perturbations to at least 118 different genes of a cell of said cell type or type of organism, and wherein said measured amounts in said first response profile and in said plurality of landmark response profiles are all measured amounts of transcripts or are all measured amounts of proteins;

(b) identifying one or more landmark response profiles in said plurality of landmark response profiles that cluster with the first response profile;

(c) characterizing the first cellular constituent as being associated with said known biological function associated with the one or more second cellular constituents that are perturbed in the one or more second cells corresponding to said respective one or more landmark response profiles identified as clustered with said first response profile in step (b); and

(d) identifying the biological function with which said first cellular constituent is associated, as characterized in step (c);

wherein steps (a), (b), (c), and (d) are implemented on a suitably programmed computer.

33. A computer system for identifying a biological function of a cellular constituent that is perturbed in one or more landmark response profiles that are most similar to a first response profile, said computer system comprising:

one or more processor units; and

one or more memory units connected to said one or more processor units, said one or more memory units containing one or more programs which cause said one or more processor units to execute steps comprising;

(a) receiving a data structure for a first response profile comprising measured amounts of a plurality of different cellular constituents in a first cell of a cell type or type of organism, said first cell having a first perturbation to said first cellular constituent;

(b) comparing said first response profile to a plurality of landmark response profiles stored in a database to determine a measure of similarity between said first response profile and each said landmark response profile in said plurality of landmark response profiles, each said landmark response profile comprising measured amounts of said plurality of different cellular constituents in a second cell of said cell type or type of organism, said second cell having a second perturbation to a second cellular constituent associated with a known biological function, wherein said plurality of landmark response profiles comprises landmark response profiles corresponding to respective perturbations to at least 118 different genes of a cell of said cell type or type of organism, and wherein said measured amounts in said first response profile and in said plurality of landmark response profiles are all measured amounts of transcripts or are all measured amounts of proteins;

(c) determining one or more landmark response profiles most similar to said first response profile based on the measures of similarity determined in step (b);

(d) determining the known biological function associated with the one or more second cellular constituents that are perturbed in the one or more second cells corresponding to the respective one or more landmark response profiles determined to be most similar to said first response profile in step (c); and

(e) outputting or displaying the known biological function determined in step (d).

34. The computer system of claim 33, wherein said step (b) of comparing said first response profile to said plurality of landmark response profiles comprises clustering said first response profile and said plurality of landmark response profiles, and wherein said step (c) of determining comprises identifying one or more landmark response profiles in said plurality of landmark response profiles that cluster with said first response profile.

36. The computer system of claim 33 or 35, wherein said programs cause the one or more processor units to carry out said steps of comparing and determining by executing the steps comprising:

(i) clustering a plurality of response profiles comprising said first response profile and said plurality of landmark response profiles so that response profiles that are correlated are located within a particular cluster; and

(ii) identifying landmark response profiles that cluster with the first response profile.

37. The computer system of claim 36, wherein said programs cause the one or more processor units to execute said step of clustering according to an agglomerative hierarchical clustering algorithm.

38. The computer system of claim 33 or 35, wherein the measured amounts of the plurality of different cellular constituents in said first response profile are values of measurements of amounts of said plurality of different cellular constituents in said first cell of said cell type or type of organism relative to measurements of amounts of respective cellular constituents in a wild-type cell of said cell type or type of organism, and wherein the measured amounts of the plurality of different cellular constituents in each said landmark response profile are values of measurements of amounts of said plurality of different cellular constituents in said second cell of said cell type or type of organism relative to measurements of amounts of respective cellular constituents in a wild-type cell of said cell type or type of organism.

39. The computer system of claim 33 or 35, wherein the measured amounts of the plurality of different cellular constituents in said first response profile and the measured amounts of the plurality of different cellular constituents in each said landmark response profile are measurements of absolute amounts of the respective cellular constituents.

35. A computer system for identifying a biological function of a cellular constituent that is perturbed in one or more landmark response profiles that are most similar to a first response profile, said computer system comprising:

one or more processor units; and

one or more memory units connected to said one or more processor units, said one or more memory units containing one or more programs which cause said one or more processor units to execute steps comprising;

(a) comparing a first response profile to a plurality of landmark response profiles stored in a database to determine a measure of similarity between said first response profile and each said landmark response profile in said plurality of landmark response profiles;

wherein said first response profile comprises measured amounts of a plurality of different cellular constituents in a first cell of a cell type or type of organism, said first cell having a first perturbation to said first cellular constituent;

wherein each said landmark response profile comprises measured amounts of said plurality of different cellular constituents in a second cell of said cell type or type of organism, said second cell having a second perturbation to a second cellular constituent associated with a known biological function, wherein said plurality of landmark response profiles comprises landmark response profiles corresponding to respective perturbations to at least 118 different genes of a cell of said cell type or type of organism, and wherein said measured amounts in said first response profile and in said plurality of landmark response profiles are all measured amounts of transcripts or are all measured amounts of proteins;

(b) determining one or more landmark response profiles most similar to said first response profile based on the measures of similarity determined in step (a);

(c) determining the known biological function associated with the one or more second cellular constituents that are perturbed in the one or more second cells corresponding to the respective one or more landmark response profiles determined to be most similar to said first response profile in step (b) and

(d) outputting or displaying the known biological function determined in step (c).

40. The computer system of claim 35, wherein said step (a) of comparing said first response profile to said plurality of landmark response profiles comprises clustering said first response profile and said plurality of landmark response profiles, and wherein said step (b) of determining comprises identifying one or more landmark response profiles in said plurality of landmark response profiles that cluster with said first response profile.

41. A computer program product for use in conjunction with a computer having one or more memory units and one or more processor units, the computer program product comprising a computer readable storage medium having a computer program mechanism encoded thereon, wherein said computer program mechanism can be loaded into the one or more memory units of said computer and cause the one or more processor units of the computer to execute steps comprising:

(a) receiving a data structure for a first response profile comprising measured amounts of a plurality of different cellular constituents in a first cell of a cell type or type of organism, said first cell having a first perturbation to a first cellular constituent; and

(b) comparing said first response profile to a plurality of landmark response profiles stored in a database to determine a measure of similarity between said first response profile and each said landmark response profile in said plurality of landmark response profiles, each landmark response profile comprising measured amounts of said plurality of different cellular constituents in a second cell of said cell type or type of organism, said second cell having a second perturbation in a second cellular constituent associated with a known biological function, wherein said plurality of landmark response profiles comprises landmark response profiles corresponding to respective perturbations to at least 118 different genes of a cell of said cell type or type of organism, and wherein said measured amounts in said first response profile and in said plurality of landmark response profiles are all measured amounts of transcripts or are all measured amounts of proteins;

(c) determining one or more landmark response profiles most similar to said first response profile based on the measures of similarity determined in step (b);

(d) determining the known biological function associated with the one or more second cellular constituents that are perturbed in the one or more second cells corresponding to the respective one or more landmark response profiles determined to be most similar to said first response profile in step (c); and

(e) outputting or displaying the known biological function determined in step (d).

42. The computer program product of claim 41, wherein said step (b) of comparing said first response profile to said plurality of landmark response profiles comprises clustering said first response profile and said plurality of landmark response profiles, and wherein said step (c) of determining comprises identifying one or more landmark response profiles in said plurality of landmark response profiles that cluster with said first response profile.

44. The computer program product of claim 41 or 43, wherein said computer program mechanism can cause the one or more processor units to carry out said steps of comparing and determining by executing the steps comprising:

(i) clustering a plurality of response profiles comprising said first response profile and said plurality of landmark response profiles so that response profiles that are correlated are located within a particular cluster; and

(ii) identifying landmark response profiles that cluster with the first response profile.

45. The computer program product of claim 41 or 43, wherein said computer program mechanism causes the one or more processor units to execute said step of clustering according to an agglomerative hierarchical clustering algorithm.

46. The computer program product of claim 41 or 43, wherein the measured amounts of the plurality of different cellular constituents in said first response profile are values of measurements of amounts of said plurality of different cellular constituents in said first cell of said cell type or type of organism relative to measurements of amounts of respective cellular constituents in a wild-type cell of said cell type or type of organism, and wherein the measured amounts of the plurality of different cellular constituents in each said landmark response profile are values of measurements of amounts of said plurality of different cellular constituents in said second cell of said cell type or type of organism relative to measurements of amounts of respective cellular constituents in a wild-type cell of said cell type or type of organism.

47. The computer program product of claim 41 or 43, wherein the measured amounts of the plurality of different cellular constituents in said response profile and the measured amounts of the plurality of different cellular constituents in each said landmark response profile are measurements of absolute amounts of the respective cellular constituents.

43. A computer program product for use in conjunction with a computer having one or more memory units and one or more processor units, the computer program product comprising a computer readable storage medium having a computer program mechanism encoded thereon, wherein said computer program mechanism can be loaded into the one or more memory units of said computer and cause the one or more processor units of the computer to execute steps comprising:

(a) comparing a first response profile to a plurality of landmark profiles stored in a database to determine a measure of similarity between said first response profile and each said landmark response profile in said plurality of landmark response profiles;

wherein said first response profile comprises measured amounts of a plurality of different cellular constituents in a first cell of a cell type or type of organism, said first cell having a first perturbation to a first cellular constituent;

wherein each landmark response profile comprises measured amounts of said plurality of different cellular constituents in a second cell of said cell type or type of organism, said second cell having a second perturbation to a second cellular constituent associated with a known biological function, wherein said plurality of landmark response profiles comprises landmark response profiles corresponding to respective perturbations to at least 118 different genes of a cell of said cell type or type of organism, and wherein said measured amounts in said first response profile and in said plurality of landmark response profiles are all measured amounts of transcripts or are all measured amounts of proteins;

(b) determining one or more landmark response profiles most similar to said first response profile based on the measures of similarity determined in step (a);

(c) determining the known biological function associated with the one or more second cellular constituents that are perturbed in the one or more second cells corresponding to the respective one or more landmark response profiles determined to be most similar to said first response profile in step (b); and

(d) outputting or displaying the known biological function determined in step (c).

48. The computer program product of claim 43, wherein said step (a) of comparing said first response profile to said plurality of landmark response profiles comprises clustering said first response profile and said plurality of landmark response profiles, and wherein said step (b) of determining comprises identifying one or more landmark response profiles in said plurality of landmark response profiles that cluster with said first response profile.