Application of the S-score algorithm for analysis of oligonucleotide microarrays

Methods

Volumn 31, Issue 4, 2003, Pages 274-281

  Kerns, Robnet T ^a   Zhang, Li ^b   Miles, Michael F ^a  

^a VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

^b UNIVERSITY OF TEXAS   (United States)

Author keywords

Data analysis; Gene expression; Oligonucleotide microarrays; S Score

Indexed keywords

ALGORITHM; ANALYTIC METHOD; ANALYTICAL ERROR; ARTICLE; COMPUTER PROGRAM; DATA ANALYSIS; DNA MICROARRAY; DNA PROBE; GENE EXPRESSION; NEUROSCIENCE; PRIORITY JOURNAL; REPRODUCIBILITY; STATISTICAL ANALYSIS; STATISTICAL SIGNIFICANCE;

EID: 0242302283     PISSN: 10462023     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1046-2023(03)00156-7     Document Type: Article

References (41)

1. Zhang L., Wang L., Ravindranathan A., Miles M.F. J. Mol. Biol. 317:2002;225-235.
2. Young R.A. Cell. 102:2000;9-15.
3. Gerhold D., Rushmore T., Caskey C.T. Trends Biochem. Sci. 24:1999;168-173.
4. Lockhart D.J., Winzeler E.A. Nature. 405:2000;827-836.
5. Schena M., Shalon D., Heller R., Chai A., Brown P.O., Davis R.W. Proc. Natl. Acad. Sci. USA. 93:1996;10614-10619.
6. DeRisi J., Penland L., Brown P.O., Bittner M.L., Meltzer P.S., Ray M., Chen Y., Su Y.A., Trent J.M. Nat. Genet. 14:1996;457-460.
7. Shalon D., Smith S.J., Brown P.O. Genome Res. 6:1996;639-645.
8. Schena M., Shalon D., Davis R.W., Brown P.O. Science. 270:1995;467-470.
9. Lockhart D.J., Dong H., Byrne M.C., Follettie M.T., Gallo M.V., Chee M.S., Mittmann M., Wang C., Kobayashi M., Horton H., Brown E.L. Nat. Biotechnol. 14:1996;1675-1680.
10. Golub T.R., Slonim D.K., Tamayo P., Huard C., Gaasenbeek M., Mesirov J.P., Coller H., Loh M.L., Downing J.R., Caligiuri M.A., Bloomfield C.D., Lander E.S. Science. 286:1999;531-537.
11. Hughes T.R., Marton M.J., Jones A.R., Roberts C.J., Stoughton R., Armour C.D., Bennett H.A., Coffey E., Dai H., He Y.D., Kidd M.J., King A.M., Meyer M.R., Slade D., Lum P.Y., Stepaniants S.B., Shoemaker D.D., Gachotte D., Chakraburtty K., Simon J., Bard M., Friend S.H. Cell. 102:2000;109-126.
12. Pease A.C., Solas D., Sullivan E.J., Cronin M.T., Holmes C.P., Fodor S.P. Proc. Natl. Acad. Sci. USA. 91:1994;5022-5026.
13. Hacia J.G., Fan J.B., Ryder O., Jin L., Edgemon K., Ghandour G., Mayer R.A., Sun B., Hsie L., Robbins C.M., Brody L.C., Wang D., Lander E.S., Lipshutz R., Fodor S.P., Collins F.S. Nat. Genet. 22:1999;164-167.
14. Yang Y.H., Dudoit S., Luu P., Lin D.M., Peng V., Ngai J., Speed T.P. Nucleic Acids Res. 30:2002;e15.
15. Bolstad B.M., Irizarry R.A., Astrand M., Speed T.P. Bioinformatics. 19:2003;185-193.
16. Affymetrix (1999) Affymetrix. Available from 〈http://www.affymetrix. com/support/technical/manuals.affx〉.
17. Affymetrix (2001) Affymetrix. Available from 〈http://www.affymetrix. com/support/technical/manuals.affx〉.
18. Li C., Wong W.H. Proc. Natl. Acad. Sci. USA. 98:2001;31-36.
19. Irizarry R.A., Bolstad B.M., Collin F., Cope L.M., Hobbs B., Speed T.P. Nucleic Acids. Res. 31:2003;e15.
20. Eisen M.B., Spellman P.T., Brown P.O., Botstein D. Proc. Natl. Acad. Sci. USA. 95:1998;14863-14868.
21. S. Dudoit, J. Shaffer, J. Boldrick, U.C. Berkeley Division of Biostatistics Working Paper Series, 2002. Available from 〈http://www. bepress.com/ucbbiostat/paper110〉.
22. Tusher V.G., Tibshirani R., Chu G. Proc. Natl. Acad. Sci. USA. 98:2001;5116-5121.
23. Dahlquist K.D., Salomonis N., Vranizan K., Lawlor S.C., Conklin B.R. Nat. Genet. 31:2002;19-20.
24. Doniger S.W., Salomonis N., Dahlquist K.D., Vranizan K., Lawlor S.C., Conklin B.R. Genome Biol. 4:2003;R7.
25. Jenssen T.K., Laegreid A., Komorowski J., Hovig E. Nat. Genet. 28:2001;21-28.
26. Luo Z., Geschwind D.H. Neurobiol. Dis. 8:2001;183-193.
27. Thibault C., Wang L., Zhang L., Miles M.F. Int. Rev. Neurobiol. 48:2001;219-253.
28. Sandberg R., Yasuda R., Pankratz D.G., Carter T.A., Del Rio J.A., Wodicka L., Mayford M., Lockhart D.J., Barlow C. Proc. Natl. Acad. Sci. USA. 97:2000;11038-11043.
29. Geschwind D.H. Proc. Natl. Acad. Sci. USA. 97:2000;10676-10678.
30. Boheler K.R., Stern M.D. Trends Biotechnol. 21:2003;55-57.
31. McConnell S.K. J. Neurosci. 15:1995;6987-6998.
32. Tanabe Y., Jessell T.M. Science. 274:1996;1115-1123.
33. Eberwine J., Yeh H., Miyashiro K., Cao Y., Nair S., Finnell R., Zettel M., Coleman P. Proc. Natl. Acad. Sci. USA. 89:1992;3010-3014.
34. Emmert-Buck M.R., Bonner R.F., Smith P.D., Chuaqui R.F., Zhuang Z., Goldstein S.R., Weiss R.A., Liotta L.A. Science. 274:1996;998-1001.
35. Elliott R.C., Miles M.F., Lowenstein D.H. J. Neurosci. 23:2003;2218-2227.
36. Quackenbush J. Nat. Rev. Genet. 2:2001;418-427.
37. Consortium T.G.O. Genome Res. 11:2001;1425-1433.
38. Kanehisa M., Goto S., Kawashima S., Nakaya A. Nucleic Acids Res. 30:2002;42-46.
39. Wheeler D.L., Church D.M., Federhen S., Lash A.E., Madden T.L., Pontius J.U., Schuler G.D., Schriml L.M., Sequeira E., Tatusova T.A., Wagner L. Nucleic Acids Res. 31:2003;28-33.
40. Diehn M., Sherlock G., Binkley G., Jin H., Matese J.C., Hernandez-Boussard T., Rees C.A., Cherry J.M., Botstein D., Brown P.O., Alizadeh A.A. Nucleic Acids Res. 31:2003;219-223.
41. Edgar R., Domrachev M., Lash A.E. Nucleic Acids Res. 30:2002;207-210.