Methods for removing artifact from biological profiles

62 Pages·2013·4.38 MB·English

US006950752B1
United States Patent
(12) (10) Patent N0.: US 6,950,752 B1
Friend et al. (45) Date of Patent: Sep. 27, 2005
(54) METHODS FOR REMOVING ARTIFACT OTHER PUBLICATIONS
FROM BIOLOGICAL PROFILES Anderson et al., 1994, “Involvement of the protein tyrosine
(75) Inventors: Stephen Hi Friend, Philadelphia, PA kinas’e p56lck in T cell signaling and thymocyte develop
(US); Roland Stoughton, San Diego, 2;? ’ Advlgglsm ‘i121 t56'151T1J8M th d C H B- 1 48.31
CA (Us); Yudong He, Kirkland, WA erson, , u agenesis , e o s‘ 'e 10 . .
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( * ) Notice: Subject to any disclaimer, the term of this 2B1'13t3129_3t33(1)' 1996 “C t H. t . . t. d
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U S C 154(k)) b 0 da S subcellular localization With a synthetic ligand that induces
' ' ' y y ' heterodimerization of proteins”, Proc Natl Acad Sci USA
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6,165,709 A 12/2000 Friend et 211.
6,232,066 B1 * 5/2001 Felder et a1. ................ .. 435/6 The invention provides methods for removing unwanted
response components (i.e., “artifacts”) from a measured
FOREIGN PATENT DOCUMENTS biological pro?le comprising measurements of a plurality of
cellular constituents of a cell or organism in response to a
E; g perturbation‘. The methods involve subtracting from the
W0 W0 88/0981() 12/1988 measured biological pro?le one or more artifact patterns,
W0 WO 90/11364 10/1990 each of Which comprises measurements of changes in cel
W0 WO 94/17208 8/1994 lular constituents as a result of deviation of one or more
W0 WO 97/10365 3/1997 experimental variables, such as cell culture density and
W0 WO 97/27317 7/1997 temperature, hybridization temperature, as Well as concen
ag trations of total RNA and/or hybridization reagents, from
W0 WO 98/41531 9/1998 deslred Values‘
W0 WO 99/58720 11/1999 13 Claims, 27 Drawing Sheets
US 6,950,752 B1
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CENESETS ANALYSIS
/
305 j 303
REFINING
BIOLOGICAL
PATHWAY DsEEENIENsTNEDTN
(BASIS VECTOR)
DATA TABLES
307 ‘J
304
PROJECTING
DATABASE
MANAGEMENT
SYSTEM
308 / f“ 313
USER
311
PROJECTED
EXPRESSION
EXPRESSION
PROFILE
PROFILE
312
U.S. Patent Sep. 27,2005 Sheet 4 0f 27 US 6,950,752 B1
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U.S. Patent Sep. 27,2005 Sheet 5 0f 27 US 6,950,752 B1
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