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1. 发明专利

HU0104050A2 METHODS FOR USING CO-REGULATED GENESETS TO ENHANCE DETECTION AND CLASSIFICATION OF GENE EXPRESSION PATTERNS 未知
公开(公告)号：HU0104050A2
公开(公告)日：2002-03-28
申请号：HU0104050
申请日：1999-10-27
申请人： ROSETTA INPHARMATICS INC
发明人： FRIEND STEPHEN H , HE YUDONG , STOUGHTON ROLAND
IPC分类号： G01N33/50 , C12M1/00 , C12N15/09 , C12P21/04 , C12Q1/68 , C40B30/02 , C40B30/04 , C40B40/02 , C40B50/02 , C40B50/06 , C40B60/12 , G01N33/15 , G01N33/68 , G06F17/10 , G06F17/16 , G06F17/18 , G06F17/30 , G06F19/20 , G06F19/24
摘要： The present invention provides methods for enhanced detection of biological response patterns. In one embodiment of the invention, genes are grouped int o basis genesets according to the co-regulation of their expression. Expressio n of individual genes within a geneset is indicated with a single gene expression value for the geneset by a projection process. The expression values of genesets, rather than the expression of individual genes, are then used as the basis for comparison and detection of biological response with greatly enhanced sensitivity. In another embodiment of the invention, biological responses are grouped according to the similarity of their biological profile. The methods of the invention have many useful applications, particularly in the fields of drug development and discovery. For example, the methods of the invention may be used to compare biological responses with greatly enhanced sensitivity. The biological responses that m ay be compared according to these methods include responses to single perturbations, such as a biological response to a mutation or temperature change, as well as graded perturbations such as titration with a particular drug. The methods are also useful to identify cellular constituents, particularly genes, associated with a particular type of biological response . Further, the methods may also be used to identify perturbations, such as nov el drugs or mutations, which effect one or more particular genesets. The method s may still further be used to remove experimental artifacts in biological response data.

2. 发明专利

AU8675001A Compositions and methods for exon profiling 未知
公开(公告)号：AU8675001A
公开(公告)日：2002-03-04
申请号：AU8675001
申请日：2001-08-24
申请人： ROSETTA INPHARMATICS INC
发明人： SHOEMAKER DANIEL D , SCHERER STEWART , FRIEND STEPHEN H
IPC分类号： C12Q1/68 , C40B40/06 , G06F19/00

3. 发明专利

AU6213500A Iterative probe design and detailed expression profiling with flexible in-situ synthesis arrays 未知
公开(公告)号：AU6213500A
公开(公告)日：2001-02-05
申请号：AU6213500
申请日：2000-07-14
申请人： ROSETTA INPHARMATICS INC
发明人： FRIEND STEPHEN H , STOUGHTON ROLAND , LINSLEY PETER S , BURCHARD JULJA
IPC分类号： C12N15/09 , C12M1/00 , C12Q1/68 , G06F19/20
摘要： Methods and compositions are provided that are useful for detecting and reporting a plurality of different target polynucleotide sequences in a sample, such as polynucleotides corresponding to a plurality of different genes expressed by a cell or cells. In particular, the invention provides methods for screening a plurality of candidate polynucleotide probes to evaluate both the sensitivity and the specificity with which each candidate probe hybridizes to a target polynucleoide sequence. Candidate polynucleotide probes can then be ranked according to both their sensitivity and specificity, and probes that have optimal sensitivity and specificity for a target polynucleotide sequence can be selected. In one embodiment, polynucleotide probes can be selected according to the methods described herein to prepare "screening chips" wherein a large number of target polynucleotide sequences are detected using a single microarray have a few (e.g., 1-5) probes for each target polynucleotide sequence. In a particularly preferred embodiment, the invention provides a screening chip that can detect genetic transcripts from the entire genome of an organism. In an alternative embodiment, polynucleotide probes can be selected according to the methods described herein to prepare "signature chips" to more accurately detect certain selected "signature genes" using several polynucleotide probes (e:g., 10-20) for each signature gene. The invention additionally provides microarrays containing polynucleotide probes for a large number of genes expressed by a cell or organism. Further, methods for detecting a plurality of polynucleotide molecules, including a large number of genes expressed by a cell or organism, are also provided.

4. 发明专利

CA2356891A1 METHODS FOR ROBUST DISCRIMINATION OF PROFILES 未知
公开(公告)号：CA2356891A1
公开(公告)日：2000-07-06
申请号：CA2356891
申请日：1999-12-21
申请人： ROSETTA INPHARMATICS INC
发明人： FRIEND STEPHEN H , STOUGHTON ROLAND
IPC分类号： G01N33/48 , C12N15/09 , C12N15/10 , C12Q1/02 , C12Q1/68 , G01N33/15 , G01N33/50
摘要： Methods for discriminating between the subtle effects of a first perturbatio n and a second perturbation on a biological sample are provided. Further, methods for identifying disease states in patients and methods for optimizin g drug therapy regiments in diseased subjects are provided. Finally, improved methods for determining the subtle effects of pharmacological agents on a biological system are provided.

5. 发明专利

CA2335299A1 METHODS OF MONITORING DISEASE STATES AND THERAPIES USING GENE EXPRESSION PROFILES 未知
公开(公告)号：CA2335299A1
公开(公告)日：1999-12-23
申请号：CA2335299
申请日：1999-06-17
申请人： ROSETTA INPHARMATICS INC
发明人： STOUGHTON ROLAND , FRIEND STEPHEN H
IPC分类号： G01D1/16 , A01N43/04 , A01N61/00 , C07H21/04 , C12M20060101 , C12M1/34 , C12M3/00 , C12N15/09 , C12P21/06 , C12Q1/02 , C12Q1/68 , C12Q1/6886 , G01N33/48 , G01N33/53 , G01N37/00 , G06G7/48
摘要： The present invention provides methods for monitoring disease states in a subject, as well as methods for monitoring the levels of effect of therapies upon a subject having one or more disease states. The methods involve: (i) measuring abundances of cellular constituents in a cell from a subject so th at a diagnostic profile is obtained, (ii) measuring abundances of cellular constituents in a cell of one or more analogous subjects so that perturbatio n response profiles are obtained which correlate to a particular disease or therapy, and (iii) determining the interpolated perturbation response profil e or profiles which best fit the diagnostic profile according to some objectiv e measure. In other aspects, the invention also provides a computer system capable of performing the methods of the invention, data bases comprising perturbation response profiles for one or more diseases and/or therapies, an d kits for determining levels of disease states and/or therapeutic effects according to the methods of the invention.

6. 发明专利

AU774059B2 Methods of determining protein activity levels using gene expression profiles 未知
公开(公告)号：AU774059B2
公开(公告)日：2004-06-17
申请号：AU3789999
申请日：1999-05-07
申请人： ROSETTA INPHARMATICS INC
发明人： FRIEND STEPHEN H , STOUGHTON ROLAND
IPC分类号： G01N33/68 , A61K38/00 , C07K14/47 , C12Q1/68 , G01N33/15 , G01N33/50 , G01N33/53 , G05B1/03
摘要： The present invention provides methods for determining the level of protein activity in a cell by: (i) measuring abundances of cellular constituents in a cell in which the activity of a specific protein is to be determined so that a diagnostic profile is thus obtained; (ii) measuring abundances of cellular constituents that occur in a cell in response to perturbations in the activity of said protein to obtain response profiles and interpolating said response profiles to generate response curves; and (iii) determining a protein activity level at which the response profile extracted from the response curves best fits the measured diagnostic profile, according to some objective measure. In alternative embodiments, the present invention also provides methods for identifying individuals having genetic mutations or polymorphisms that disrupt protein activity, and methods for identifying drug activity in vivo by determining the activity levels of proteins which interact with said drugs.

7. 发明专利

BR9914913A 未知
公开(公告)号：BR9914913A
公开(公告)日：2001-10-16
申请号：BR9914913
申请日：1999-10-27
申请人： ROSETTA INPHARMATICS INC
发明人： FRIEND STEPHEN H , STOUGHTON ROLAND , HE YUDONG
IPC分类号： G01N33/50 , C12M1/00 , C12N15/09 , C12P21/04 , C12Q1/68 , C40B30/02 , C40B30/04 , C40B40/02 , C40B50/02 , C40B50/06 , C40B60/12 , G01N33/15 , G01N33/68 , G06F17/10 , G06F17/16 , G06F17/18 , G06F17/30 , G06F19/20 , G06F19/24
摘要： The present invention provides methods for enhanced detection of biological response patterns. In one embodiment of the invention, genes are grouped int o basis genesets according to the co-regulation of their expression. Expressio n of individual genes within a geneset is indicated with a single gene expression value for the geneset by a projection process. The expression values of genesets, rather than the expression of individual genes, are then used as the basis for comparison and detection of biological response with greatly enhanced sensitivity. In another embodiment of the invention, biological responses are grouped according to the similarity of their biological profile. The methods of the invention have many useful applications, particularly in the fields of drug development and discovery. For example, the methods of the invention may be used to compare biological responses with greatly enhanced sensitivity. The biological responses that m ay be compared according to these methods include responses to single perturbations, such as a biological response to a mutation or temperature change, as well as graded perturbations such as titration with a particular drug. The methods are also useful to identify cellular constituents, particularly genes, associated with a particular type of biological response . Further, the methods may also be used to identify perturbations, such as nov el drugs or mutations, which effect one or more particular genesets. The method s may still further be used to remove experimental artifacts in biological response data.

8. 发明专利

NO20012036D0 未知
公开(公告)号：NO20012036D0
公开(公告)日：2001-04-25
申请号：NO20012036
申请日：2001-04-25
申请人： ROSETTA INPHARMATICS INC
发明人： FRIEND STEPHEN H , STOUGHTON ROLAND , HE YUDONG
IPC分类号： G01N33/50 , C12M1/00 , C12N15/09 , C12P21/04 , C12Q1/68 , C40B30/02 , C40B30/04 , C40B40/02 , C40B50/02 , C40B50/06 , C40B60/12 , G01N33/15 , G01N33/68 , G06F17/10 , G06F17/16 , G06F17/18 , G06F17/30 , G06F19/20 , G06F19/24 , C12Q
摘要： The present invention provides methods for enhanced detection of biological response patterns. In one embodiment of the invention, genes are grouped int o basis genesets according to the co-regulation of their expression. Expressio n of individual genes within a geneset is indicated with a single gene expression value for the geneset by a projection process. The expression values of genesets, rather than the expression of individual genes, are then used as the basis for comparison and detection of biological response with greatly enhanced sensitivity. In another embodiment of the invention, biological responses are grouped according to the similarity of their biological profile. The methods of the invention have many useful applications, particularly in the fields of drug development and discovery. For example, the methods of the invention may be used to compare biological responses with greatly enhanced sensitivity. The biological responses that m ay be compared according to these methods include responses to single perturbations, such as a biological response to a mutation or temperature change, as well as graded perturbations such as titration with a particular drug. The methods are also useful to identify cellular constituents, particularly genes, associated with a particular type of biological response . Further, the methods may also be used to identify perturbations, such as nov el drugs or mutations, which effect one or more particular genesets. The method s may still further be used to remove experimental artifacts in biological response data.

9. 发明专利

CA2348837A1 METHODS FOR USING CO-REGULATED GENESETS TO ENHANCE DETECTIONAND CLASSIFICATION OF GENE EXPRESSION PATTERNS 未知
公开(公告)号：CA2348837A1
公开(公告)日：2000-05-04
申请号：CA2348837
申请日：1999-10-27
申请人： ROSETTA INPHARMATICS INC
发明人： FRIEND STEPHEN H , HE YUDONG , STOUGHTON ROLAND
IPC分类号： G01N33/50 , C12M1/00 , C12N15/09 , C12P21/04 , C12Q1/68 , C40B30/02 , C40B30/04 , C40B40/02 , C40B50/02 , C40B50/06 , C40B60/12 , G01N33/15 , G01N33/68 , G06F17/10 , G06F17/16 , G06F17/18 , G06F17/30 , G06F19/20 , G06F19/24
摘要： The present invention provides methods for enhanced detection of biological response patterns. In one embodiment of the invention, genes are grouped int o basis genesets according to the co-regulation of their expression. Expressio n of individual genes within a geneset is indicated with a single gene expression value for the geneset by a projection process. The expression values of genesets, rather than the expression of individual genes, are then used as the basis for comparison and detection of biological response with greatly enhanced sensitivity. In another embodiment of the invention, biological responses are grouped according to the similarity of their biological profile. The methods of the invention have many useful applications, particularly in the fields of drug development and discovery. For example, the methods of the invention may be used to compare biological responses with greatly enhanced sensitivity. The biological responses that m ay be compared according to these methods include responses to single perturbations, such as a biological response to a mutation or temperature change, as well as graded perturbations such as titration with a particular drug. The methods are also useful to identify cellular constituents, particularly genes, associated with a particular type of biological response . Further, the methods may also be used to identify perturbations, such as nov el drugs or mutations, which effect one or more particular genesets. The method s may still further be used to remove experimental artifacts in biological response data.

10. 发明专利

AU3890699A Methods for identifying pathways of drug action 未知
公开(公告)号：AU3890699A
公开(公告)日：1999-11-29
申请号：AU3890699
申请日：1999-05-07
申请人： ROSETTA INPHARMATICS INC
发明人： FRIEND STEPHEN H , STOUGHTON ROLAND
IPC分类号： G01N33/53 , C12N15/09 , C12Q1/02 , C12Q1/04 , C12Q1/68 , G06F19/12 , C12Q1/00 , A61K48/00 , G06F17/00
摘要： The present invention provides methods and computer systems for identifying and representing the biological pathways of drug action on a cell The present invention also provides methods and computer systems for assessing the significance of the identified representation and for verifying that the identified pathways are actual pathway of drug action. The present invention also provides methods and computer systems for drug development based on the methods for identifying biological pathways of drug action, and methods and computer systems for representing the biological pathways involved in the effect of an environmental change upon a cell.

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