WO2001021839A3 - Gene expression profiles - Google Patents

Gene expression profiles Download PDF

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Publication number
WO2001021839A3
WO2001021839A3 PCT/US2000/026055 US0026055W WO0121839A3 WO 2001021839 A3 WO2001021839 A3 WO 2001021839A3 US 0026055 W US0026055 W US 0026055W WO 0121839 A3 WO0121839 A3 WO 0121839A3
Authority
WO
WIPO (PCT)
Prior art keywords
expression profiles
gene expression
identification
pathogens
drug compounds
Prior art date
Application number
PCT/US2000/026055
Other languages
French (fr)
Other versions
WO2001021839A2 (en
Inventor
Jennifer M Fostel
Gary F Bammert
Original Assignee
Upjohn Co
Jennifer M Fostel
Gary F Bammert
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Upjohn Co, Jennifer M Fostel, Gary F Bammert filed Critical Upjohn Co
Priority to AU76061/00A priority Critical patent/AU7606100A/en
Publication of WO2001021839A2 publication Critical patent/WO2001021839A2/en
Publication of WO2001021839A3 publication Critical patent/WO2001021839A3/en

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/136—Screening for pharmacological compounds
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression

Landscapes

  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Physics & Mathematics (AREA)
  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Molecular Biology (AREA)
  • Organic Chemistry (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Analytical Chemistry (AREA)
  • Zoology (AREA)
  • Theoretical Computer Science (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Medical Informatics (AREA)
  • Evolutionary Biology (AREA)
  • Wood Science & Technology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Microbiology (AREA)
  • Immunology (AREA)
  • Pathology (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

This invention provides a simplified method of analysis of data generated by microarrays permitting those of skill in the art to generate expression profiles of pathogens. The methods of the invention allow the rapid screening of candidate drug compounds, identification of drug candidates predicted to be effective against particular pathogens, and identification of genes involved in the pathway affected by such drug compounds.
PCT/US2000/026055 1999-09-24 2000-09-22 Gene expression profiles WO2001021839A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU76061/00A AU7606100A (en) 1999-09-24 2000-09-22 Gene expression profiles

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US15605099P 1999-09-24 1999-09-24
US60/156,050 1999-09-24
US20902600P 2000-06-02 2000-06-02
US60/209,026 2000-06-02

Publications (2)

Publication Number Publication Date
WO2001021839A2 WO2001021839A2 (en) 2001-03-29
WO2001021839A3 true WO2001021839A3 (en) 2002-01-17

Family

ID=26852821

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2000/026055 WO2001021839A2 (en) 1999-09-24 2000-09-22 Gene expression profiles

Country Status (2)

Country Link
AU (1) AU7606100A (en)
WO (1) WO2001021839A2 (en)

Families Citing this family (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7031846B2 (en) 2001-08-16 2006-04-18 Affymetrix, Inc. Method, system, and computer software for the presentation and storage of analysis results
CA2469695A1 (en) * 2001-12-06 2003-06-19 Paradigm Genetics, Inc. Methods for the identification of inhibitors of asparagine synthase, 5-aminolevulinate synthase, histidinol-phosphatase, 3-isopropylmalate and threonine synthase as antibiotics
US6689578B2 (en) * 2001-12-06 2004-02-10 Paradigm Genetics, Inc. Methods for the identification of inhibitors of 5-aminolevulinate synthase as antibiotics
US20040142351A1 (en) * 2002-10-24 2004-07-22 Oklahoma Medical Research Foundation Associative analysis of gene expression array data
US8594942B2 (en) * 2004-07-30 2013-11-26 Metabolon, Inc. Computational method and system for identifying network patterns in complex biological systems data
US8200440B2 (en) 2007-05-18 2012-06-12 Affymetrix, Inc. System, method, and computer software product for genotype determination using probe array data
AU2011220736C1 (en) * 2010-02-24 2014-12-18 The Broad Institute, Inc Methods of diagnosing infectious disease pathogens and their drug sensitivity
CN112662800B (en) * 2020-12-28 2022-12-20 广西大学 Molecular marker primer of rice cold-resistant major QTL CTS12 as well as marking method and application thereof

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1997015676A2 (en) * 1995-10-27 1997-05-01 Abbott Laboratories Candida topoisomeraseigene
WO1998035659A1 (en) * 1997-02-18 1998-08-20 Lxr Biotechnology Inc. Bak promotor expression system
WO1999047709A2 (en) * 1998-03-18 1999-09-23 Chinook Acquisition Corporation Methods for identifying anti-cancer agents

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1997015676A2 (en) * 1995-10-27 1997-05-01 Abbott Laboratories Candida topoisomeraseigene
WO1998035659A1 (en) * 1997-02-18 1998-08-20 Lxr Biotechnology Inc. Bak promotor expression system
WO1999047709A2 (en) * 1998-03-18 1999-09-23 Chinook Acquisition Corporation Methods for identifying anti-cancer agents

Non-Patent Citations (10)

* Cited by examiner, † Cited by third party
Title
BAMMERT G F AND FOSTEL J M: "Gene expression patterns in Saccharomyces cerevisiae: Comparing response to drug treatment with mutations in ergosterol biosynthetic genes.", ABSTRACTS OF THE INTERSCIENCE CONFERENCE ON ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, vol. 39, 26 September 1999 (1999-09-26), pages 550, XP001001100 *
BAMMERT G F AND FOSTEL J M: "Genome-wide expression patterns in Saccharomyces cerevisiae: Comparison of drug treatment and genetic alterations affecting biosynthesis of ergosterol", ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, vol. 44, no. 5, May 2000 (2000-05-01), pages 1255 - 1265, XP000998080 *
DERISI J L ET AL: "Exploring the metabolic and genetic control of gene expression on a genomic scale", SCIENCE,AMERICAN ASSOCIATION FOR THE ADVANCEMENT OF SCIENCE,,US, vol. 278, 24 October 1997 (1997-10-24), pages 680 - 686, XP002110854, ISSN: 0036-8075 *
DOUGHERTY E R AND BATMAN S: "Clustering analysis for gene expression data", SPIE, vol. 3802, January 1999 (1999-01-01), pages 422 - 428, XP001001103 *
FOSTEL J M ET AL.: "Use of quantitative real time PCR to characterize the specificity of yeast transcriptional profiles determined by microarray analysis following exposure of Saccharomyces cerevisiae to antifungal agents", ABSTRACTS OF THE INTERSCIENCE CONFERENCE ON ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, vol. 40, September 2000 (2000-09-01), pages 227, XP001001147 *
JELINSKY S A AND SAMSON L D: "Global response of Saccharomyces cerevisiae to an alkylating agent", PORCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES USA, vol. 96, February 1999 (1999-02-01), pages 1486 - 1491, XP002168522 *
LOCKHART ET AL: "EXPRESSION MONITORING BY HYBRIDIZATION TO HIGH-DENSITY OLIGONUCLEOTIDE ARRAYS", NATURE BIOTECHNOLOGY,US,NATURE PUBLISHING, vol. 14, 1 December 1996 (1996-12-01), pages 1675 - 1680, XP002094438, ISSN: 1087-0156 *
MARTON M J ET AL.: "Drug target validation and identification of secondary drug target effects using DNA microarrays", NATURE MEDICINE, vol. 4, no. 11, November 1998 (1998-11-01), pages 1293 - 1301, XP002168523 *
ROTH F P ET AL: "FInding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation", NATURE BIOTECHNOLOGY,NATURE PUBLISHING,US, vol. 16, October 1998 (1998-10-01), pages 939 - 945, XP002153325, ISSN: 1087-0156 *
WODICKA ET AL: "GENOME-WIDE EXPRESSION MONITORING IN SACCHAROMYCES CEREVISIAE", NATURE BIOTECHNOLOGY,NATURE PUBLISHING,US, vol. 15, December 1997 (1997-12-01), pages 1359 - 1367, XP002100297, ISSN: 1087-0156 *

Also Published As

Publication number Publication date
AU7606100A (en) 2001-04-24
WO2001021839A2 (en) 2001-03-29

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