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BR9914913A - Processes for analyzing a biological sample, for grouping biological response profiles, for analyzing a n-dimensional network of data, for removing one or more artifacts from a measured biological profile, and, polynucleotide probe network - Google Patents

Processes for analyzing a biological sample, for grouping biological response profiles, for analyzing a n-dimensional network of data, for removing one or more artifacts from a measured biological profile, and, polynucleotide probe network

Info

Publication number
BR9914913A
BR9914913A BR9914913-3A BR9914913A BR9914913A BR 9914913 A BR9914913 A BR 9914913A BR 9914913 A BR9914913 A BR 9914913A BR 9914913 A BR9914913 A BR 9914913A
Authority
BR
Brazil
Prior art keywords
biological
processes
genes
biological response
analyzing
Prior art date
Application number
BR9914913-3A
Other languages
Portuguese (pt)
Inventor
Stephen H Friend
Roland Stoughton
Yudong He
Original Assignee
Rosetta Inpharmatics Inc
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
Priority claimed from US09/179,569 external-priority patent/US6203987B1/en
Priority claimed from US09/220,275 external-priority patent/US6950752B1/en
Application filed by Rosetta Inpharmatics Inc filed Critical Rosetta Inpharmatics Inc
Publication of BR9914913A publication Critical patent/BR9914913A/en

Links

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
    • 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
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/30—Unsupervised data analysis
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6803—General methods of protein analysis not limited to specific proteins or families of proteins
    • 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
    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection
    • 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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • 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
    • 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
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • 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

  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Chemical & Material Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Medical Informatics (AREA)
  • General Health & Medical Sciences (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Organic Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Theoretical Computer Science (AREA)
  • Data Mining & Analysis (AREA)
  • Evolutionary Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Analytical Chemistry (AREA)
  • Immunology (AREA)
  • Biochemistry (AREA)
  • Evolutionary Computation (AREA)
  • Artificial Intelligence (AREA)
  • Public Health (AREA)
  • Microbiology (AREA)
  • Epidemiology (AREA)
  • Bioethics (AREA)
  • Software Systems (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Databases & Information Systems (AREA)
  • General Engineering & Computer Science (AREA)
  • Urology & Nephrology (AREA)
  • Biomedical Technology (AREA)
  • Hematology (AREA)
  • Food Science & Technology (AREA)
  • Pathology (AREA)
  • Medicinal Chemistry (AREA)

Abstract

"PROCESSOS PARA ANALISAR UMA AMOSTRA BIOLóGICA, PARA AGRUPAR PERFIS DE RESPOSTA BIOLóGICA, PARA ANALISAR UMA REDE N-DIMENSIONAL DE DADOS, PARA REMOVER UM OU MAIS ARTEFATOS DE UM PERFIL BIOLóGICO MEDIDO, E, REDE DE SONDAS DE POLINUCLEOTìDEOS". A presente invenção provê processos para melhorada detecção de padrões de resposta biológica. Em uma forma de realização da invenção, os genes são agrupados em conjuntos de genes de base para a co-regulagem de sua expressão. A expressão de genes individuais dentro de um conjunto de genes é indicada com um valor de expressão de gene único para o conjunto de genes por um processo de projeção. Os valores de expressão de conjuntos de genes, em vez da expressão de genes individuais, são então usados como a base para comparação e detecção de resposta biológica com sensibilidade muito melhorada. Em uma forma de realização da invenção, as respostas biológicas são agrupadas de acordo com a similaridade de seu perfil biológico. Os processos da invenção tem muitas aplicações utilizáveis, particularmente nos campos de desenvolvimento e descoberta de drogas. Por exemplo, os processos da invenção podem ser usados para comparar respostas biológicas com sensibilidade muito melhorada. As respostas biológicas que podem ser comparadas de acordo com estes processos incluem respostas a perturbações únicas como a resposta biológica a uma mutação ou mudança de temperatura, assim como perturbações graduadas como titulação com uma droga em particular. Os processos são também utilizáveis para identificar constituintes celulares, particularmente genes, associados com um tipo particular de resposta biológica. Além disso, os processos também podem ser usados para identificar perturbações, como novas drogas ou mutações, que afetam um ou mais conjuntos de genes em particular. Os processos podem ainda ser usados para remover artefatos experimentais em dados de resposta biológica."PROCESSES TO ANALYZE A BIOLOGICAL SAMPLE, TO GROUP BIOLOGICAL RESPONSE PROFILES, TO ANALYZE A N-DIMENSIONAL NETWORK OF DATA, TO REMOVE ONE OR MORE MEASURES FROM A MEASURED BIOLOGICAL PROFILE, AND, NET OF POLINUCLEOTID PROBES". The present invention provides processes for improved detection of biological response patterns. In an embodiment of the invention, the genes are grouped into sets of base genes for the co-regulation of their expression. The expression of individual genes within a set of genes is indicated with a unique gene expression value for the set of genes by a projection process. The expression values of sets of genes, instead of the expression of individual genes, are then used as the basis for comparison and detection of biological response with much improved sensitivity. In an embodiment of the invention, biological responses are grouped according to the similarity of their biological profile. The processes of the invention have many usable applications, particularly in the fields of drug development and discovery. For example, the processes of the invention can be used to compare biological responses with much improved sensitivity. The biological responses that can be compared according to these processes include responses to unique disorders such as the biological response to a mutation or change in temperature, as well as graded disorders such as titration with a particular drug. The processes are also usable to identify cellular constituents, particularly genes, associated with a particular type of biological response. In addition, processes can also be used to identify disorders, such as new drugs or mutations, that affect one or more particular sets of genes. The processes can also be used to remove experimental artifacts from biological response data.

BR9914913-3A 1998-10-27 1999-10-27 Processes for analyzing a biological sample, for grouping biological response profiles, for analyzing a n-dimensional network of data, for removing one or more artifacts from a measured biological profile, and, polynucleotide probe network BR9914913A (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US09/179,569 US6203987B1 (en) 1998-10-27 1998-10-27 Methods for using co-regulated genesets to enhance detection and classification of gene expression patterns
US09/220,275 US6950752B1 (en) 1998-10-27 1998-12-23 Methods for removing artifact from biological profiles
PCT/US1999/025025 WO2000024936A1 (en) 1998-10-27 1999-10-27 Methods for using co-regulated genesets to enhance detection and classification of gene expression patterns

Publications (1)

Publication Number Publication Date
BR9914913A true BR9914913A (en) 2001-10-16

Family

ID=26875445

Family Applications (1)

Application Number Title Priority Date Filing Date
BR9914913-3A BR9914913A (en) 1998-10-27 1999-10-27 Processes for analyzing a biological sample, for grouping biological response profiles, for analyzing a n-dimensional network of data, for removing one or more artifacts from a measured biological profile, and, polynucleotide probe network

Country Status (11)

Country Link
EP (1) EP1124992A4 (en)
JP (1) JP2002528095A (en)
KR (1) KR20010081098A (en)
AU (1) AU773456B2 (en)
BR (1) BR9914913A (en)
CA (1) CA2348837A1 (en)
HU (1) HUP0104050A2 (en)
IL (1) IL142840A0 (en)
IS (1) IS5929A (en)
NO (1) NO20012036L (en)
PL (1) PL347495A1 (en)

Families Citing this family (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9183349B2 (en) 2005-12-16 2015-11-10 Nextbio Sequence-centric scientific information management
JP2009520278A (en) 2005-12-16 2009-05-21 ネクストバイオ Systems and methods for scientific information knowledge management
WO2009111581A1 (en) 2008-03-04 2009-09-11 Nextbio Categorization and filtering of scientific data
CN102356163A (en) * 2009-01-19 2012-02-15 西斯特米克苏格兰有限公司 Methods employing non-coding rna expression assays
JP5133368B2 (en) * 2010-05-30 2013-01-30 株式会社 ワールドフュージョン Expression data prediction system
WO2015198620A1 (en) * 2014-06-23 2015-12-30 オリンパス株式会社 Tissue mapping method
CN111507649B (en) * 2020-06-30 2020-11-27 上海竞动科技有限公司 A blockchain-based financial big data risk control platform
CN117933579B (en) * 2024-03-25 2024-06-25 中国农业科学院草原研究所 Efficient artificial grassland comprehensive management method

Also Published As

Publication number Publication date
JP2002528095A (en) 2002-09-03
AU1451700A (en) 2000-05-15
NO20012036D0 (en) 2001-04-25
CA2348837A1 (en) 2000-05-04
HUP0104050A2 (en) 2002-03-28
NO20012036L (en) 2001-06-25
PL347495A1 (en) 2002-04-08
AU773456B2 (en) 2004-05-27
IS5929A (en) 2001-04-27
EP1124992A4 (en) 2006-09-06
IL142840A0 (en) 2002-03-10
KR20010081098A (en) 2001-08-27
EP1124992A1 (en) 2001-08-22

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