SG11201902925PA - Phenotype/disease specific gene ranking using curated, gene library and network based data structures - Google Patents

Phenotype/disease specific gene ranking using curated, gene library and network based data structures

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Publication number
SG11201902925PA
SG11201902925PA SG11201902925PA SG11201902925PA SG11201902925PA SG 11201902925P A SG11201902925P A SG 11201902925PA SG 11201902925P A SG11201902925P A SG 11201902925PA SG 11201902925P A SG11201902925P A SG 11201902925PA SG 11201902925P A SG11201902925P A SG 11201902925PA
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Singapore
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international
california
gene
data
san diego
Prior art date
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SG11201902925PA
Inventor
Marc Jung
Sam Ng
Joseph R Delaney
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Illumina Inc
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Publication of SG11201902925PA publication Critical patent/SG11201902925PA/en

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    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F16/00—Information retrieval; Database structures therefor; File system structures therefor
    • G06F16/20—Information retrieval; Database structures therefor; File system structures therefor of structured data, e.g. relational data
    • G06F16/24—Querying
    • G06F16/245—Query processing
    • G06F16/2457—Query processing with adaptation to user needs
    • G06F16/24578—Query processing with adaptation to user needs using ranking
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/10—Complex mathematical operations
    • G06F17/15—Correlation function computation including computation of convolution operations
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/10—Complex mathematical operations
    • G06F17/16—Matrix or vector computation, e.g. matrix-matrix or matrix-vector multiplication, matrix factorization
    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino 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
    • G16B5/00—ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
    • 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
    • G16B5/00—ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
    • G16B5/20—Probabilistic models

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  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Theoretical Computer Science (AREA)
  • Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Physics & Mathematics (AREA)
  • Medical Informatics (AREA)
  • Biotechnology (AREA)
  • Evolutionary Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Biophysics (AREA)
  • Molecular Biology (AREA)
  • Data Mining & Analysis (AREA)
  • Mathematical Physics (AREA)
  • Chemical & Material Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Computational Mathematics (AREA)
  • Pure & Applied Mathematics (AREA)
  • Mathematical Analysis (AREA)
  • Mathematical Optimization (AREA)
  • General Engineering & Computer Science (AREA)
  • Databases & Information Systems (AREA)
  • Genetics & Genomics (AREA)
  • Physiology (AREA)
  • Computing Systems (AREA)
  • Algebra (AREA)
  • Software Systems (AREA)
  • Computational Linguistics (AREA)
  • Probability & Statistics with Applications (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Information Retrieval, Db Structures And Fs Structures Therefor (AREA)
  • Management, Administration, Business Operations System, And Electronic Commerce (AREA)

Abstract

608 Knowledge-based In ico gene data 4—* gene data (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date 12 April 2018 (12.04.2018) WIP0 1 PCT °Ens °nolo omoiloo im Eno oimIE (10) International Publication Number WO 2018/067595 Al (51) International Patent Classification: GOOF 19/18 (2011.01) (21) International Application Number: PCT/US2017/054977 (22) International Filing Date: 03 October 2017 (03.10.2017) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: 62/403,206 03 October 2016 (03.10.2016) US (71) Applicant: ILLUMINIA, INC. [US/US]; 5200 Illumina Way, San Diego, California 92122 (US). (72) Inventors: JUNG, Marc; 5200 Illumina Way, San Diego, California 92122 (US). NG, Sam; 5200 Illumina Way, San Diego, California 92122 (US). DELANEY, Joseph R.; 5200 Illumina Way, San Diego, California 92122 (US). (74) Agent: ZHOU, Feng et al.; Weaver Austin Villeneuve & Sampson LLP, P. 0. Box 70250, Oakland, California 94612-0250 (US). Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, KM, ML, MR, NE, SN, TD, TG). Published: with international search report (Art. 21(3)) N O cc O C (54) Title: PHENOTYPE/DISEASE SPECIFIC GENE RANKING USING CURATED, GENE LIBRARY AND NETWORK BASED DATA STRUCTURES 602 604 Experimental gene data FIG. 6 (57) : The present invention relates to methods, systems and apparatus for capturing, integrating, organizing, navigating and querying large-scale data from high-throughput biological and chemical assay platforms. It provides a highly efficient meta-analysis infrastructure for performing research queries across a large number of studies and experiments from different biological and chemical assays, data types and organisms, as well as systems to build and add to such an infrastructure. According to various embodiments, methods, systems and interfaces for identifying genes that are potentially associated with a biological, chemical or medical concept of interest.
SG11201902925PA 2016-10-03 2017-10-03 Phenotype/disease specific gene ranking using curated, gene library and network based data structures SG11201902925PA (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201662403206P 2016-10-03 2016-10-03
PCT/US2017/054977 WO2018067595A1 (en) 2016-10-03 2017-10-03 Phenotype/disease specific gene ranking using curated, gene library and network based data structures

Publications (1)

Publication Number Publication Date
SG11201902925PA true SG11201902925PA (en) 2019-05-30

Family

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SG11201902925PA SG11201902925PA (en) 2016-10-03 2017-10-03 Phenotype/disease specific gene ranking using curated, gene library and network based data structures

Country Status (11)

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US (1) US10810213B2 (en)
EP (1) EP3520006B1 (en)
JP (1) JP2020502697A (en)
KR (1) KR20190077372A (en)
CN (1) CN109906486B (en)
AU (2) AU2017338775B2 (en)
CA (1) CA3039201A1 (en)
MX (1) MX2019003765A (en)
RU (1) RU2019110756A (en)
SG (1) SG11201902925PA (en)
WO (1) WO2018067595A1 (en)

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CN104956225B (en) 2012-10-29 2018-10-02 约翰·霍普金斯大学 Ovary and the test of the Pap test of carcinoma of endometrium
US11286531B2 (en) 2015-08-11 2022-03-29 The Johns Hopkins University Assaying ovarian cyst fluid
US11948662B2 (en) * 2017-02-17 2024-04-02 The Regents Of The University Of California Metabolite, annotation, and gene integration system and method
MX2020001575A (en) 2017-08-07 2020-11-18 Univ Johns Hopkins Methods and materials for assessing and treating cancer.
EP3550568B1 (en) * 2018-04-07 2023-07-05 Tata Consultancy Services Limited Graph convolution based gene prioritization on heterogeneous networks
US11354591B2 (en) 2018-10-11 2022-06-07 International Business Machines Corporation Identifying gene signatures and corresponding biological pathways based on an automatically curated genomic database
CA3115991A1 (en) * 2018-10-12 2020-04-16 Human Longevity, Inc. Multi-omic search engine for integrative analysis of cancer genomic and clinical data
KR102230156B1 (en) * 2018-10-15 2021-03-19 연세대학교 산학협력단 A drug repositioning system using network-based gene set enrichment analysis method
CN109684286B (en) * 2018-12-28 2021-10-22 中国科学院苏州生物医学工程技术研究所 Digital periodical experiment data sharing method and system, storage medium and electronic equipment
US20220223225A1 (en) * 2019-05-24 2022-07-14 Northeastern University Chemical-disease perturbation ranking
CN110310708A (en) * 2019-06-18 2019-10-08 广东省生态环境技术研究所 A method of building alienation arsenic reductase enzyme protein database
CN110364266A (en) * 2019-06-28 2019-10-22 深圳裕策生物科技有限公司 For instructing the database and its construction method and device of clinical tumor personalized medicine
WO2021033179A1 (en) * 2019-08-20 2021-02-25 Technion Research & Development Foundation Limited Automated literature meta analysis using hypothesis generators and automated search
CN110797080A (en) * 2019-10-18 2020-02-14 湖南大学 Predicting synthetic lethal genes based on cross-species migratory learning
CN110729022B (en) * 2019-10-24 2023-06-23 江西中烟工业有限责任公司 Method for establishing early liver injury model of passive smoke-absorbing rat and related gene screening method
CN111028883B (en) * 2019-11-20 2023-07-18 广州达美智能科技有限公司 Gene processing method and device based on Boolean algebra and readable storage medium
EP3855114A1 (en) * 2020-01-22 2021-07-28 Siemens Gamesa Renewable Energy A/S A method and an apparatus for computer-implemented analyzing of a road transport route
CN111540405B (en) * 2020-04-29 2023-07-07 新疆大学 Disease gene prediction method based on rapid network embedding
JP7402140B2 (en) * 2020-09-23 2023-12-20 株式会社日立製作所 Registration device, registration method, and registration program
CN112802546B (en) * 2020-12-29 2024-05-03 中国人民解放军军事科学院军事医学研究院 Biological state characterization method, device, equipment and storage medium
TWI755261B (en) * 2021-01-25 2022-02-11 沐恩生醫光電股份有限公司 Genes evaluation device and method
US11823440B2 (en) 2021-08-19 2023-11-21 Rehrig Pacific Company Imaging system with unsupervised learning
CN115240772B (en) * 2022-08-22 2023-08-22 南京医科大学 Method for analyzing single cell pathway activity based on graph neural network

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US9183349B2 (en) * 2005-12-16 2015-11-10 Nextbio Sequence-centric scientific information management
US8364665B2 (en) 2005-12-16 2013-01-29 Nextbio Directional expression-based scientific information knowledge management
EP1964037A4 (en) 2005-12-16 2012-04-25 Nextbio System and method for scientific information knowledge management
CN101989297A (en) * 2009-07-30 2011-03-23 陈越 System for excavating medicine related with disease gene in computer
CN102855398B (en) 2012-08-28 2016-03-02 中国科学院自动化研究所 The acquisition methods of the potential associated gene of the disease based on Multi-source Information Fusion
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AU2017338775B2 (en) 2022-08-11
US10810213B2 (en) 2020-10-20
MX2019003765A (en) 2019-09-26
AU2022268283A1 (en) 2022-12-15
JP2020502697A (en) 2020-01-23
KR20190077372A (en) 2019-07-03
CA3039201A1 (en) 2018-04-12
CN109906486A (en) 2019-06-18
EP3520006B1 (en) 2023-11-29
AU2017338775A1 (en) 2019-05-02
CN109906486B (en) 2023-07-14
US20180095969A1 (en) 2018-04-05
WO2018067595A1 (en) 2018-04-12
AU2022268283B2 (en) 2024-03-28
RU2019110756A (en) 2020-11-06
EP3520006A1 (en) 2019-08-07

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