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SG11201903139SA - Methods for expression profile classification - Google Patents

Methods for expression profile classification

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Publication number
SG11201903139SA
SG11201903139SA SG11201903139SA SG11201903139SA SG11201903139SA SG 11201903139S A SG11201903139S A SG 11201903139SA SG 11201903139S A SG11201903139S A SG 11201903139SA SG 11201903139S A SG11201903139S A SG 11201903139SA SG 11201903139S A SG11201903139S A SG 11201903139SA
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Singapore
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SG11201903139SA
Inventor
Jue Fan
Jesse Zhang
Jing Hu
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Cellular Res Inc
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Publication of SG11201903139SA publication Critical patent/SG11201903139SA/en

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    • 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
    • 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
    • G06F16/22—Indexing; Data structures therefor; Storage structures
    • G06F16/2228—Indexing structures
    • G06F16/2246—Trees, e.g. B+trees
    • 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
    • G06F16/28—Databases characterised by their database models, e.g. relational or object models
    • G06F16/283—Multi-dimensional databases or data warehouses, e.g. MOLAP or ROLAP
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F18/00—Pattern recognition
    • G06F18/20—Analysing
    • G06F18/23—Clustering techniques
    • G06F18/231—Hierarchical techniques, i.e. dividing or merging pattern sets so as to obtain a dendrogram
    • 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
    • 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
    • G16B40/30—Unsupervised data analysis
    • 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
    • G16B99/00—Subject matter not provided for in other groups of this subclass

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  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Theoretical Computer Science (AREA)
  • Medical Informatics (AREA)
  • Databases & Information Systems (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Data Mining & Analysis (AREA)
  • General Health & Medical Sciences (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Software Systems (AREA)
  • Genetics & Genomics (AREA)
  • Evolutionary Computation (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Artificial Intelligence (AREA)
  • General Engineering & Computer Science (AREA)
  • General Physics & Mathematics (AREA)
  • Public Health (AREA)
  • Epidemiology (AREA)
  • Bioethics (AREA)
  • Molecular Biology (AREA)
  • Information Retrieval, Db Structures And Fs Structures Therefor (AREA)
  • Image Analysis (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Other Investigation Or Analysis Of Materials By Electrical Means (AREA)

Abstract

INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (43) International Publication Date 17 May 2018 (17.05.2018) WIPO I PCT ill~~~~~~~~ 011101010VIIIOH olo oluolui lino Elio oimIE (10) International Publication Number WO 2018/089378 Al (51) International Patent Classification: GOOF 19/10 (2011.01) GOOF 19/24 (2011.01) GOOF 19/20 (2011.01) (21) International Application Number: PCT/US2017/060451 (22) International Filing Date: 07 November 2017 (07.11.2017) (25) Filing Language: English (26) Publication Language: English (30) Priority Data: 62/419,291 08 November 2016 (08.11.2016) US 62/446,227 13 January 2017 (13.01.2017) US (71) Applicant: CELLULAR RESEARCH, INC. [US/US]; 4040 Campbell Avenue, Suite 110, Menlo Park, CA 94025 (US). (72) Inventors: FAN, Jue; c/o Cellular Research, Inc., 4040 Campbell Avenue, Suite 110, Menlo Park, CA 94025 (US). ZHANG, Jesse; c/o Cellular Research, INC., 4040 Camp- bell Avenue, Suite 110, Menlo Park, CA 94025 (US). HU, Jing; c/o Cellular Research, INC., 4040 Campbell Avenue, Suite 110, Menlo Park, CA 94025 (US). (74) Agent: MALLON, Joseph, J.; 2040 Main Street, Four- teenth Floor, Irvine, CA 92614 (US). (81) 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, = (54) Title: METHODS FOR EXPRESSION PROFILE CLASSIFICATION 400 Receive a molecular counts matrix 408,---d Preprocess the molecular counts matrix to generate a dista ce matrix Hierarchical 412 cluster expression profiles of cells to generate a dendrogram 416 Split and test the dendrogram to generate a set of labels Merge the first set of labels to generate a second set of labels Select features from the second set of labels to identify features for distinguishing cell types (57) : Disclosed herein are methods and systems for identifying targets for distinguishing cell types. In some embodiments, the method comprises: hierarchically clustering expression profiles of cells to generate a dendrogram with each leaf representing the expression profile of a different individual cell. The dendrogram can be pruned by eliminating invalid splits (and their children). The remaining leaves in the dendrogram can be merged, independent of their locations in the dendrogram, based on their distances to one another to generate clusters of expression profiles. The method can identify targets for distinguishing cell types based on targets that are expressed differentially in the clusters. [Continued on next page] WO 2018/089378 Al MIDEDIMOMOIDEIREEMOOMMEITOMMOVOIMIE 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))
SG11201903139SA 2016-11-08 2017-11-07 Methods for expression profile classification SG11201903139SA (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201662419291P 2016-11-08 2016-11-08
US201762446227P 2017-01-13 2017-01-13
PCT/US2017/060451 WO2018089378A1 (en) 2016-11-08 2017-11-07 Methods for expression profile classification

Publications (1)

Publication Number Publication Date
SG11201903139SA true SG11201903139SA (en) 2019-05-30

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
SG11201903139SA SG11201903139SA (en) 2016-11-08 2017-11-07 Methods for expression profile classification

Country Status (8)

Country Link
US (1) US11164659B2 (en)
EP (1) EP3539035B1 (en)
JP (2) JP7232180B2 (en)
CN (2) CN117594126A (en)
AU (2) AU2017359048B2 (en)
ES (1) ES2980967T3 (en)
SG (1) SG11201903139SA (en)
WO (1) WO2018089378A1 (en)

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