Data processing: database and file management or data structures – Database design – Data structure types
Reexamination Certificate
1998-07-24
2001-10-23
Choules, Jack (Department: 2177)
Data processing: database and file management or data structures
Database design
Data structure types
C707S793000, C702S019000, C435S006120
Reexamination Certificate
active
06308170
ABSTRACT:
The subject matter of the present application is related to the subject matter of the following three co-assigned applications filed on the same day as the present application: METHOD AND APPARATUS FOR PROVIDING A BIOINFORMATICS DATABASE Ser. No. 09/122,167, METHOD AND SYSTEM FOR PROVIDING A POLYMORPHISM DATABASE Ser. No. 09/122,169, METHOD AND SYSTEM FOR PROVIDING A PROBE ARRAY CHIP DESIGN DATABASE Ser. No. 09/122,304. The contents of these three applications are herein incorporated by reference.
BACKGROUND OF THE INVENTION
The present invention relates to computer systems and more particularly to computer systems for analyzing expression levels or concentrations.
Devices and computer systems have been developed for collecting information about gene expression or expressed sequence tag (EST) expression in large numbers of tissue samples. For example, PCT application WO92/10588, incorporated herein by reference for all purposes, describes techniques for sequencing or sequence checking nucleic acids and other materials. Probes for performing these operations may be formed in arrays according to the methods of, for example, the pioneering techniques disclosed in U.S. Pat. No. 5,143,854 and U.S. Pat. No. 5,571,639, both incorporated herein by reference for all purposes.
According to one aspect of the techniques described therein, an array of nucleic acid probes is fabricated at known locations on a chip or substrate. A fluorescently labeled nucleic acid is then brought into contact with the chip and a scanner generates an image file indicating the locations where the labeled nucleic acids bound to the chip. Based upon the identities of the probes at these locations, it becomes possible to extract information such as the monomer sequence of DNA or RNA.
Computer-aided techniques for monitoring gene expression using such arrays of probes have been developed as disclosed in EP Pub. No. 0848067 and PCT publication No. WO 97/10365, the contents of which are herein incorporated by reference. Many disease states are characterized by differences in the expression levels of various genes either through changes in the copy number of the genetic DNA or through changes in levels of transcription (e.g., through control of initiation, provision of RNA precursors, RNA processing, etc.) of particular genes. For example, losses and gains of genetic material play an important role in malignant transformation and progression. Furthermore, changes in the expression (transcription) levels of particular genes (e.g., oncogenes or tumor suppressors), serve as signposts for the presence and progression of various cancers.
Information on expression of genes or expressed sequence tags may be collected on a large scale in many ways, including the probe array techniques described above. One of the objectives in collecting this information is the identification of genes or ESTs whose expression is of particular importance. Researchers wish to answer questions such as: 1) Which genes are expressed in cells of a malignant tumor but not expressed in either healthy tissue or tissue treated according to a particular regime? 2) Which genes or ESTs are expressed in particular organs but not in others? 3) Which genes or ESTs are expressed in particular species but not in others?.
Collecting vast amounts of expression data from large numbers of samples including all the tissue types mentioned above is but the first step in answering these questions. To derive full value from the investment made in collecting and storing expression data, one must be able to efficiently mine the data to find items of particular relevance. What is needed is an efficient and easy to use query system for a gene expression database.
SUMMARY OF THE INVENTION
An efficient and easy to use query system for a gene expression database is provided by virtue of the present invention. Using such a system, one can easily identify genes or expressed sequence tags whose expression correlates to particular tissue types. Various tissue types may correspond to different diseases, states of disease progression, different organs, different species, etc. Researchers may now use large scale gene expression databases to full advantage.
According to a first aspect of the present invention, a method is provided in a computer system for operating a database storing information about compound concentration. The method includes: providing a database including concentrations of a plurality of compounds as measured in a plurality of samples, accepting a user query to the database to identify desired ones of the plurality of compounds, the user query specifying concentration characteristics of the desired compounds in selected ones of the plurality of samples, and comparing the concentration characteristics to the concentrations stored in the database to identify the desired compounds.
A further understanding of the nature and advantages of the inventions herein may be realized by reference to the remaining portions of the specification and the attached drawings.
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Affymetrix Inc.
Choules Jack
Townsend & Townsend & Crew LLP
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