Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Reexamination Certificate
1998-02-09
2002-07-16
Siew, Jeffrey (Department: 1634)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
C435S007100, C536S024300, C536S024310, C536S024330, C702S019000, C702S020000
Reexamination Certificate
active
06420108
ABSTRACT:
BACKGROUND OF THE INVENTION
The present invention relates to the field of computer systems. More specifically, the present invention relates to computer systems for visualizing analysis results.
Devices and computer systems for forming and using arrays of materials on a substrate are known. For example, PCT Publication No. WO92/10588, incorporated herein by reference for all purposes, describes techniques for sequencing or sequence checking nucleic acids and other materials. Arrays for performing these operations may be formed according to the methods of, for example, the pioneering techniques disclosed in U.S. Pat. No. 5,143,854 and U.S. Pat. No. 5,593,839 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 substrate or chip. A fluorescently labeled nucleic acid is then brought into contact with the chip and a scanner generates an image file (which is processed into a cell file) indicating the locations where the labeled nucleic acids bound to the chip. Based upon the cell file and identities of the probes at specific locations, it becomes possible to extract information such as the monomer sequence of DNA or RNA. Such systems have been used to form, for example, arrays of DNA that may be used to study and detect mutations relevant to cystic fibrosis, the P53 gene (relevant to certain cancers), HIV, and other genetic characteristics.
Computer-aided techniques for monitoring gene expression using such arrays of probes have also been developed as disclosed in U.S. patent application Ser. No. 08/828,952 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.
It is desirable to identify genes having expression levels relevant to diagnosis of a diseased state by analyzing the expression levels of large numbers of genes in both diseased and normal individuals. Methods for collecting the expression level information have been developed. However, the user interfaces for gene expression monitoring systems that have been developed until now are designed to clearly present the expression of particular pre-selected genes. A user seeking to identify, e.g., an oncogene or a tumor suppressor gene, must individually review the expression level of large numbers of genes and compare the expression levels between diseased and normal individuals. What is needed is a user interface that takes advantage of collected gene expression information to help the user to identify particular genes of interest.
SUMMARY OF THE INVENTION
The present invention provides innovative systems and methods for visualizing information collected from analyzing samples. The samples may include nucleic acids, proteins, or other polymers. Gene expression level as determined from analysis of a nucleic acid sample is one possible analysis result that may be visualized. In one embodiment, a computer system may display the expression levels of multiple genes simultaneously in a way that facilitates user identification of genes whose expression is significant to a characteristic such as disease or resistance to disease. Additionally, the computer system may facilitate display of further information about relevant genes once they are identified.
A first aspect of the invention provides a computer-implemented method for presenting expression level information as collected from first and second samples. The method includes steps of: displaying a first axis corresponding to expression level in the first sample, and displaying a second axis substantially perpendicular to the first axis, the second axis corresponding to expression level in the second sample. The method further includes a step of: for a selected expressed sequence, displaying a mark at a position. The position is selected relative to the first axis in accordance with an expression level of the selected expressed sequence in the first sample and relative to the second axis in accordance with an expression level of the selected expressed sequence in the second sample. A particularly useful application is displaying many marks simultaneously for many selected genes to discover which ones of the selected genes may be relevant to the characteristic.
A second aspect of the invention provides a computer-implemented method of presenting sample analysis information. The method includes steps of: displaying a first axis corresponding to a concentration of a compound in a first sample as determined by monitoring binding of the compound to a selected polymer having binding affinity to the compound, and displaying a second axis substantially perpendicular to the first axis. The second axis corresponds to a concentration of the compound in the second sample as determined by monitoring binding of the compound to the selected polymer. The method further preferably includes a step of displaying a mark at a position. The position is selected relative to the first axis in accordance with the concentration in the first sample and relative to the second axis in accordance with the concentration in the second sample.
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Matsubara e
Balaban David
Dai Josie
Gish Kurt
Khurgin Elina
Mack David H.
Affymetrix Inc.
Siew Jeffrey
Townsend and Townsend / and Crew LLP
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