System, method, and computer software product for linked window interfaces

• US 7,992,098 B2
• Filed: 03/27/2006
• Issued: 08/02/2011
• Est. Priority Date: 08/22/2000
• Status: Active Grant

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Jevons, Luis, Kaushikkar, Shantanu V.
• Primary Examiner(s): Pitaro; Ryan F
• Application Number:
  US11/389,690
• Publication Number:
  US 20060259874A1
• Time in Patent Office: 1,954 Days
• Field of Search: 422/63, 715/764, 715/700, 715/762, 715/763, 715/765, 715/769, 715/771, 715/809, 715/810
• US Class Current: 715/803
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00533 essentially rectangular
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00675 In-situ synthesis on the substrate
• CPC Class Codes: B01J 2219/00677 Ex-situ synthesis followed by deposition on the substrate
• CPC Class Codes: B01J 2219/00689 using computers
• CPC Class Codes: B01J 2219/00695 Synthesis control routines, e.g. using computer programs
• CPC Class Codes: B01J 2219/00702 Processes involving means for analysing and characterising the products
• CPC Class Codes: B01J 2219/00707 separated from the reactor apparatus
• CPC Class Codes: C40B 50/14 Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support
• CPC Class Codes: G01N 2021/6419 Excitation at two or more wavelengths
• CPC Class Codes: G01N 2021/6421 Measuring at two or more wavelengths
• CPC Class Codes: G01N 2021/6441 with two or more labels
• CPC Class Codes: G01N 2021/6471 Special filters, filter wheel
• CPC Class Codes: G01N 2035/00158 Elements containing microarrays, i.e. "biochip"
• CPC Class Codes: G01N 2035/0494 Detecting or compensating piositioning errors
• CPC Class Codes: G01N 21/6452 : Individual samples arranged in a regular 2D-array, e.g. multiwell plates
• CPC Class Codes: G01N 27/44717 : Arrangements for investigating the separated zones, e.g. localising zones
• CPC Class Codes: G01N 27/44721 : by optical means
• CPC Class Codes: G16B 25/00 : ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 45/00 : ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks

Abstract

Systems, methods, and computer program products are described for providing a graphical user interface (GUI) that may include a first openable window of image features constituting, for example, a pseudo-image of a scanned probe array. The image features each have one or more characteristics representing one or more hybridization reactions associated with a probe of the probe array. The GUI also has a second openable window including data features, each relating to one or more quantifications of one or more hybridization reactions associated with a probe of the probe array. This second window may be, for example, a scatter plot of hybridization intensities of probes to two or more labeled samples. The GUI further includes a third openable window including descriptive features such as rows of a spreadsheet. Each row may include descriptive elements associated with a probe. When a user selects a feature from any of the two or more windows, a corresponding feature in at least one other of the two or more windows is highlighted.

Claims

1. A method comprising the steps of:

(a) providing a laser source, a detector and scanner optics, said laser source being constructed and arranged to produce excitation radiation being delivered to an array including hybridized probe-target pairs, said detector being constructed to detect emitted radiation excited in a fluorophore in response to the excitation radiation, and said scanner being constructed to scan the probe array to generate image data based on sampled emission radiation received from said detector over a pixel array corresponding to the scanned probe array;

(b) providing in a graphical user interface (GUI) at least the following windows;

(i) a first window having a plurality of image features based on the image data, each having one or more characteristics representing one or more hybridization reactions associated with a probe of a probe array,

(ii) a second window having a plurality of data features, each relating to one or more quantifications of one or more hybridization reactions associated with a probe of the probe array, and

(iii) a third window having a plurality of descriptive features, each feature including at least two descriptive elements selected from the group consisting of;

absolute image intensity value, probe data links, pin identifier, well plate identifier, chromosome location of a gene represented by the probe, chromosome location of an expressed sequence tag represented by the probe, band location on the chromosome, a single-nucleotide polymorphism (SNP) identifying the location on the chromosome, a non-SNP marker identifying the location on the chromosome, data related to the production of hybridization intensity data displayed in the first window, and information about the targets that hybridized with the probes.

2. The method of claim 1, further comprising the steps of:

(c) receiving a user selection of a feature from any of the windows; and

(d) causing a corresponding feature in at least one other window to be highlighted.

3. The method of claim 1, further comprising:

a fourth openable window having a plurality of second image features, each having one or more characteristics representing one or more hybridization reactions associated with a probe of the array.

4. The method of claim 1, wherein the scanner provides light of two wavelengths and wherein the first image features are generated based on emissions of a first wavelength and the second image features are generated based on emissions of a second wavelength different from the first wavelength.

5. The method of claim 1, wherein the one or more characteristics of the plurality of first image features include a chromatic value representing degree, efficiency, or intensity of hybridization.

6. The method of claim 1, wherein the one or more characteristics of the plurality of first image features include an intensity value representing degree, efficiency, or intensity of hybridization.

7. The method of claim 1, wherein:

the plurality of first image features comprises a pseudo-image of the array.

8. The method of claim 1, wherein the plurality of data features each represent a quantification of degree, efficiency, or intensity of hybridization of a probe based on the probe hybridizing with none, one or a plurality of targets.

9. The method of claim 1, wherein the plurality of descriptive features comprises rows of a spreadsheet wherein each row includes one or more descriptive elements associated with a probe.

10. The method of claim 1, wherein the descriptive elements comprise probe data links comprising links to remotely stored user-supplied data related to the probe, links to locally stored user-supplied data related to the probe, links to remotely stored biological information related to the probe, and links to locally stored biological information related to the probe.

11. The method of claim 1, wherein:

the plurality of data features comprises a three dimensional scatter plot of emission intensity values, where each axis shows the emission intensity values of a different fluorescent dye.

12. The method of claim 1, wherein the laser source can generate the excitation radiation between successive scans, groups of successive scans, or between full scans of the scanned probe array.

13. The method of claim 1, wherein the third window comprises at least the descriptive feature of data linked to an internet-based database which contains information about the probes and/or the targets that hybridize with the probes.

14. The method of claim 13, wherein the descriptive feature in the third window is a gene sequence accession number which links the data to an internet-based genetic sequence databank.

15. The method according to claim 14, wherein the accession number corresponds to accession numbers found in GenBank or UniGene.

16. The method of claim 1, wherein each feature of the third window includes at least three descriptive elements.

17. A scanning system, comprising:

(a) a scanner comprising a laser source, a detector and scanner optics, said laser source being constructed and arranged to produce excitation radiation being delivered to an array comprising hybridized probe-target pairs, said detector being constructed to detect emitted radiation excited in a fluorophore in response to said excitation radiation, and said scanner being constructed to scan the array to generate image data based on sampled emission radiation received from said detector over a pixel array corresponding to the scanned array;

(b) an image processor constructed and arranged to receive image data from the scanner and to process the image data; and

(c) a graphical user interface (GUI) manager constructed and arranged to provide at least the following windows;

(i) a first window having a plurality of image features based on the processed image data, each having one or more characteristics representing one or more hybridization reactions associated with a probe of the probe array,

(ii) a second window having a plurality of data features, each relating to one or more quantifications of one or more hybridization reactions associated with a probe of the probe array, and

(iii) a third window having a plurality of descriptive features, each feature including at least two descriptive elements selected from the group consisting of;

absolute image intensity value, probe data links, pin identifier, well plate identifier, chromosome location of a gene represented by the probe, chromosome location of an expressed sequence tag represented by the probe, band location on the chromosome, a single-nucleotide polymorphism (SNP) identifying the location on the chromosome, a non-SNP marker identifying the location on the chromosome, data related to the production of hybridization intensity data displayed in the first window, and information about the targets that hybridized with the probes.

18. The scanning system of claim 17, wherein the first, second, and third openable windows are all open in the interface at a same time.

19. The scanning system of claim 17, further comprising:

a fourth openable window having a plurality of second image features, each having one or more characteristics representing one or more hybridization reactions associated with a probe of the array.

20. The scanning system of claim 19, wherein the scanner provides light of two wavelengths and wherein the first image features are generated based on emissions of a first wavelength and the second image features are generated based on emissions of a second wavelength different from the first wavelength.

21. The scanning system of claim 17, wherein the one or more characteristics of the plurality of first image features include a chromatic value representing degree, efficiency, or intensity of hybridization.

22. The scanning system of claim 17, wherein:

the plurality of first image features comprises a pseudo-image of the array.

23. The scanning system of claim 17, wherein the plurality of data features each represent a quantification of degree, efficiency, or intensity of hybridization of a probe based on the probe hybridizing with none, one or a plurality of targets.

24. The scanning system of claim 17, wherein the plurality of descriptive features comprises rows of a spreadsheet wherein each row includes one or more descriptive elements associated with a probe.

25. The scanning system of claim 17, wherein the descriptive elements comprise probe data links comprising links to remotely stored user-supplied data related to the probe, links to locally stored user-supplied data related to the probe, links to remotely stored biological information related to the probe, and links to locally stored biological information related to the probe.

26. The scanning system of claim 17, wherein the GUI manager enables a user to select a first image feature associated with a first probe, a data feature or a descriptive feature associated with the first probe, or both, for highlighting.

27. The scanning system of claim 17, wherein the array is a spotted array.

28. The scanning system of claim 17, wherein the array is a synthesized array.

29. The scanning system of claim 17, wherein the third window comprises at least the descriptive feature of data linked to an internet-based database which contains information about the probes and/or the targets that hybridize with the probes.

30. The system of claim 17, wherein each feature of the third window includes at least three descriptive elements.

31. A scanning system, comprising:

a scanner constructed and arranged to receive probe array data and to scan a probe array to generate image data;

a computer; and

a computer program product that, when executed on the computer, performs a method comprising the steps of;

(a) receiving image data from said scanner and processing the image data, and

(b) providing in a graphical user interface (GUI) at least the following windows;

(i) a first window having a plurality of image features based on the processed image data, each having one or more characteristics representing one or more hybridization reactions associated with a probe of a probe array,

(ii) a second window having a plurality of data features, each relating to one or more quantifications of one or more hybridization reactions associated with a probe of the probe array, and

(iii) a third window having a plurality of descriptive features, each including one or more descriptive elements selected from the group consisting of;

absolute image intensity value, probe data links, pin identifier, well plate identifier, chromosome location of a gene represented by the probe, chromosome location of an expressed sequence tag represented by the probe, band location on the chromosome, a single-nucleotide polymorphism (SNP) identifying the location on the chromosome, a non-SNP marker identifying the location on the chromosome, data related to the production of hybridization intensity data displayed in the first window, and information about the targets that hybridized with the probes.

32. The scanning system of claim 31, wherein:

the method performed by the computer program product further comprises the steps of

(c) receiving a user selection of a feature from any of the windows, and

(d) causing a corresponding feature in at least one other window to be highlighted.

33. The scanning system of claim 31, wherein the GUI enables a user to select a first image feature associated with a first probe, a data feature or a descriptive feature associated with the first probe, or both, for highlighting.

34. The scanning system of claim 31, wherein the descriptive elements comprise probe data links comprising links to remotely stored user-supplied data related to the probe, links to locally stored user-supplied data related to the probe, links to remotely stored biological information related to the probe, and links to locally stored biological information related to the probe.

35. The scanning system of claim 31, further comprising:

a fourth openable window having a plurality of second image features, each having one or more characteristics representing one or more hybridization reactions associated with a probe of the same probe array.

36. The scanning system of claim 31, wherein the scanner provides light of two wavelengths and wherein the first image features are generated based on emissions of a first wavelength and the second image features are generated based on emissions of a second wavelength different from the first wavelength.

37. The scanning system of claim 31, wherein the scanner provides an x-ray source constructed and arranged to produce excitation radiation.

38. The scanning system of claim 31, wherein the third window comprises at least the descriptive feature of data linked to an internet-based database which contains information about the probes and/or the targets that hybridize with the probes.