Method and computer-program product for detecting and quantifying protein spots
AssigneeBoard of Regents, The University of Texas System
InventorsJeffrey S. Morris, Howard Gutstein
Life of this patent
Estimating the term…
Abstract
The present inventions is directed to a method and computer program product for detecting and quantifying protein spots, including: generating an average gel image by taking a pixel-by-pixel average of the intensities of a plurality of aligned gel images; detecting spots on the average gel image using pinnacle detection; and quantifying spots on individual gels using the maximum intensity within fixed neighborhoods surrounding pinnacle locations found in the average gel image.
Claims18
A method for detecting and quantifying protein spots in a plurality of two-dimensional electrophoresis gel images that have been aligned to one another, each gel image having a two-dimensional array of pixels, the method comprising:
- a) generating an average gel image by taking a pixel-by-pixel average of the intensities of individual gel images, as aligned to one another;
- b) detecting spots on the average gel image using pinnacle detection, each detected spot of the average gel image having a pinnacle and a pinnacle location;
- and
- c) quantifying spots on one or more of the individual gel images using maximum intensities within fixed neighborhoods surrounding pinnacle locations found in the average gel image.
A computer program product for directing a computer processor to detect and quantify protein spots in a plurality of two-dimensional gel electrophoresis images that have been aligned to one another, each gel image having a two-dimensional array of pixels, the computer program product comprising:
- a computer readable medium;
- an initial set of instructions embodied on the computer readable medium adapted to direct a data processor to receive data representative of the plurality of two-dimensional gel electrophoresis images;
- a first set of instructions embodied on the computer readable medium adapted to direct the data processor to generate an average gel image by taking a pixel-by-pixel average of the intensities of the individual gel images, as aligned to one another;
- a second set of instructions embodied on the computer readable medium adapted to direct the data processor to detect spots on the average gel image by detecting pinnacles, each detected spot of the average gel image having a corresponding pinnacle and pinnacle location;
- a third set of instructions embodied on the computer readable medium adapted to direct the data processor to quantify spots on one or more of the individual gel images using maximum intensities within fixed neighborhoods surrounding pinnacle locations found in the average gel image.
A computer program to be installed in a computer for controlling the computer to perform a process for detecting and quantifying protein spots in 2-dimensional gel electrophoresis data, the process comprising:
- a) receiving data related to superimposition of corresponding gel features across gels;
- b) generating an average gel by taking a pixel-by-pixel average of aligned gel intensities;
- c) detecting spots on the average gel by applying a wavelet-based de-noising filter and then detecting pinnacles;
- d) quantifying spots on each individual gel using the maximum intensity within fixed neighborhoods surrounding the pinnacle locations found in the average gel.
Dependencies are inferred from the claim text.