Unwarping and Analysing Electrophoresis Gels
Doktorsavhandling, 2005

Gel electrophoresis is a technology in molecular biology that is used to separate and quantify biomolecules, for example DNA and proteins. Ideally the position in a gel image corresponds to one or several properties of the molecules, such as size and net charge, but in practise the separation pattern is often warped, that is, geometrically distorted. This thesis presents methods for unwarping and analysing electrophoresis gel images. There are three main contributions in the thesis: (i) An image analysis method for simultaneous unwarping and classification of multi-track 1-D gels using a database of track profiles. The main advantage of this method is that the two analysis steps are done automatically and simultaneously. The method is motivated by and applied to pulse-field electrophoresis gels from a genotyping of potentially antibiotic-resistant bacteria. (ii) A physical model and methods for individual unwarping and pair-wise alignment of 2-D gel images. Here, the main advantages are an explicit control of image deformations and that the pair-wise alignment is automatic. The methods are evaluated on a set of protein gels from a study of the adaptation of yeast cells to saline conditions. The image alignment method is also applied and found to be robust in a comparative study of different yeast strains where the protein spot pattern differs substantially between the strains. (iii) The final main contribution is a statistical exploration of variation in quantitative 2-D gel data from three gel sets. Here, parallels to the design and analysis of microarray experiments are discussed and utilised.

Gel matching

Yeast

Variation

Classification

Curved field lines

Pulse-field gel electrophoresis

Image warping

Two-dimensional electrophoresis

Image alignment

Proteomics

10.00 Föreläsningssal Pascal, Matematiska vetenskaper, Chalmers tvärgata 3
Opponent: Professor Fred Godtliebsen, University of Tromsö, Norway

Författare

John Gustafsson

Göteborgs universitet

Chalmers, Matematiska vetenskaper, matematisk statistik

A statistical model for unwarping of 1-D electrophoresis gels

Electrophoresis,; Vol. 26(2005)p. 4237-4242

Artikel i vetenskaplig tidskrift

Warping two-dimensional electrophoresis gel images to correct for geometric distortions of the spot pattern

Electrophoresis,; Vol. 23(2002)p. 1731-1744

Artikel i vetenskaplig tidskrift

Ämneskategorier

Biokemi och molekylärbiologi

Sannolikhetsteori och statistik

Datorseende och robotik (autonoma system)

ISBN

91-7291-722-9

Doktorsavhandlingar vid Chalmers tekniska högskola. Ny serie: 2404

10.00 Föreläsningssal Pascal, Matematiska vetenskaper, Chalmers tvärgata 3

Opponent: Professor Fred Godtliebsen, University of Tromsö, Norway

Mer information

Skapat

2017-10-06