Warping two-dimensional electrophoresis gel images to correct for geometric distortions of the spot pattern
Artikel i vetenskaplig tidskrift, 2002

A crucial step in two-dimensional gel based protein expression analysis is to match spots in different gel images that correspond to the same protein. It still requires extensive and time-consuming manual interference, although several semiautomatic techniques exist. Geometric distortion of the protein patterns inherent to the electrophoresis procedure is one of the main causes of these difficulties. An image warping method to reduce this problem is presented. A warping is a function that deforms images by mapping between image domains. The method proceeds in two steps. Firstly, a simple physicochemical model is formulated and applied for warping of each gel image to correct for what might be one of the main causes of the distortions: current leakage across the sides during the second-dimensional electrophoresis. Secondly, the images are automatically aligned by maximizing a penalized likelihood criterion. The method is applied to a set of ten gel images showing the radioactively labeled proteome of yeast Saccharomyces cerevisiae during normal and steady-state saline growth. The improvement in matching when given the warped images instead of the original ones is exemplified by a comparison within a commercially available software.

Alignment

Image analysis

Proteomics

Curved field lines

Two-dimensional gel electrophoresis

Författare

John Gustafsson

Göteborgs universitet

Chalmers, Institutionen för matematisk statistik

Anders Blomberg

Mats Rudemo

Göteborgs universitet

Chalmers, Institutionen för matematisk statistik

Electrophoresis

0173-0835 (ISSN) 1522-2683 (eISSN)

Vol. 23 1731-1744

Ämneskategorier

Biokemi och molekylärbiologi

Annan fysik

Sannolikhetsteori och statistik

Datorseende och robotik (autonoma system)

DOI

10.1002/1522-2683(200206)23

PubMed

12179995