Dwuwymiarowa elektroforeza żelowa: od eksperymentu po profile ekspresji. Część druga - analiza obrazu

Suchwałko, A.; Podbielska, H.

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Dwuwymiarowa elektroforeza żelowa: od eksperymentu po profile ekspresji. Część druga - analiza obrazu

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Suchwałko A. , Podbielska H.

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Warianty tytułu

Two-dimensional gel electrophoresis: from experiment to protein expresion profiles. Part two - image analysis

Języki publikacji

Abstrakty

Dwuwymiarowa (dwukierunkowa) elektroforeza żelowa (2-DE) jest metodą znaną od lat siedemdziesiątych poprzedniego stulecia. Zainteresowanie badaczy metodą 2-DE wynika z możliwości separacji nawet kilku tysięcy białek w jednym żelu, co pozwala na i ch detekcję i identyfikację. Dzięki wysokiej rozdzielczości wyników separacji możliwe staje się ustalenie roli biologicznej poszczególnych białek czy odkrywanie wpływu czynników zewnętrznych na organizmy żywe na poziomie proteomu. Metoda 2-DE wciąż ewoluuje. W ostatniej dekadzie nastąpił ogromny postęp w sposobie przeprowadzania eksperymentów z dużą powtarzalnością. Zmieniło się też całkowicie podejście do analizy obrazów żeli i wykorzystywane do tego celu algorytmy. Ze względu na tak szybki rozwój technik dwuwymiarowej elektroforezy żelowej, autorzy postanowili przedstawić obecny stan wiedzy w tym zakresie. Praca składa się z dwu części. W pierwszej opisano zmiany, jakie zaszły w technikach przeprowadzania eksperymentów elektroforetycznych. Draga część skupia się na analizie obrazów uzyskanych za pomocą metody 2-DE, z uwzględnien i em zmian w schemacie analizy. Druga część pracy to opis dwóch schematów analizy: klasycznego i obecnie stosowanego. Szczegółowo opracowane zostały metody analizy pojedynczego obrazu 2-DE oraz analizy porównawczej serii obrazów. Przedstawione są algorytmy stosowane do normalizacji, segmentacji obrazu, detekcji plam, dopasowywania do siebie obrazów czy tworzenia map proteomowych jako najważniejsze w całej analizie. Opisano również generowanie profili ekspresji, metody identyfikacji protein oraz internetowe bazy danych 2-DE. Autorzy nie pominęli tak ważnego zagadnienia, jak sposoby porównywania systemów analizujących dane 2-DE. Ta część pracy podsumowuje rozwój, jaki nastąpił wostatnim dziesięcioleciu w metodach stosowanych w analizie komputerowej obrazów 2-DE, którego najważniejszym krokiem było opracowanie nowego schematu analizy, opartego na tworzeniu map proteomowych.

Two-dimensional gel electrophoresis (2-DE) is a method commonly used since seventies of the previous cesatury. It owns its non weakening interest of researchers because of the possibility of separation even a few thousands of proteins in one gel, what allows for protein detection a n d identification. Thanks to high resolution of separation results, it is possible to determine a biological role of particular proteins or to discover influence of extemal factors on living organisms on t h e proteome level. 2-DE i s stilł evolving. In t h e last decade, a great progress has be en made in t h e way of performing experiments and their reproducibility. Approach to the analysis of gel images and algorthms used for the analysis have been entirely changed. For the reason of suchinstant changes of methods a n d techniques of the two-dimensional gel electrophoresis, the authors decided to describe state of the art. This work consists of two parts. The first part describes changes that have b e e n made in performing of electrophoretic experiments. The second part concentrates on the analysis of obtained images, with emphasis the analysis workflow. Second part is a description of two analysis workflows: the classical one and the currentiy used one. Analysis methods of the single 2-DE image and differential analysis of the image series are discussed in detail. Algorthms used for normalization, image segmentation, spot detection, image warping and creation of proteome maps are intrcduced as th e most crucial in the whole analysis. Generation of expression profiles, protein Identification methods, and the Internet databases of the 2-DE data are described. Authors have not missed as important issue as methods of comparison of systems for 2-DE data analysis. This part of the work summarises development that has been made for the last ten years in th e methods used for the computer analysis of 2-DE images. The most important step of this development was elaborat i on of the workflow based on creation of proteome maps.

Słowa kluczowe

elektroforeza żelowa 2DE analiza porównawcza schemat analizy 2-DE mapa proteomowa segmentacja obrazu detekcja plam identyfikacja protein

gel electrophoresis 2-DE differential image analysis 2-DE analysis workflow proteome map image segmentation spot detection protein identification

Wydawca

Jacek Doskocz

Czasopismo

Acta Bio-Optica et Informatica Medica. Inżynieria Biomedyczna

Rocznik

2010

Tom

Vol. 16, nr 4

Strony

372--380

Opis fizyczny

Bibliogr. 64 poz.

Twórcy

autor

Suchwałko A.

autor

Podbielska H.

Instytut Inżynierii Biomedycznej i Pomiarowej, Wydział Podstawowych Problemów Techniki, Politechnika Wrocławska tel. 71 320-28- 25, agnieszka.suchwalko@pwr.wroc.pl

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