A new method for 2D gel spot alignment: application to the analysis of large sample sets in clinical proteomics
Open Access
- 28 October 2008
- journal article
- Published by Springer Science and Business Media LLC in BMC Bioinformatics
- Vol. 9 (1), 460
- https://doi.org/10.1186/1471-2105-9-460
Abstract
In current comparative proteomics studies, the large number of images generated by 2D gels is currently compared using spot matching algorithms. Unfortunately, differences in gel migration and sample variability make efficient spot alignment very difficult to obtain, and, as consequence most of the software alignments return noisy gel matching which needs to be manually adjusted by the user. We present Sili2DGel an algorithm for automatic spot alignment that uses data from recursive gel matching and returns meaningful Spot Alignment Positions (SAP) for a given set of gels. In the algorithm, the data are represented by a graph and SAP by specific subgraphs. The results are returned under various forms (clickable synthetic gel, text file, etc.). We have applied Sili2DGel to study the variability of the urinary proteome from 20 healthy subjects. Sili2DGel performs noiseless automatic spot alignment for variability studies (as well as classical differential expression studies) of biological samples. It is very useful for typical clinical proteomic studies with large number of experiments.Keywords
This publication has 21 references indexed in Scilit:
- Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipelineBioinformatics, 2008
- Pixel‐based analysis of multiple images for the identification of changes: A novel approach applied to unravel proteome patters of 2‐D electrophoresis gel imagesProteomics, 2007
- Proteomic analysis of the cellular responses induced in uninfected immune cells by cell‐expressed X4 HIV‐1 envelopeProteomics, 2007
- The state of the art in the analysis of two-dimensional gel electrophoresis imagesApplied Microbiology and Biotechnology, 2007
- Characterization of the human urine proteome by preparative electrophoresis in combination with 2-DEProteomics, 2006
- Numerical approaches for quantitative analysis of two‐dimensional maps: A review of commercial software and home‐made systemsProteomics, 2005
- Using standard positions and image fusion to create proteome maps from collections of two‐dimensional gel electrophoresis imagesProteomics, 2003
- Enumerating all connected maximal common subgraphs in two graphsTheoretical Computer Science, 2001
- Melanie II – a third‐generation software package for analysis of two‐dimensional electrophoresis images: II. AlgorithmsElectrophoresis, 1997
- Algorithm 457: finding all cliques of an undirected graphCommunications of the ACM, 1973