RETRACTED ARTICLE Oncogenes and pathway identification using filter-based approaches between various carcinoma types in lung. This paper, "Oncogenes and pathway identification using filter-based approaches between various carcinoma types in lung", submitted to a special issue of the IJCBDD, was based on a paper presented at the IEEE conference on bioinformatics and biomedicine held 1-4 November, 2009. However, the IEEE notified one of the authors (Mahesh Visvanathan) that the 2009 conference paper, "PathMapper - An Integrative Approach for Oncogene Pathway Identification", used a paragraph originally taken from a paper by Goffard and Weiller [below]. It is accepted that the paragraph originally taken from the paper by Goffard and Weiller was not clearly referenced or specifically identified in IJCBDD paper. Mahesh Visvanathan, the author notified by IEEE, asked for the IJCBDD paper to be withdrawn and therefore the IJCBDD paper is retracted. The full details of the passage in question are: "PathExpress: A Web-based Tool to Identify Relevant Pathways in Gene Expression Data" by Nicolas Goffard and Georg Weiller, in Nucleic Acids Research, Vol 35, Web Server Issue, Oxford, June 2007, pp. W176-W181 Although generation of high-throughput expression data is becoming customary, the fast, easy, and methodical presentation and analysis of these data in a biological context is still an obstruction. To tackle this necessity we have developed PathMapper, a standalone application which maps expression profiles of genes or proteins concurrently onto major, currently available regulatory, metabolic and cellular pathways. PathMapper automatically predicts protein functions directly from genes and can systematically identify differences between metabolic pathways and map genes onto pathways. MYSQL database is used to store, query, and manipulate the large amounts of data that are involved. PathMapper allows its users to (i) upload microarray data into a database; (ii) integrate gene expression with enzymes of the pathways; (iii) generate pathway diagrams (iv) visualize gene expression for each pathway. A graphical pathway representation permits the visualization of the expressed genes in a functional context. Based on publicly available pathway databases, PathMapper can be adapted to any organism and is currently available for human, mouse and rat genome arrays. About 20% of the probe sets of each array have been assigned to EC numbers by homology relationship and linked to its corresponding metabolic pathways. This tool can be downloaded and evaluated using the following Web link: (http://parasakti.amrita.ac.in/~amm07bi008/PathMapper). Online publication date: Thu, 10-Dec-2009
by Mahesh Visvanathan, Michael Netzer, Michael Seger, Bhargav S. Adagarla, Christian Baumgartner, Sitta Sittampalam, Gerald H. Lushington
International Journal of Computational Biology and Drug Design (IJCBDD), Vol. 2, No. 3, 2009
Abstract:
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