Notice of Violation of IEEE Publication Principles: PathMapper-an integrative approach for oncogene pathway identification

Notice of Violation of IEEE Publication Principles

"PathMapper-An Integrative Approach for Oncogene Pathway Identification"
by Asha Vijayan, Bessey Elen Skariah, Bipin G. Nair, Gerald H. Lushington, Sabarinath Subramanian, Mahesh Visvanathan
in the Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine Workshop, 2009. BIBMW 2009, November 2009, pp. 267-271

After careful and considered review of the content and authorship of this paper by a duly constituted expert committee, this paper has been found to be in violation of IEEE's Publication Principles.

This paper contains portions of text from the paper(s) cited below. A credit notice is used, but due to the absence of quotation marks or offset text, copied material is not clearly referenced or specifically identified.

"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).