Title: Associating functional groups to multiple clinical types using combined t-test scores and contingency-based measures: a study on breast cancer genes

Authors: Noha A. Yousri; Dalal M. Elkaffash

Addresses: Computer and System Engineering, Faculty of Engineering, Alexandria University, Alexandria, Egypt. ' Department of Clinical Pathology, Faculty of Medicine, Alexandria University Alexandria, Egypt; Alexandria Regional Centre for Women's Health and Development, Ramleh Station Square, Abdel Hamid Badawy St., Alexandria Corniche, 21653 Alexandria, Egypt

Abstract: Stemming from the need to score relations between functional groups of genes and multiple clinical types associated with a tumour, this study proposes to use contingency-based measures to quantify such relations. It aims at reflecting a relative measure of association within a specific set of functional groups, and a specific set of clinical statuses. The proposed methodology is based on extracting features (scores) from expression sets that relate genes to multiple cancer subtypes (clinical statuses), and use those features (scores) to associate cancer subtypes with functional groups. It proposes combining t-test scores at several levels of cancer statuses' differentiation to calculate such gene features. It also proposes using contingency based measures as Jaccard and F-measure to associate gene functional groups to multiple cancer subtypes/statuses. Variations from the original Jaccard measure are proposed to reflect scores of genes' relations to classes/groups rather than using binary relations. The core objective of the experimental study is to identify the functional categories of genes that mark the change in lymph node status under each of oestrogen receptor positive and negative statuses in breast cancer expression sets.

Keywords: gene expression analysis; enrichment analysis; Jaccard similarity; F-measure; t-test; clinical status; functional groups; gene ontology; breast cancer; lymph nodes; oestrogen receptors; clinical types; cancer genes; tumours; lymph node status.

DOI: 10.1504/IJCBDD.2012.049208

International Journal of Computational Biology and Drug Design, 2012 Vol.5 No.3/4, pp.261 - 283

Published online: 05 Dec 2014 *

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