title: Gene expression analysis with integrated fuzzy C-means and pathway analysis.
abstract: A workflow for associating fuzzy clusters to biological pathways has been implemented as a Java-based software tool. Its software implementation is comprised of a correlation-based fuzzy c-means algorithm and an enrichment test on Kyoto Encyclopedia of Genes and Genomes' pathways. We applied this workflow to gene expression in classification of lung cancer cell types and achieved satisfactory results. The software could aid in the validation of results of fuzzy clustering algorithms and the exploration of un-annotated associations between genes and gene ontology categories.
authors.affiliation: Computer Science Department, Winona State University, Winona, MN 55987, USA. MZhang@winona.edu
authors.forename: Mingrui
authors.initials: M
authors.lastname: Zhang
authors.forename: Beya
authors.initials: B
authors.lastname: Adamu
authors.forename: Chi-Cheng
authors.initials: CC
authors.lastname: Lin
authors.forename: Ping
authors.initials: P
authors.lastname: Yang
mesh_terms: D000465:Algorithms; D017143:Fuzzy Logic; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D008175:Lung Neoplasms / Q000145:classification* / Q000378:metabolism*; D009363:Neoplasm Proteins / Q000378:metabolism*; D011381:Programming Languages; D015398:Signal Transduction; D012984:Software; D018511:Systems Integration
chemical_list: D009363:Neoplasm Proteins