title: The use of logic relationships to model colon cancer gene expression networks with mRNA microarray data.
abstract: The ultimate goal of genomics research is to describe the network of molecules and interactions that govern all biological functions and disease processes in cells. Nonlinear interactions among genes in terms of their logic relationships play a key role for deciphering the networks of molecules that underlie cellular function. We present a method based on a graph coloring scheme and information theory to identify the gene expression network with lower and higher order logic interactions of genes. The analysis of oncogenes and suppressor genes from a colon cancer mRNA microarray dataset identifies a gene expression network with directionality and weights that reflects intracellular communication pathways. The success of the proposed method in mining hidden, complicated gene interactions and reliably interpreting experimental results suggests that the proposed method is a useful tool for understanding cancer systems. Extension of this method holds the potential to be fruitful for understanding other complex, nonsymmetric systems.
authors.affiliation: College of Electronic Information and Control Engineering, Beijing University of Technology, Pingleyuan 100#, Chaoyang District 100022, PR China. adrxg@bjut.edu.cn
authors.forename: Xiaogang
authors.initials: X
authors.lastname: Ruan
authors.forename: Jinlian
authors.initials: J
authors.lastname: Wang
authors.forename: Hui
authors.initials: H
authors.lastname: Li
authors.forename: Rhoda E
authors.initials: RE
authors.lastname: Perozzi
authors.forename: Edmund F
authors.initials: EF
authors.lastname: Perozzi
mesh_terms: D003110:Colonic Neoplasms / Q000378:metabolism*; D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D016015:Logistic Models; D008954:Models, Biological; D009363:Neoplasm Proteins / Q000235:genetics / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D012333:RNA, Messenger / Q000235:genetics*; D015398:Signal Transduction
chemical_list: D009363:Neoplasm Proteins; D012333:RNA, Messenger