title: Multimodel pathway enrichment methods for functional evaluation of expression regulation.
abstract: Functional analysis of quantitative expression data is becoming common practice within the proteomics and transcriptomics fields; however, a gold standard for this type of analysis has yet not emerged. To grasp the systemic changes in biological systems, efficient and robust methods are needed for data analysis following expression regulation experiments. We discuss several conceptual and practical challenges potentially hindering the emergence of such methods and present a novel method, called FEvER, that utilizes two enrichment models in parallel. We also present analysis of three disparate differential expression data sets using our method and compare our results to other established methods. With many useful features such as pathway hierarchy overview, we believe the FEvER method and its software implementation will provide a useful tool for peers in the field of proteomics. Furthermore, we show that the method is also applicable to other types of expression data.
authors.affiliation: Department of Immunotechnology,  Lund University Biomedical Centre  D13, SE-221 84 Lund, Sweden.
authors.forename: Ufuk
authors.initials: U
authors.lastname: Kirik
authors.forename: Paolo
authors.initials: P
authors.lastname: Cifani
authors.forename: Ann-Sofie
authors.initials: AS
authors.lastname: Albrekt
authors.forename: Malin
authors.initials: M
authors.lastname: Lindstedt
authors.forename: Anders
authors.initials: A
authors.lastname: Heyden
authors.forename: Fredrik
authors.initials: F
authors.lastname: Levander
mesh_terms: D053898:Biosynthetic Pathways; D045744:Cell Line, Tumor; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D004137:Dinitrochlorobenzene / Q000494:pharmacology; D005656:Fungal Proteins / Q000737:chemistry; D020869:Gene Expression Profiling; D006801:Humans; D008938:Mitosis; D008954:Models, Biological; D009363:Neoplasm Proteins / Q000737:chemistry; D009369:Neoplasms / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000201:enzymology; D012984:Software; D059467:Transcriptome
chemical_list: D004137:Dinitrochlorobenzene; D005656:Fungal Proteins; D009363:Neoplasm Proteins