title: Prediction of microbial infection of cultured cells using DNA microarray gene-expression profiles of host responses.
abstract: Infection by microorganisms may cause fatally erroneous interpretations in the biologic researches based on cell culture. The contamination by microorganism in the cell culture is quite frequent (5% to 35%). However, current approaches to identify the presence of contamination have many limitations such as high cost of time and labor, and difficulty in interpreting the result. In this paper, we propose a model to predict cell infection, using a microarray technique which gives an overview of the whole genome profile. By analysis of 62 microarray expression profiles under various experimental conditions altering cell type, source of infection and collection time, we discovered 5 marker genes, NM_005298, NM_016408, NM_014588, S76389, and NM_001853. In addition, we discovered two of these genes, S76389, and NM_001853, are involved in a Mycolplasma-specific infection process. We also suggest models to predict the source of infection, cell type or time after infection. We implemented a web based prediction tool in microarray data, named Prediction of Microbial Infection (http://www.snubi.org/software/PMI).
authors.affiliation: Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine, Seoul, Korea.
authors.forename: Yu Rang
authors.initials: YR
authors.lastname: Park
authors.forename: Tae Su
authors.initials: TS
authors.lastname: Chung
authors.forename: Young Joo
authors.initials: YJ
authors.lastname: Lee
authors.forename: Yeong Wook
authors.initials: YW
authors.lastname: Song
authors.forename: Eun Young
authors.initials: EY
authors.lastname: Lee
authors.forename: Yeo Won
authors.initials: YW
authors.lastname: Sohn
authors.forename: Sukgil
authors.initials: S
authors.lastname: Song
authors.forename: Woong Yang
authors.initials: WY
authors.lastname: Park
authors.forename: Ju Han
authors.initials: JH
authors.lastname: Kim
mesh_terms: D000465:Algorithms; D002460:Cell Line; D019902:Chondrocytes / Q000166:cytology / Q000378:metabolism / Q000382:microbiology; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D054884:Host-Pathogen Interactions; D006801:Humans; D015603:Keratinocytes / Q000166:cytology / Q000378:metabolism / Q000382:microbiology; D008957:Models, Genetic; D009174:Mycoplasma / Q000235:genetics / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis
keywords: DNA Microarray; Microbial Infection; Mycoplasma; Prediction Model