title: Computational dissection of tissue contamination for identification of colon cancer-specific expression profiles.
abstract: Microarray profiles of bulk tumor tissues reflect gene expression corresponding to malignant cells as well as to many different types of contaminating normal cells. In this report, we assess the feasibility of querying baseline multitissue transcriptome databases to dissect disease-specific genes. Using colon cancer as a model tumor, we show that the application of Boolean operators (AND, OR, BUTNOT) for database searches leads to genes with expression patterns of interest. The BUTNOT operator for example allows the assignment of "expression signatures" to normal tissue specimens. These expression signatures were then used to computationally identify contaminating cells within conventionally dissected tissue specimens. The combination of several logic operators together with an expression database based on multiple human tissue specimens can resolve the problem of tissue contamination, revealing novel cancer-specific gene expression. Several markers, previously not known to be colon cancer associated, are provided.
authors.affiliation: III. Medizinische Klinik und Poliklinik, Johannes Gutenberg Universität Mainz, D-55131 Mainz, Germany. Tureci@mail.uni-mainz.de
authors.forename: Ozlem
authors.initials: O
authors.lastname: Türeci
authors.forename: Jiayi
authors.initials: J
authors.lastname: Ding
authors.forename: Holly
authors.initials: H
authors.lastname: Hilton
authors.forename: Hongjin
authors.initials: H
authors.lastname: Bian
authors.forename: Hitomi
authors.initials: H
authors.lastname: Ohkawa
authors.forename: Michael
authors.initials: M
authors.lastname: Braxenthaler
authors.forename: Gerhard
authors.initials: G
authors.lastname: Seitz
authors.forename: Laura
authors.initials: L
authors.lastname: Raddrizzani
authors.forename: Helmut
authors.initials: H
authors.lastname: Friess
authors.forename: Markus
authors.initials: M
authors.lastname: Buchler
authors.forename: Ugur
authors.initials: U
authors.lastname: Sahin
authors.forename: Juergen
authors.initials: J
authors.lastname: Hammer
mesh_terms: D003106:Colon / Q000033:anatomy & histology / Q000378:metabolism; D003110:Colonic Neoplasms / Q000235:genetics* / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D014158:Transcription, Genetic