title: Biomarker discovery: identification of a growth factor gene signature.
abstract: Gene expression signatures can be developed as comprehensive pathway readouts and used as pharmacodynamic or patient-stratification biomarkers. While a consensus on the best practices for selecting gene expression signatures from microarray data is evolving, we have developed basic guidelines to ensure consistency and quality. Here we illustrate these guidelines through the identification of a growth factor gene expression signature that is responsive to phosphatidylinositol 3-kinase (PI3K) pathway perturbations in vitro and related to phosphatase and tensin homolog (PTEN) deregulation in vivo.
authors.affiliation: Department of Molecular Profiling, Merck Research Laboratories, West Point, Pennsylvania, USA.
authors.forename: A
authors.initials: A
authors.lastname: Loboda
authors.forename: M
authors.initials: M
authors.lastname: Nebozhyn
authors.forename: C
authors.initials: C
authors.lastname: Cheng
authors.forename: R
authors.initials: R
authors.lastname: Vessey
authors.forename: P
authors.initials: P
authors.lastname: Huang
authors.forename: H
authors.initials: H
authors.lastname: Dai
authors.forename: J W
authors.initials: JW
authors.lastname: Watters
mesh_terms: D015415:Biomarkers / Q000378:metabolism*; D045744:Cell Line, Tumor; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000502:physiology*; D005819:Genetic Markers / Q000502:physiology; D006801:Humans; D036341:Intercellular Signaling Peptides and Proteins / Q000096:biosynthesis / Q000235:genetics* / Q000502:physiology; D020411:Oligonucleotide Array Sequence Analysis; D051059:PTEN Phosphohydrolase / Q000096:biosynthesis / Q000235:genetics* / Q000502:physiology; D019869:Phosphatidylinositol 3-Kinases / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction / Q000235:genetics
chemical_list: D015415:Biomarkers; D005819:Genetic Markers; D036341:Intercellular Signaling Peptides and Proteins; D019869:Phosphatidylinositol 3-Kinases; D051059:PTEN Phosphohydrolase; C494929:PTEN protein, human