title: Highly informative marker sets consisting of genes with low individual degree of differential expression.
abstract: Genes with significant differential expression are traditionally used to reveal the genetic background underlying phenotypic differences between cancer cells. We hypothesized that informative marker sets can be obtained by combining genes with a relatively low degree of individual differential expression. We developed a method for construction of highly informative gene combinations aimed at the maximization of the cumulative informative power and identified sets of 2-5 genes efficiently predicting recurrence for ER-positive breast cancer patients. The gene combinations constructed on the basis of microarray data were successfully applied to data acquired by RNA-seq. The developed method provides the basis for the generation of highly efficient prognostic and predictive gene signatures for cancer and other diseases. The identified gene sets can potentially reveal novel essential segments of gene interaction networks and pathways implied in cancer progression.
authors.affiliation: Moscow State University, Leninskie Gory, 119991 Moscow, Russia.|SRC Bioclinicum, Ugreshskaya str 2/85, 115088 Moscow, Russia.
authors.forename: V V
authors.initials: VV
authors.lastname: Galatenko
authors.affiliation: P. Hertsen Moscow Oncology Research Institute, National Center of Medical Radiological Research, 3 Second Botkinsky Lane, Moscow, 125284, Russia.
authors.forename: M Yu
authors.initials: MY
authors.lastname: Shkurnikov
authors.affiliation: SRC Bioclinicum, Ugreshskaya str 2/85, 115088 Moscow, Russia.|Moscow State University of Mechanical Engineering, Bolshaya Semenovskaya str 38, 107023 Moscow, Russia.
authors.forename: T R
authors.initials: TR
authors.lastname: Samatov
authors.affiliation: Moscow State University, Leninskie Gory, 119991 Moscow, Russia.
authors.forename: A V
authors.initials: AV
authors.lastname: Galatenko
authors.affiliation: SRC Bioclinicum, Ugreshskaya str 2/85, 115088 Moscow, Russia.
authors.forename: I A
authors.initials: IA
authors.lastname: Mityakina
authors.affiliation: P. Hertsen Moscow Oncology Research Institute, National Center of Medical Radiological Research, 3 Second Botkinsky Lane, Moscow, 125284, Russia.
authors.forename: A D
authors.initials: AD
authors.lastname: Kaprin
authors.affiliation: Department of Anatomy and Experimental Morphology, University Cancer Center, University Medical Center Hamburg-Eppendorf, Martinistr. 52, Hamburg D-20246, Germany.
authors.forename: U
authors.initials: U
authors.lastname: Schumacher
authors.affiliation: Moscow State University, Leninskie Gory, 119991 Moscow, Russia.|P. Hertsen Moscow Oncology Research Institute, National Center of Medical Radiological Research, 3 Second Botkinsky Lane, Moscow, 125284, Russia.
authors.forename: A G
authors.initials: AG
authors.lastname: Tonevitsky
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics* / Q000378:metabolism; D001943:Breast Neoplasms / Q000175:diagnosis / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009363:Neoplasm Proteins / Q000235:genetics* / Q000378:metabolism; D009364:Neoplasm Recurrence, Local / Q000175:diagnosis / Q000235:genetics* / Q000473:pathology; D020411:Oligonucleotide Array Sequence Analysis; D011960:Receptors, Estrogen / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome
chemical_list: D014408:Biomarkers, Tumor; D009363:Neoplasm Proteins; D011960:Receptors, Estrogen