title: Individual-level analysis of differential expression of genes and pathways for personalized medicine.
abstract: BACKGROUND
  The differential expression analysis focusing on inter-group comparison can capture only differentially expressed genes (DE genes) at the population level, which may mask the heterogeneity of differential expression in individuals. Thus, to provide patient-specific information for personalized medicine, it is necessary to conduct differential expression analysis at the individual level.
  
  
  RESULTS
  We proposed a method to detect DE genes in individual disease samples by using the disrupted ordering in individual disease samples. In both simulated data and real paired cancer-normal sample data, this method showed excellent performance. It was found to be insensitive to experimental batch effects and data normalization. The landscape of stable gene pairs in a particular type of normal tissue could be predetermined using previously accumulated data, based on which dysregulated genes and pathways for any disease sample can be readily detected. The usefulness of the RankComp method in clinical settings was exemplified by the identification and application of prognostic markers for lung cancer.
  
  
  METHODS
  RankComp is implemented in R script that is freely available from Supplementary Materials.
authors.affiliation: College of Bioinformatics Science and Technology, Genomics Research Center, Harbin Medical University, Harbin 150086, China, Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, AB, T2N 4N1, Canada and Bioinformatics Department, Basic Medical College, Fujian Medical University, Fuzhou 350004, China.
authors.forename: Hongwei
authors.initials: H
authors.lastname: Wang
authors.affiliation: College of Bioinformatics Science and Technology, Genomics Research Center, Harbin Medical University, Harbin 150086, China, Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, AB, T2N 4N1, Canada and Bioinformatics Department, Basic Medical College, Fujian Medical University, Fuzhou 350004, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Sun
authors.affiliation: College of Bioinformatics Science and Technology, Genomics Research Center, Harbin Medical University, Harbin 150086, China, Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, AB, T2N 4N1, Canada and Bioinformatics Department, Basic Medical College, Fujian Medical University, Fuzhou 350004, China.
authors.forename: Wenyuan
authors.initials: W
authors.lastname: Zhao
authors.affiliation: College of Bioinformatics Science and Technology, Genomics Research Center, Harbin Medical University, Harbin 150086, China, Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, AB, T2N 4N1, Canada and Bioinformatics Department, Basic Medical College, Fujian Medical University, Fuzhou 350004, China.
authors.forename: Lishuang
authors.initials: L
authors.lastname: Qi
authors.affiliation: College of Bioinformatics Science and Technology, Genomics Research Center, Harbin Medical University, Harbin 150086, China, Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, AB, T2N 4N1, Canada and Bioinformatics Department, Basic Medical College, Fujian Medical University, Fuzhou 350004, China.
authors.forename: Yunyan
authors.initials: Y
authors.lastname: Gu
authors.affiliation: College of Bioinformatics Science and Technology, Genomics Research Center, Harbin Medical University, Harbin 150086, China, Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, AB, T2N 4N1, Canada and Bioinformatics Department, Basic Medical College, Fujian Medical University, Fuzhou 350004, China.
authors.forename: Pengfei
authors.initials: P
authors.lastname: Li
authors.affiliation: College of Bioinformatics Science and Technology, Genomics Research Center, Harbin Medical University, Harbin 150086, China, Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, AB, T2N 4N1, Canada and Bioinformatics Department, Basic Medical College, Fujian Medical University, Fuzhou 350004, China.
authors.forename: Mengmeng
authors.initials: M
authors.lastname: Zhang
authors.affiliation: College of Bioinformatics Science and Technology, Genomics Research Center, Harbin Medical University, Harbin 150086, China, Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, AB, T2N 4N1, Canada and Bioinformatics Department, Basic Medical College, Fujian Medical University, Fuzhou 350004, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Li
authors.affiliation: College of Bioinformatics Science and Technology, Genomics Research Center, Harbin Medical University, Harbin 150086, China, Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, AB, T2N 4N1, Canada and Bioinformatics Department, Basic Medical College, Fujian Medical University, Fuzhou 350004, China College of Bioinformatics Science and Technology, Genomics Research Center, Harbin Medical University, Harbin 150086, China, Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, AB, T2N 4N1, Canada and Bioinformatics Department, Basic Medical College, Fujian Medical University, Fuzhou 350004, China.
authors.forename: Shu-Lin
authors.initials: SL
authors.lastname: Liu
authors.affiliation: College of Bioinformatics Science and Technology, Genomics Research Center, Harbin Medical University, Harbin 150086, China, Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, AB, T2N 4N1, Canada and Bioinformatics Department, Basic Medical College, Fujian Medical University, Fuzhou 350004, China College of Bioinformatics Science and Technology, Genomics Research Center, Harbin Medical University, Harbin 150086, China, Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, AB, T2N 4N1, Canada and Bioinformatics Department, Basic Medical College, Fujian Medical University, Fuzhou 350004, China.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Guo
mesh_terms: D014408:Biomarkers, Tumor / Q000032:analysis / Q000235:genetics*; D001940:Breast / Q000378:metabolism; D001943:Breast Neoplasms / Q000235:genetics* / Q000401:mortality; D016022:Case-Control Studies; D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D016002:Discriminant Analysis; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D008168:Lung / Q000378:metabolism; D008175:Lung Neoplasms / Q000235:genetics* / Q000401:mortality; D057285:Precision Medicine; D015398:Signal Transduction
chemical_list: D014408:Biomarkers, Tumor