title: Stratification of gene coexpression patterns and GO function mining for a RNA-Seq data series.
abstract: RNA-Seq is emerging as an increasingly important tool in biological research, and it provides the most direct evidence of the relationship between the physiological state and molecular changes in cells. A large amount of RNA-Seq data across diverse experimental conditions have been generated and deposited in public databases. However, most developed approaches for coexpression analyses focus on the coexpression pattern mining of the transcriptome, thereby ignoring the magnitude of gene differences in one pattern. Furthermore, the functional relationships of genes in one pattern, and notably among patterns, were not always recognized. In this study, we developed an integrated strategy to identify differential coexpression patterns of genes and probed the functional mechanisms of the modules. Two real datasets were used to validate the method and allow comparisons with other methods. One of the datasets was selected to illustrate the flow of a typical analysis. In summary, we present an approach to robustly detect coexpression patterns in transcriptomes and to stratify patterns according to their relative differences. Furthermore, a global relationship between patterns and biological functions was constructed. In addition, a freely accessible web toolkit "coexpression pattern mining and GO functional analysis" (COGO) was developed.
authors: Department of Hematology, The First Affiliated Hospital, Harbin Medical University, Harbin 150001, China ; Health Ministry Key Lab of Cell Transplantation, Harbin 150001, China ; Heilongjiang Institute of Hematology and Oncology, Harbin 150001, China ; College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors: Hui
authors: H
authors: Zhao
authors: Department of Hematology, The First Affiliated Hospital, Harbin Medical University, Harbin 150001, China ; Health Ministry Key Lab of Cell Transplantation, Harbin 150001, China ; Heilongjiang Institute of Hematology and Oncology, Harbin 150001, China.
authors: Fenglin
authors: F
authors: Cao
authors: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors: Yonghui
authors: 0000-0003-4622-1442
authors: Y
authors: Gong
authors: College of Life Science, Heilongjiang University, Harbin 150080, China.
authors: Huafeng
authors: H
authors: Xu
authors: Department of Hematology, The First Affiliated Hospital, Harbin Medical University, Harbin 150001, China ; Health Ministry Key Lab of Cell Transplantation, Harbin 150001, China ; Heilongjiang Institute of Hematology and Oncology, Harbin 150001, China.
authors: Yiping
authors: Y
authors: Fei
authors: Department of Hematology, The First Affiliated Hospital, Harbin Medical University, Harbin 150001, China ; Health Ministry Key Lab of Cell Transplantation, Harbin 150001, China ; Heilongjiang Institute of Hematology and Oncology, Harbin 150001, China.
authors: Longyue
authors: L
authors: Wu
authors: Department of Hematology, The First Affiliated Hospital, Harbin Medical University, Harbin 150001, China ; Health Ministry Key Lab of Cell Transplantation, Harbin 150001, China ; Heilongjiang Institute of Hematology and Oncology, Harbin 150001, China.
authors: Xiangmei
authors: X
authors: Ye
authors: Department of Hematology, The First Affiliated Hospital, Harbin Medical University, Harbin 150001, China ; Health Ministry Key Lab of Cell Transplantation, Harbin 150001, China ; Heilongjiang Institute of Hematology and Oncology, Harbin 150001, China.
authors: Dongguang
authors: D
authors: Yang
authors: Department of Hematology, The First Affiliated Hospital, Harbin Medical University, Harbin 150001, China ; Health Ministry Key Lab of Cell Transplantation, Harbin 150001, China ; Heilongjiang Institute of Hematology and Oncology, Harbin 150001, China.
authors: Xiuhua
authors: X
authors: Liu
authors: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
authors: Xia
authors: X
authors: Li
authors: Department of Hematology, The First Affiliated Hospital, Harbin Medical University, Harbin 150001, China ; Health Ministry Key Lab of Cell Transplantation, Harbin 150001, China ; Heilongjiang Institute of Hematology and Oncology, Harbin 150001, China.
authors: Jin
authors: J
authors: Zhou
mesh_terms: D000465:Algorithms; D057225:Data Mining / Q000379:methods*; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000235:genetics; D053263:Gene Regulatory Networks; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics