title: Identification of a lncRNA involved functional module for esophageal cancer subtypes.
abstract: Esophageal cancer (EC) is the sixth most common cause of death from cancer and has two principal histological subtypes: esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC). In addition, Barrett's esophagus (BE), due to its strong association with EAC, is generally considered to be a premalignant condition of EAC. lncRNAs are believed to function in initiation and progression of multiple cancers, and therefore should play prominent, but unknown roles in the determination and behavior of different EC subtypes. In this study, by using expression profile re-annotation and differential expression (DE) analysis, we identified DE-lncRNAs and DE-protein-coding genes (DE-PCGs), and then constructed a lncRNA-PCG network, using co-expressed DE-lncRNAs (550) and DE-PCGs (5236), which was also annotated for EC subtypes. After module mining of the network, we obtained twenty candidate lncRNA-PCG modules that were ranked by gene expression and subtype-specification. Within the top four modules, we identified an ESCC specific module, two EAC-BE-specific modules and a heterologous module. Novel candidate lncRNAs were identified, in addition to lncRNAs known to be functionally connected to EC, and could be responsible for the subtype disparities in the GO biological process and at pathway levels.
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China. lixia@hrbmu.edu.cn lcqbio@163.com.
authors.forename: Shang
authors.initials: S
authors.lastname: Li
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China. lixia@hrbmu.edu.cn lcqbio@163.com.
authors.forename: Yanjun
authors.initials: Y
authors.lastname: Xu
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China. lixia@hrbmu.edu.cn lcqbio@163.com.
authors.forename: Zeguo
authors.initials: Z
authors.lastname: Sun
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China. lixia@hrbmu.edu.cn lcqbio@163.com.
authors.forename: Li
authors.initials: L
authors.lastname: Feng
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China. lixia@hrbmu.edu.cn lcqbio@163.com.
authors.forename: Desi
authors.initials: D
authors.lastname: Shang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China. lixia@hrbmu.edu.cn lcqbio@163.com.
authors.forename: Chunlong
authors.initials: C
authors.lastname: Zhang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China. lixia@hrbmu.edu.cn lcqbio@163.com.
authors.forename: Xinrui
authors.initials: X
authors.lastname: Shi
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China. lixia@hrbmu.edu.cn lcqbio@163.com.
authors.forename: Junwei
authors.initials: J
authors.lastname: Han
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China. lixia@hrbmu.edu.cn lcqbio@163.com.
authors.forename: Fei
authors.initials: F
authors.lastname: Su
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China. lixia@hrbmu.edu.cn lcqbio@163.com.
authors.forename: Haixiu
authors.initials: H
authors.lastname: Yang
authors.affiliation: School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China.
authors.forename: Jianmei
authors.initials: J
authors.lastname: Zhao
authors.affiliation: School of Pharmacology, Daqing Campus, Harbin Medical University, Daqing 163319, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Song
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China. lixia@hrbmu.edu.cn lcqbio@163.com.
authors.forename: Yunpeng
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China. lixia@hrbmu.edu.cn lcqbio@163.com and School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China.
authors.forename: Chunquan
authors.initials: C
authors.lastname: Li
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China. lixia@hrbmu.edu.cn lcqbio@163.com.
authors.forename: Xia
authors.initials: X
authors.lastname: Li
mesh_terms: D000465:Algorithms; D014408:Biomarkers, Tumor; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining; D004938:Esophageal Neoplasms / Q000235:genetics* / Q000473:pathology*; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D056726:Genetic Association Studies; D006801:Humans; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames; D062085:RNA, Long Noncoding / Q000235:genetics*; D059467:Transcriptome
chemical_list: D014408:Biomarkers, Tumor; D062085:RNA, Long Noncoding