title: Cancer-Related Triplets of mRNA-lncRNA-miRNA Revealed by Integrative Network in Uterine Corpus Endometrial Carcinoma.
abstract: The regulation of transcriptome expression level is a complex process involving multiple-level interactions among molecules such as protein coding RNA (mRNA), long noncoding RNA (lncRNA), and microRNA (miRNA), which are essential for the transcriptome stability and maintenance and regulation of body homeostasis. The availability of multilevel expression data enables a comprehensive view of the regulatory network. In this study, we analyzed the coding and noncoding gene expression profiles of 301 patients with uterine corpus endometrial carcinoma (UCEC). A new method was proposed to construct a genome-wide integrative network based on variance inflation factor (VIF) regression method. The cross-regulation relations of mRNA, lncRNA, and miRNA were then selected based on clique-searching algorithm from the network, when any two molecules of the three were shown as interacting according to the integrative network. Such relation, which we call the mRNA-lncRNA-miRNA triplet, demonstrated the complexity in transcriptome regulation process. Finally, six UCEC-related triplets were selected in which the mRNA participates in endometrial carcinoma pathway, such as CDH1 and TP53. The multi-type RNAs are proved to be cross-regulated as to each of the six triplets according to literature. All the triplets demonstrated the association with the initiation and progression of UCEC. Our method provides a comprehensive strategy for the investigation of transcriptome regulation mechanism.
authors.affiliation: School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai 200240, China.
authors.forename: Chenglin
authors.identifier: 0000-0003-4411-8548
authors.initials: C
authors.lastname: Liu
authors.affiliation: Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: Yu-Hang
authors.initials: YH
authors.lastname: Zhang
authors.affiliation: Department of Medical Oncology, Shanghai Pulmonary Hospital, Cancer Institute, Tongji University Medical School, Shanghai 200433, China.
authors.forename: Qinfang
authors.initials: Q
authors.lastname: Deng
authors.affiliation: School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai 200240, China; Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200433, China.
authors.forename: Yixue
authors.identifier: 0000-0002-1198-7176
authors.initials: Y
authors.lastname: Li
authors.affiliation: Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
authors.forename: Tao
authors.identifier: 0000-0003-1975-9693
authors.initials: T
authors.lastname: Huang
authors.affiliation: Department of Medical Oncology, Shanghai Pulmonary Hospital, Cancer Institute, Tongji University Medical School, Shanghai 200433, China.
authors.forename: Songwen
authors.identifier: 0000-0002-9377-320X
authors.initials: S
authors.lastname: Zhou
authors.affiliation: School of Life Sciences, Shanghai University, Shanghai 200444, China.
authors.forename: Yu-Dong
authors.identifier: 0000-0001-5664-7979
authors.initials: YD
authors.lastname: Cai
mesh_terms: D016889:Endometrial Neoplasms / Q000235:genetics*; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D052138:Genes, Neoplasm; D006801:Humans; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D062085:RNA, Long Noncoding; D012333:RNA, Messenger