title: Network based analyses of gene expression profile of LCN2 overexpression in esophageal squamous cell carcinoma.
abstract: LCN2 (lipocalin 2) is a member of the lipocalin family of proteins that transport small, hydrophobic ligands. LCN2 is elevated in various cancers including esophageal squamous cell carcinoma (ESCC). In this study, LCN2 was overexpressed in the EC109 ESCC cell line and we applied integrated analyses of the gene expression data to identify protein-protein interactions (PPI) network to enhance our understanding of the role of LCN2 in ESCC. Through further mining of PPI sub-networks, hundreds of differentially expressed genes (DEGs) were identified to interact with thousands of other proteins. Subcellular localization analyses found the DEGs and their directly or indirectly interacting proteins distributed in multiple layers, which was applied to analyze the possible paths between two DEGs. Gene Ontology annotation generated a functional annotation map and found hundreds of significant terms, especially those associated with the known and potential roles of LCN2 protein. The algorithm of Random Walk with Restart was applied to prioritize the DEGs and identified several cancer-related DEGs ranked closest to LCN2 protein. These analyses based on PPI network have greatly expanded our understanding of the mRNA expression profile of LCN2 overexpression for future examination of the roles and mechanisms of LCN2.
authors: 1] Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou515041, China [2].
authors: Bingli
authors: B
authors: Wu
authors: 1] Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou515041, China [2] College of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing163319, China [3].
authors: Chunquan
authors: C
authors: Li
authors: Department of Pathology, Shantou Central Hospital, Shantou515041, China.
authors: Zepeng
authors: Z
authors: Du
authors: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin150081, China.
authors: Qianlan
authors: Q
authors: Yao
authors: Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou515041, China.
authors: Jianyi
authors: J
authors: Wu
authors: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin150081, China.
authors: Li
authors: L
authors: Feng
authors: Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou515041, China.
authors: Pixian
authors: P
authors: Zhang
authors: College of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing163319, China.
authors: Shang
authors: S
authors: Li
authors: Institute of Oncologic Pathology, Shantou University Medical College, Shantou515041, China.
authors: Liyan
authors: L
authors: Xu
authors: Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou515041, China.
authors: Enmin
authors: E
authors: Li
mesh_terms: D000209:Acute-Phase Proteins / Q000378:metabolism*; D000465:Algorithms; D002294:Carcinoma, Squamous Cell / Q000378:metabolism*; D003198:Computer Simulation; D004938:Esophageal Neoplasms / Q000378:metabolism*; D020869:Gene Expression Profiling / Q000379:methods; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D000071068:Lipocalin-2; D054834:Lipocalins / Q000378:metabolism*; D008954:Models, Biological; D009363:Neoplasm Proteins / Q000378:metabolism*; D011518:Proto-Oncogene Proteins / Q000378:metabolism*; D015398:Signal Transduction; D015854:Up-Regulation
chemical_list: D000209:Acute-Phase Proteins; C489506:LCN2 protein, human; D000071068:Lipocalin-2; D054834:Lipocalins; D009363:Neoplasm Proteins; D011518:Proto-Oncogene Proteins