title: PPI network analysis of mRNA expression profile of ezrin knockdown in esophageal squamous cell carcinoma.
abstract: Ezrin, coding protein EZR which cross-links actin filaments, overexpresses and involves invasion, metastasis, and poor prognosis in various cancers including esophageal squamous cell carcinoma (ESCC). In our previous study, Ezrin was knock down and analyzed by mRNA expression profile which has not been fully mined. In this study, we applied protein-protein interactions (PPI) network knowledge and methods to explore our understanding of these differentially expressed genes (DEGs). PPI subnetworks showed that hundreds of DEGs interact with thousands of other proteins. Subcellular localization analyses found that the DEGs and their directly or indirectly interacting proteins distribute in multiple layers, which was applied to analyze the shortest paths between EZR and other DEGs. Gene ontology annotation generated a functional annotation map and found hundreds of significant terms, especially those associated with cytoskeleton organization of Ezrin protein, such as "cytoskeleton organization," "regulation of actin filament-based process," and "regulation of actin cytoskeleton organization." The algorithm of Random Walk with Restart was applied to prioritize the DEGs and identified several cancer related DEGs ranked closest to EZR. These analyses based on PPI network have greatly expanded our comprehension of the mRNA expression profile of Ezrin knockdown for future examination of the roles and mechanisms of Ezrin.
authors.affiliation: Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China.
authors.forename: Bingli
authors.initials: B
authors.lastname: Wu
authors.affiliation: Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China.
authors.forename: Jianjun
authors.initials: J
authors.lastname: Xie
authors.affiliation: Department of Pathology, Shantou Central Hospital, Shantou 515041, China.
authors.forename: Zepeng
authors.initials: Z
authors.lastname: Du
authors.affiliation: Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China.
authors.forename: Jianyi
authors.initials: J
authors.lastname: Wu
authors.affiliation: Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China.
authors.forename: Pixian
authors.initials: P
authors.lastname: Zhang
authors.affiliation: Institute of Oncologic Pathology, Shantou University Medical College, Shantou 515041, China.
authors.forename: Liyan
authors.initials: L
authors.lastname: Xu
authors.affiliation: Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China.
authors.forename: Enmin
authors.initials: E
authors.lastname: Li
mesh_terms: D008841:Actin Cytoskeleton / Q000235:genetics / Q000473:pathology; D002294:Carcinoma, Squamous Cell / Q000235:genetics* / Q000473:pathology; D045744:Cell Line, Tumor; D003598:Cytoskeletal Proteins / Q000096:biosynthesis* / Q000235:genetics; D003599:Cytoskeleton / Q000235:genetics / Q000473:pathology; D004938:Esophageal Neoplasms / Q000235:genetics* / Q000473:pathology; D000077277:Esophageal Squamous Cell Carcinoma; D015972:Gene Expression Regulation, Neoplastic; D055785:Gene Knockdown Techniques; D006801:Humans; D058977:Molecular Sequence Annotation; D060066:Protein Interaction Maps / Q000235:genetics*; D012333:RNA, Messenger / Q000096:biosynthesis; D000099149:Ezrin
chemical_list: D003598:Cytoskeletal Proteins; D012333:RNA, Messenger; D000099149:Ezrin