Analysis of co-expression networks for circular RNAs and mRNAs reveals that circular RNAs hsa_circ_0047905, hsa_circ_0138960 and has-circRNA7690-15 are candidate oncogenes in gastric cancer

References

• Torre LA, Bray F, Siegel RL, Ferlay J, Lortet-Tieulent J, Jemal A. Global cancer statistics, 2012. CA Cancer J Clin. 2015;65:87-108. doi:10.3322/caac.21262. PMID:25651787
   PubMed Web of Science ®Google Scholar
• Chen W, Zheng R, Baade PD, Zhang S, Zeng H, Bray F, Jemal A, Yu XQ, He J. Cancer statistics in China, 2015. CA: A Cancer Journal for Clinicians. 2016;66:115-32. PMID:26808342
   PubMed Web of Science ®Google Scholar
• Ferlay J, Soerjomataram I, Dikshit R, Eser S, Mathers C, Rebelo M, Parkin DM, Forman D, Bray F. Cancer incidence and mortality worldwide: sources, methods and major patterns in GLOBOCAN 2012. Int J Cancer. 2015;136:E359-86. doi:10.1002/ijc.29210. PMID:25220842
   PubMed Web of Science ®Google Scholar
• Kolakofsky D. Isolation and characterization of Sendai virus DI-RNAs. Cell. 1976;8:547-55. doi:10.1016/0092-8674(76)90223-3. PMID:182384
   PubMed Web of Science ®Google Scholar
• Hsu MT, Coca-Prados M. Electron microscopic evidence for the circular form of RNA in the cytoplasm of eukaryotic cells. Nature. 1979;280:339-40. doi:10.1038/280339a0. PMID:460409.
   PubMedGoogle Scholar
• Hansen TB, Jensen TI, Clausen BH, Bramsen JB, Finsen B, Damgaard CK, Kjems J. Natural RNA circles function as efficient microRNA sponges. Nature. 2013;495:384-8. doi:10.1038/nature11993. PMID:23446346
   PubMed Web of Science ®Google Scholar
• Li Z, Huang C, Bao C, Chen L, Lin M, Wang X, Zhong G, Yu B, Hu W, Dai L, et al. Exon-intron circular RNAs regulate transcription in the nucleus. Nat Struct Mol Biol. 2015;22:256-64. doi:10.1038/nsmb.2959. PMID:25664725
   PubMed Web of Science ®Google Scholar
• Granados-Riveron JT, Aquino-Jarquin G. The complexity of the translation ability of circRNAs. Biochim Biophys Acta. 2016;1859:1245-51. doi:10.1016/j.bbagrm.2016.07.009. PMID:27449861
   PubMed Web of Science ®Google Scholar
• Szabo L, Salzman J. Detecting circular RNAs: bioinformatic and experimental challenges. Nat Rev Genet. 2016;17:679-92. doi:10.1038/nrg.2016.114. PMID:27739534
   PubMed Web of Science ®Google Scholar
• Chen Y, Li C, Tan C, Liu X. Circular RNAs: a new frontier in the study of human diseases. J Med Genet. 2016;53:359-65. doi:10.1136/jmedgenet-2016-103758. PMID:26945092
   PubMed Web of Science ®Google Scholar
• Wang Y, Mo Y, Gong Z, Yang X, Yang M, Zhang S, Xiong F, Xiang B, Zhou M, Liao Q, et al. Circular RNAs in human cancer. Mol Cancer. 2017;16:25. doi:10.1186/s12943-017-0598-7.
   PubMed Web of Science ®Google Scholar
• Huang G, Li S, Yang N, Zou Y, Zheng D, Xiao T. Recent progress in circular RNAs in human cancers. Cancer Lett. 2017;404:8-18. doi:10.1016/j.canlet.2017.07.002. PMID:28705773
   PubMed Web of Science ®Google Scholar
• Li W, Song Y, Zhang H, Zhou Z, Xie X, Zeng Q, Guo K, Wang T, Xia P, Chang D. Decreased expression of Hsa_circ_00001649 in Gastric cancer and its clinical significance. Dis Markers. 2017;2017:1-6. doi:10.1155/2017/7089493.
   Web of Science ®Google Scholar
• Chen S, Li T, Zhao Q, Xiao B, Guo J. Using circular RNA hsa_circ_0000190 as a new biomarker in the diagnosis of gastric cancer. Clin Chim Acta. 2017;466:167-71. doi:10.1016/j.cca.2017.01.025. PMID:28130019
   PubMed Web of Science ®Google Scholar
• Zhang Y, Li J, Yu J, Liu H, Shen ZY, Ye GT, Mou TY, Qi XL, Li GX. Circular RNAs signature predicts the early recurrence of stage III gastric cancer after radical surgery. 2017;8:22936-43.
   Google Scholar
• Chen J, Li Y, Zheng Q, Bao C, He J, Chen B, Lyu D, Zheng B, Xu Y, Long Z, et al. Circular RNA profile identifies circPVT1 as a proliferative factor and prognostic marker in gastric cancer. Cancer Lett. 2017;388:208-19. doi:10.1016/j.canlet.2016.12.006. PMID:27986464
   PubMed Web of Science ®Google Scholar
• Sun TT, He J, Liang Q, Ren LL, Yan TT, Yu TC, Tang JY, Bao YJ, Hu Y, Lin Y, et al. LncRNA GClnc1 promotes Gastric Carcinogenesis and may act as a modular Scaffold of WDR5 and KAT2A complexes to specify the Histone modification pattern. Cancer Discov. 2016;6:784-801. doi:10.1158/2159-8290.CD-15-0921. PMID:27147598
   PubMed Web of Science ®Google Scholar
• Prieto C, Risueno A, Fontanillo C, De Las RJ. Human gene coexpression landscape: confident network derived from tissue transcriptomic profiles. Plos One. 2008;3:e3911. doi:10.1371/journal.pone.0003911. PMID:19081792
   PubMed Web of Science ®Google Scholar
• Barabasi AL, Oltvai ZN. Network biology: understanding the cell's functional organization. Nat Rev Genet. 2004;5:101-13. doi:10.1038/nrg1272. PMID:14735121
   PubMed Web of Science ®Google Scholar
• Suzuki H, Zuo Y, Wang J, Zhang MQ, Malhotra A, Mayeda A. Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing. Nucleic Acids Res. 2006;34:e63. doi:10.1093/nar/gkl151. PMID:16682442
   PubMed Web of Science ®Google Scholar
• Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, Maier L, Mackowiak SD, Gregersen LH, Munschauer M, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013;495:333-8. doi:10.1038/nature11928. PMID:23446348
   PubMed Web of Science ®Google Scholar
• Salzman J, Chen RE, Olsen MN, Wang PL, Brown PO. Cell-type specific features of circular RNA expression. Plos Genet. 2013;9:e1003777. doi:10.1371/journal.pgen.1003777. PMID:24039610
   PubMed Web of Science ®Google Scholar
• Chen Y, Li C, Tan C, Liu X. Circular RNAs: a new frontier in the study of human diseases. J Med Genet. 2016;53:359-65. doi:10.1136/jmedgenet-2016-103758. PMID:26945092
   PubMed Web of Science ®Google Scholar
• Zou Z, Anisowicz A, Hendrix MJ, Thor A, Neveu M, Sheng S, Rafidi K, Seftor E, Sager R. Maspin, a serpin with tumor-suppressing activity in human mammary epithelial cells. Science. 1994;263:526-9. doi:10.1126/science.8290962. PMID:8290962
   PubMed Web of Science ®Google Scholar
• Kim SM, Cho SJ, Jang WY, Kim DH, Shin HS, Jang MK, Kim HY, Nam ES. Expression of maspin is associated with the intestinal type of gastric adenocarcinoma. Cancer Res Treat. 2005;37:228-32. doi:10.4143/crt.2005.37.4.228. PMID:19956519
   PubMedGoogle Scholar
• Song SY, Son HJ, Kim MH, Nam ES, Rhee JC, Park C. Prognostic significance of maspin expression in human gastric adenocarcinoma. Hepatogastroenterology. 2007;54:973-6. PMID:17591106
   PubMedGoogle Scholar
• Yu M, Zheng H, Tsuneyama K, Takahashi H, Nomoto K, Xu H, Takano Y. Paradoxical expression of maspin in gastric carcinomas: correlation with carcinogenesis and progression. Hum Pathol. 2007;38:1248-55. doi:10.1016/j.humpath.2006.11.025. PMID:17490717
   PubMed Web of Science ®Google Scholar
• Lei KF, Liu BY, Wang YF, Chen XH, Yu BQ, Guo Y, Zhu ZG. SerpinB5 interacts with KHDRBS3 and FBXO32 in gastric cancer cells. Oncol Rep. 2011;26:1115-20. PMID:21725612
   PubMed Web of Science ®Google Scholar
• Guo JU, Agarwal V, Guo H, Bartel DP. Expanded identification and characterization of mammalian circular RNAs. Genome Biol. 2014;15:409. doi:10.1186/s13059-014-0409-z. PMID:25070500
   PubMed Web of Science ®Google Scholar
• Li Z, Huang C, Bao C, Chen L, Lin M, Wang X, Zhong G, Yu B, Hu W, Dai L, et al. Exon-intron circular RNAs regulate transcription in the nucleus. Nat Struct Mol Biol. 2015;22:256-64. doi:10.1038/nsmb.2959. PMID:25664725
   PubMed Web of Science ®Google Scholar
• Li Z, Huang C, Bao C, Chen L, Lin M, Wang X, Zhong G, Yu B, Hu W, Dai L, et al. Corrigendum: Exon-intron circular RNAs regulate transcription in the nucleus. Nat Struct Mol Biol. 2017;24:194. doi:10.1038/nsmb0217-194a. PMID:28170000
   PubMed Web of Science ®Google Scholar
• Prieto C, Risueno A, Fontanillo C, De Las RJ. Human gene coexpression landscape: confident network derived from tissue transcriptomic profiles. Plos One. 2008;3:e3911. doi:10.1371/journal.pone.0003911. PMID:19081792
   PubMed Web of Science ®Google Scholar
• Vazquez A, Dobrin R, Sergi D, Eckmann JP, Oltvai ZN, Barabasi AL. The topological relationship between the large-scale attributes and local interaction patterns of complex networks. Proc Natl Acad Sci U S A. 2004;101:17940-5. doi:10.1073/pnas.0406024101. PMID:15598746
   PubMed Web of Science ®Google Scholar