1,440
Views
23
CrossRef citations to date
0
Altmetric
Research Paper

Co-expression network analysis of long noncoding RNAs (IncRNAs) and cancer genes revealsSFTA1P and CASC2abnormalities in lung squamous cell carcinoma

, , &
Pages 115-122 | Received 23 Sep 2016, Accepted 08 Jan 2017, Published online: 13 Mar 2017

References

  • Network C. Comprehensive genomic characterization of squamous cell lung cancers. Nature 2012; 489(7417): 519-25; PMID:22960745; http://dx.doi.org/10.1038/nature11404
  • Chiba I, Takahashi T, Nau MM, D'Amico D, Curiel DT, Mitsudomi T, Buchhagen DL, Carbone D, Piantadosi S, Koga H, et al. Mutations in the p53 gene are frequent in primary, resected non-small cell lung cancer. lung cancer study group. Oncogene 1990; 5(10): 1603-10; PMID:1979160.
  • Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Research 2012; 22(9): 1775-1789; PMID:22955988; http://dx.doi.org/10.1101/gr.132159.111
  • Wang K, Chang H. Molecular mechanisms of long noncoding RNAs. Molecular cell 2011; 43(6): 904-14; PMID:21925379; http://dx.doi.org/10.1016/j.molcel.2011.08.018
  • Gupta R, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 2010; 464(7291): 1071-76; PMID:20393566; http://dx.doi.org/10.1038/nature08975
  • Wilusz J, Sunwoo H, Spector D. Long noncoding RNAs: functional surprises from the RNA world. Genes & Development 2009; 23(13): 1494-1504; http://dx.doi.org/10.1101/gad.1800909
  • Yu W, Gius D, Onyango P, Muldoon-Jacobs K, Karp J, Feinberg AP, Cui H. Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature 2008; 451(7175): 202-206; PMID:18185590; http://dx.doi.org/10.1038/nature06468
  • Wang N, Sanborn Z, Arnett KL, Bayston LJ, Liao W, Proby CM, Leigh IM, Collisson EA, Gordon PB, Jakkula L, et al. Loss-of-function mutations in Notch receptors in cutaneous and lung squamous cell carcinoma. Proceedings of the National Academy of Sciences 2011; 108(43): 17761-66; ; http://dx.doi.org/10.1073/pnas.1114669108
  • Guffanti A, et al. A transcriptional sketch of a primary human breast cancer by 454 deep sequencing. BMC Genomics 2009; 10(1): 1; PMID:19121221; http://dx.doi.org/10.1186/1471-2164-10-163
  • Yamada K, Kano J, Tsunoda H, Yoshikawa H, Okubo C, Ishiyama T, Noguchi M. Phenotypic characterization of endometrial stromal sarcoma of the uterus. Cancer Science 2006; 97(2): 106-12; PMID:16441420; http://dx.doi.org/10.1111/j.1349-7006.2006.00147.x
  • Lin R, Maeda S, Liu C, Karin M, Edgington TS. A large noncoding RNA is a marker for murine hepatocellular carcinomas and a spectrum of human carcinomas. Oncogene 2007; 26(6): 851-58; PMID:16878148; http://dx.doi.org/10.1038/sj.onc.1209846
  • Luo J, Ren B, Keryanov S, Tseng GC, Rao UN, Monga SP, Strom S, Demetris AJ, Nalesnik M, Yu YP, et al. Transcriptomic and genomic analysis of human hepatocellular carcinomas and hepatoblastomas. Hepatology 2006; 44(4): 1012-24; PMID:17006932; http://dx.doi.org/10.1002/hep.21328
  • He X, et al. Low expression of long noncoding RNA CASC2 indicates a poor prognosis and regulates cell proliferation in non-small cell lung cancer. Tumor Biology 2016; 37(7):9503-9510.
  • Du Z, et al. Integrative analyses reveal a long noncoding RNA-mediated sponge regulatory network in prostate cancer. Nature Communications 2016; 7:10982; http://dx.doi.org/10.1038/ncomms10982
  • Di Martino M, Guzzi PH, Caracciolo D, Agnelli L, Neri A, Walker BA, Morgan GJ, Cannataro M, Tassone P, Tagliaferri P, et al. Integrated analysis of microRNAs, transcription factors and target genes expression discloses a specific molecular architecture of hyperdiploid multiple myeloma. Oncotarget 2015; 6(22): 19132; PMID:26056083; http://dx.doi.org/10.18632/oncotarget.4302
  • Ritchie M, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research 2015; 43(7):e47; http://dx.doi.org/10.1093/nar/gkv007
  • Jiang Q, et al. LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data. BMC Genomics 2015; 16(3): 1. PMID:25553907; http://dx.doi.org/10.1186/1471-2164-16-S3-S2
  • Futreal P, Coin L, Marshall M, Down T, Hubbard T, Wooster R, Rahman N, Stratton MR. A census of human cancer genes. Nat Rev Cancer 2004; 4(3): 177-83; PMID:14993899; http://dx.doi.org/10.1038/nrc1299
  • Chen J, Hung WS, Chan HH, Tsai SJ, Sun HS. In silico identification of oncogenic potential of fyn-related kinase in hepatocellular carcinoma. Bioinformatics 2013; 29(4): 420-7; PMID:23267173; http://dx.doi.org/10.1093/bioinformatics/bts715
  • Mootha V, Lindgren CM, Eriksson KF, Subramanian A, Sihag S, Lehar J, Puigserver P, Carlsson E, Ridderstråle M, Laurila E, et al. PGC-1[alpha]-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet 2003; 34(3): 267-73; PMID:12808457; http://dx.doi.org/10.1038/ng1180
  • Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 2005; 102(43): 15545-50; PMID:16199517; http://dx.doi.org/10.1073/pnas.0506580102
  • Yang F, Lyu S, Dong S, Liu Y, Zhang X, Wang O. Expression profile analysis of long noncoding RNA in HER-2-enriched subtype breast cancer by next-generation sequencing and bioinformatics. OncoTargets and Therapy 2016; 9: 761; PMID:26929647; http://dx.doi.org/10.2147/OTT.S97664
  • Sørlie T, Tibshirani R, Parker J, Hastie T, Marron JS, Nobel A, Deng S, Johnsen H, Pesich R, Geisler S, et al. Repeated observation of breast tumor subtypes in independent gene expression data sets. Proceedings of the National Academy of Sciences 2003; 100(14): 8418-23; PMID:12829800; http://dx.doi.org/10.1073/pnas.0932692100
  • Sørlie T, et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proceedings of the National Academy of Sciences 2001; 98(19): 10869-74; PMID:11553815; http://dx.doi.org/10.1073/pnas.191367098
  • Zhao W, Luo J, Jiao S. Comprehensive characterization of cancer subtype associated long non-coding RNAs and their clinical implications. Scientific Reports 2014; 4: 6591; PMID:25307233; http://dx.doi.org/10.1038/srep06591
  • Wang P, Liu YH, Yao YL, Li Z, Li ZQ, Ma J, Xue YX. Long non-coding RNA CASC2 suppresses malignancy in human gliomas by miR-21. Cellular Signalling 2015; 27(2): 275-82; PMID:25446261; http://dx.doi.org/10.1016/j.cellsig.2014.11.011
  • Zhang J, Zhu N, Chen X. A novel long noncoding RNA LINC01133 is upregulated in lung squamous cell cancer and predicts survival. Tumor Biology 2015; 36(10): 7465-1; PMID:25908174; http://dx.doi.org/10.1007/s13277-015-3460-9
  • Dimitrova N, Zamudio JR, Jong RM, Soukup D, Resnick R, Sarma K, Ward AJ, Raj A, Lee JT, Sharp PA, et al. LincRNA-p21 activates p21 in cis to promote polycomb target gene expression and to enforce the G1/S checkpoint. Molecular Cell 2014; 54(5): 777-90; PMID:24857549; http://dx.doi.org/10.1016/j.molcel.2014.04.025

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.