Identification of crucial regulatory relationships between long non-coding RNAs and protein-coding genes in lung squamous cell carcinoma

Molecular and Cellular Probes - Tập 30 - Trang 146-152 - 2016
Xiaofen Wu1, Lei Ruan1, Yi Yang1, Qi Mei2
1Department of Gerontology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
2Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China

Tài liệu tham khảo

Network CGAR, 2012, Comprehensive genomic characterization of squamous cell lung cancers, Nature, 489, 519, 10.1038/nature11404 Siegel, 2013, Cancer statistics, CA Cancer J. Clin., 2013, 11, 10.3322/caac.21166 Xu, 2014, Loss of Lkb1 and Pten leads to lung squamous cell carcinoma with elevated PD-L1 expression, Cancer Cell., 25, 590, 10.1016/j.ccr.2014.03.033 Justilien, 2014, The PRKCI and SOX2 oncogenes are coamplified and cooperate to activate Hedgehog signaling in lung squamous cell carcinoma, Cancer Cell, 25, 139, 10.1016/j.ccr.2014.01.008 Heist, 2012, FGFR1 amplification in squamous cell carcinoma of the lung, J. Thorac. Oncol., 7, 1775, 10.1097/JTO.0b013e31826aed28 JiP, 2003, MALAT-1, a novel noncoding RNA, and thymosin β4 predict metastasis and survival in early-stage non-small cell lung cancer, Oncogene, 22, 8031, 10.1038/sj.onc.1206928 X-h, 2013, The long non-coding RNA HOTAIR indicates a poor prognosis and promotes metastasis in non-small cell lung cancer, BMC Cancer, 13, 464, 10.1186/1471-2407-13-464 Zhang, 2015, A novel long noncoding RNA LINC01133 is upregulated in lung squamous cell cancer and predicts survival, Tumor Biol., 1 Benjamini, 1995, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J. R. Stat. Soc. Ser. B Methodol., 289 Harrow, 2012, GENCODE: the reference human genome annotation for The ENCODE Project, Genome Res., 22, 1760, 10.1101/gr.135350.111 Yu, 2012, clusterProfiler: an R package for comparing biological themes among gene clusters, OMICS, 16, 284, 10.1089/omi.2011.0118 Eisen, 1998, Cluster analysis and display of genome-wide expression patterns, Proc. Natl. Acad. Sci. U. S. A., 95, 14863, 10.1073/pnas.95.25.14863 Herzel, 2001, Extracting information from cDNA arrays, CHAOS Interdiscip. J. Nonlinear Sci., 11, 98, 10.1063/1.1336843 Kohl, 2011, Cytoscape: software for visualization and analysis of biological networks, 291 Wingender, 2008, The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation, Brief. Bioinform., 9, 326, 10.1093/bib/bbn016 Shannon, 2014 Beckstette, 2006, Fast index based algorithms and software for matching position specific scoring matrices, BMC Bioinforma., 7, 389, 10.1186/1471-2105-7-389 Colombo, 2015, PVT1: a rising star among oncogenic long noncoding RNAs, BioMed Res. Int., 2015 Parsons, 2007, DNA polymerase δ-dependent repair of DNA single strand breaks containing 3′-end proximal lesions, Nucleic Acids Res., 35, 1054, 10.1093/nar/gkl1115 Baserga, 1965, The relationship of the cell cycle to tumor growth and control of cell division: a review, Cancer Res., 25, 581 Kikuchi, 2011, Minichromosome maintenance (MCM) protein 4 as a marker for proliferation and its clinical and clinicopathological significance in non-small cell lung cancer, Lung Cancer, 72, 229, 10.1016/j.lungcan.2010.08.020 Baik, 2009, DNA profiling by array comparative genomic hybridization (CGH) of peripheral blood mononuclear cells (PBMC) and tumor tissue cell in non-small cell lung cancer (NSCLC), Mol. Biol. Rep., 36, 1767, 10.1007/s11033-008-9380-7 Blomquist, 2013, CEBPG exhibits allele-specific expression in human bronchial epithelial cells, Gene Regul. Syst. Biol., 7, 125, 10.4137/GRSB.S11879 Groenen, 1996, Structure, sequence, and chromosome 19 localization of HumanUSF2and its rearrangement in a patient with multicystic renal dysplasia, Genomics, 38, 141, 10.1006/geno.1996.0609 Ocejo-Garcia, 2005, Roles for USF-2 in lung cancer proliferation and bronchial carcinogenesis, J. Pathol., 206, 151, 10.1002/path.1775 Soder, 1998, Tumour specific regulation of telomerase RNA gene expression visualized by in situ hybridization, Oncogene, 16, 979, 10.1038/sj.onc.1201620 Yokoi, 2003, TERC identified as a probable target within the 3q26 amplicon that is detected frequently in non-small cell lung cancers, Clin. Cancer Res., 9, 4705 Mamelak, 2005, Downregulation of NDUFA1 and other oxidative phosphorylation-related genes is a consistent feature of basal cell carcinoma, Exp. Dermatol., 14, 336, 10.1111/j.0906-6705.2005.00278.x Teh, 2012, FOXM1 induces a global methylation signature that mimics the cancer epigenome in head and neck squamous cell carcinoma, Plos One, 7, e34329, 10.1371/journal.pone.0034329 Wendler, 1997, Identification of pirin, a novel highly conserved nuclear protein, J. Biol. Chem., 272, 8482, 10.1074/jbc.272.13.8482 Pang, 2004, Crystal structure of human pirin An iron-binding nuclear protein and transcription cofactor, J. Biol. Chem., 279, 1491, 10.1074/jbc.M310022200