[1]
Li Y, Padmanabha D, Gentile LB, Dumur CI, Beckstead RB, Baker KD. HIF- and non-HIF-regulated hypoxic responses require the estrogen-related receptor in Drosophila melanogaster. PLoS Genet 2013; 9(1): e1003230.
[2]
Semenza GL. HIF-1 and human disease: one highly involved factor. Genes Dev 2000; 14(16): 1983-91.
[3]
Gupta A, Sugadev R, Sharma YK, Yahmad Y, Khurana P. Role of miRNAs in hypoxia-related disorders. J Biosci 2018; 43(4): 739-49.
[4]
Majmundar AJ, Wong WJ, Simon MC. Hypoxia-inducible factors and the response to hypoxic stress. Mol Cell 2010; 40(2): 294-309.
[5]
Kunz M, Ibrahim SM. Molecular responses to hypoxia in tumor cells. Mol Cancer 2003; 2: 23.
[6]
Hubbi ME, Semenza GL. Regulation of cell proliferation by hypoxia-inducible factors. Am J Physiol Cell Physiol 2015; 309(12): C775-82.
[7]
Goda N, Ryan HE, Khadivi B, McNulty W, Rickert RC, Johnson RS. Hypoxia-inducible factor 1 alpha is essential for cell cycle arrest during hypoxia. Mol Cell Biol 2003; 23(1): 359-69.
[8]
Hu CJ, Wang LY, Chodosh LA, Keith B, Simon MC. Differential roles of hypoxia-inducible factor 1alpha (HIF-1alpha) and HIF-2alpha in hypoxic gene regulation. Mol Cell Biol 2003; 23(24): 9361-74.
[9]
Fandrey J, Gorr TA, Gassmann M. Regulating cellular oxygen sensing by hydroxylation. Cardiovasc Res 2006; 71(4): 642-51.
[10]
Kunz M, Moeller S, Koczan D, et al. Mechanisms of hypoxic gene regulation of angiogenesis factor Cyr61 in melanoma cells. The J Boil Chem 2003; 278(46): 45651-60.
[11]
Semenza GL. Targeting HIF-1 for cancer therapy. Nat Rev Cancer 2003; 3(10): 721-32.
[12]
Manalo DJ, Rowan A, Lavoie T, et al. Transcriptional regulation of vascular endothelial cell responses to hypoxia by HIF-1. Blood 2005; 105(2): 659-69.
[13]
Wang V, Davis DA, Haque M, Huang LE, Yarchoan R. Differential gene up-regulation by hypoxia-inducible factor-1alpha and hypoxia-inducible factor-2alpha in HEK293T cells. Cancer Res 2005; 65(8): 3299-306.
[14]
Benita Y, Kikuchi H, Smith AD, Zhang MQ, Chung DC, Xavier RJ. An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia. Nucleic Acids Res 2009; 37(14): 4587-602.
[15]
Zhang HM, Kuang S, Xiong X, Gao T, Liu C, Guo AY. Transcription factor and microRNA co-regulatory loops: important regulatory motifs in biological processes and diseases. Brief Bioinform 2015; 16(1): 45-58.
[16]
Slomiany MG, Rosenzweig SA. Hypoxia-inducible factor-1-dependent and -independent regulation of insulin-like growth factor-1-stimulated vascular endothelial growth factor secretion. The J Pharmacol Exp Ther 2006; 318(2): 666-75.
[17]
Mizukami Y, Kohgo Y, Chung DC. Hypoxia inducible factor-1 independent pathways in tumor angiogenesis. Clin Cancer Res 2007; 13(19): 5670-4.
[18]
Fujisue Y, Nakagawa T, Takahara K, et al. Induction of erythropoietin increases the cell proliferation rate in a hypoxia-inducible factor-1-dependent and -independent manner in renal cell carcinoma cell lines. Oncol Lett 2013; 5(6): 1765-70.
[19]
Lee J, Lee J. Hypoxia-inducible Factor-1 (HIF-1)-independent hypoxia response of the small heat shock protein hsp-16.1 gene regulated by chromatin-remodeling factors in the nematode Caenorhabditis elegans. The J Boil Chem 2013; 288(3): 1582-9.
[20]
Joyce D, Albanese C, Steer J, Fu M, Bouzahzah B, Pestell RG. NF-kappaB and cell-cycle regulation: the cyclin connection. Cytokine Growth Factor Rev 2001; 12(1): 73-90.
[21]
Weiler-Mithoff EM, Friederich HC, Horn W, Issing K. Increase of oxygen partial pressure and acceleration of wound healing by tetrachlorodecaoxide. Zeitschrift fur Hautkrankheiten 1989; 64(3): 208-11.
[22]
Ledoux AC, Perkins ND. NF-kappaB and the cell cycle. Biochem Soc Trans 2014; 42(1): 76-81.
[23]
Cummins EP, Berra E, Comerford KM, et al. Prolyl hydroxylase-1 negatively regulates IkappaB kinase-beta, giving insight into hypoxia-induced NFkappaB activity. Proc Natl Acad Sci USA 2006; 103(48): 18154-9.
[24]
Gilmore TD. Introduction to NF-kappaB: players, pathways, perspectives. Oncogene 2006; 25(51): 6680-4.
[25]
Wouters BG, Koritzinsky M. Hypoxia signalling through mTOR and the unfolded protein response in cancer. Nat Rev Cancer 2008; 8(11): 851-64.
[26]
Kulshreshtha R, Ferracin M, Wojcik SE, et al. A microRNA signature of hypoxia. Mol Cell Biol 2007; 27(5): 1859-67.
[27]
Huang X, Le QT, Giaccia AJ. MiR-210--micromanager of the hypoxia pathway. Trends Mol Med 2010; 16(5): 230-7.
[28]
Chivukula RR, Mendell JT. Circular reasoning: microRNAs and cell-cycle control. Trends Biochem Sci 2008; 33(10): 474-81.
[29]
Bandi N, Zbinden S, Gugger M, et al. miR-15a and miR-16 are implicated in cell cycle regulation in a Rb-dependent manner and are frequently deleted or down-regulated in non-small cell lung cancer. Cancer Res 2009; 69(13): 5553-9.
[30]
Chen J, Wang DZ. microRNAs in cardiovascular development. J Mol Cell Cardiol 2012; 52(5): 949-57.
[31]
Chan YC, Khanna S, Roy S, Sen CK. miR-200b targets Ets-1 and is down-regulated by hypoxia to induce angiogenic response of endothelial cells. The J Biol Chem 2011; 286(3): 2047-56.
[32]
Tili E, Croce CM, Michaille JJ. MiR-155: on the crosstalk between inflammation and cancer. Int Rev Immunol 2009; 28(5): 264-84.
[33]
Li T, Li RS, Li YH, et al. miR-21 as an independent biochemical recurrence predictor and potential therapeutic target for prostate cancer. The J Urol 2012; 187(4): 1466-72.
[34]
Gulyaeva LF, Kushlinskiy NE. Regulatory mechanisms of microRNA expression. J Transl Med 2016; 14(1): 143.
[35]
Zhang G, Shi H, Wang L, et al. MicroRNA and transcription factor mediated regulatory network analysis reveals critical regulators and regulatory modules in myocardial infarction. PLoS One 2015; 10(8): e0135339.
[36]
Zhang G, Xu Z, Wang N. Network of microRNA, transcription factors, target genes and host genes in human mesothelioma. Exp Therapeut Med 2017; 13(6): 3039-46.
[37]
Khurana SR, Sarkar S, Singh SB. A network-based analysis of proteins involved in hypoxia-stress and identification of leader proteins. J Proteomics Enzymol 2016; 5(1)
[38]
Tsang J, Zhu J, van Oudenaarden A. MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals. Mol Cell 2007; 26(5): 753-67.
[39]
Liang C, Li Y, Luo J, Zhang Z. A novel motif-discovery algorithm to identify co-regulatory motifs in large transcription factor and microRNA co-regulatory networks in human. Bioinformatics 2015; 31(14): 2348-55.
[40]
Franco E, Galloway KE. Feedback loops in biological networks. Methods Mol Biol 2015; 1244: 193-214.
[41]
Mangan S, Alon U. Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci USA 2003; 100(21): 11980-5.
[42]
Su N, Wang Y, Qian M, Deng M. Combinatorial regulation of transcription factors and microRNAs. BMC Syst Biol 2010; 4: 150.
[43]
Li G, Ross KE, Arighi CN, Peng Y, Wu CH, Vijay-Shanker K. miRTex: a text mining system for miRNA-gene relation extraction. PLOS Comput Biol 2015; 11(9): e1004391.
[44]
Griffiths-Jones S. miRBase: the microRNA sequence database. Methods Mol Biol 2006; 342: 129-38.
[45]
Ru Y, Kechris KJ, Tabakoff B, et al. The multiMiR R package and database: integration of microRNA-target interactions along with their disease and drug associations. Nucleic Acids Res 2014; 42(17): e133.
[46]
Chou CH, Chang NW, Shrestha S, et al. miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database. Nucleic Acids Res 2016; 44(D1): D239-47.
[47]
Sethupathy P, Corda B, Hatzigeorgiou AG. TarBase: a comprehensive database of experimentally supported animal microRNA targets. RNA 2006; 12(2): 192-7.
[48]
Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T. miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res 2009; 37(Database issue): D105-10.
[49]
Fontaine JF, Priller F, Barbosa-Silva A, Andrade-Navarro MA. Genie: literature-based gene prioritization at multi genomic scaleNucleic Acids Res 2011; 39(Web Server issue): W455-61
[50]
Khurana P, Sugadev R, Jain J, Singh SB. HypoxiaDB: a database of hypoxia-regulated proteinsDatabase: The J Biol Databases Curat 2013; 2013: bat074
[51]
Jeanquartier F, Jean-Quartier C, Holzinger A. Integrated web visualizations for protein-protein interaction databases. BMC Bioinformatics 2015; 16: 195.
[52]
Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T. Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 2011; 27(3): 431-2.
[53]
Dennis G Jr, Sherman BT, Hosack DA, et al. DAVID: database for annotation, visualization, and integrated discovery. Genome Biol 2003; 4(5): 3.
[54]
Merico D, Isserlin R, Stueker O, Emili A, Bader GD. Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS One 2010; 5(11): e13984.
[55]
Schuierer S, Tranchevent LC, Dengler U, Moreau Y. Large-scale benchmark of endeavour using metacore maps. Bioinformatics 2010; 26(15): 1922-3.
[56]
Nishimura D. BioCarta. Biotech Softw Internet Rep 2004; 2(3): 117.
[57]
Pankaj K, Sugadev R, Sarkar S, Shashi BS. A comprehensive assessment of networks and pathways of hypoxia-associated proteins and identification of responsive protein modules. Netw Model Anal Health Inform Bioinform 2016; 5(1): 1-13.
[58]
Rezaei-Tavirani M, Rezaei-Tavirani M, Mansouri V, et al. Introducing crucial protein panel of gastric adenocarcinoma disease. Gastroenterol Hepatol From Bed To Bench 2017; 10(1): 21-8.
[59]
Safari-Alighiarloo N, Taghizadeh M, Tabatabaei SM, et al. Identification of new key genes for type 1 diabetes through construction and analysis of protein-protein interaction networks based on blood and pancreatic islet transcriptomes. J Diabetes 2017; 9(8): 764-77.
[60]
Hamed M, Spaniol C, Nazarieh M, Helms V. TFmiR: a web server for constructing and analyzing disease-specific transcription factor and miRNA co-regulatory networks. Nucleic Acids Res 2015; 43(W1): W283-8.
[61]
Matys V, Fricke E, Geffers R, et al. TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res 2003; 31(1): 374-8.
[62]
Griffith OL, Montgomery SB, Bernier B, et al. ORegAnno: an open-access community-driven resource for regulatory annotation. Nucleic Acids Res 2008; 36(Database issue): D107-13.
[63]
Liberzon A, Subramanian A, Pinchback R, Thorvaldsdottir H, Tamayo P, Mesirov JP. Molecular signatures database (MSigDB) 3.0. Bioinformatics 2011; 27(12): 1739-40.
[64]
Wang J, Lu M, Qiu C, Cui Q. TransmiR: a transcription factor-microRNA regulation database. Nucleic Acids Res 2010; 38(Database issue): D119-22.
[65]
Zhou KR, Liu S, Sun WJ, et al. ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data. Nucleic Acids Res 2017; 45(D1): D43-50.
[66]
Li JH, Liu S, Zhou H, Qu LH, Yang JH. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res 2014; 42(Database issue): D92-7.
[67]
Sengupta D, Bandyopadhyay S. Participation of microRNAs in human interactome: extraction of microRNA-microRNA regulations. Mol Biosyst 2011; 7(6): 1966-73.
[68]
Shalgi R, Lieber D, Oren M, Pilpel Y. Global and local architecture of the mammalian microRNA-transcription factor regulatory network. PLOS Comput Biol 2007; 3(7): e131.
[69]
Zhu H, Fan GC. Role of microRNAs in the reperfused myocardium towards post-infarct remodelling. Cardiovasc Res 2012; 94(2): 284-92.
[70]
Volm M, Koomagi R. Hypoxia-Inducible Factor (HIF-1) and its relationship to apoptosis and proliferation in lung cancer. Anticancer Res 2000; 20(3A): 1527-33.
[71]
Schmidt M, Fernandez de Mattos S, van der Horst A, et al. Cell cycle inhibition by FoxO forkhead transcription factors involves downregulation of cyclin D. Mol Cell Biol 2002; 22(22): 7842-52.
[72]
Papageorgis P, Cheng K, Ozturk S, et al. Smad4 inactivation promotes malignancy and drug resistance of colon cancer. Cancer Res 2011; 71(3): 998-1008.
[73]
Wierenga AT, Vellenga E, Schuringa JJ. Convergence of hypoxia and TGF beta pathways on cell cycle regulation in human hematopoietic stem/progenitor cells. PLoS One 2014; 9(3): e93494.
[74]
Zhang H, Akman HO, Smith EL, Zhao J, Murphy-Ullrich JE, Batuman OA. Cellular response to hypoxia involves signaling via Smad proteins. Blood 2003; 101(6): 2253-60.
[75]
Ijichi H, Otsuka M, Tateishi K, et al. Smad4-independent regulation of p21/WAF1 by transforming growth factor-beta. Oncogene 2004; 23(5): 1043-51.
[76]
Guttilla IK, White BA. Coordinate regulation of FOXO1 by miR-27a, miR-96, and miR-182 in breast cancer cells. The J Biol Chem 2009; 284(35): 23204-16.
[77]
Zhou CH, Zhang XP, Liu F, Wang W. Modeling the interplay between the HIF-1 and p53 pathways in hypoxia. Sci Rep 2015; 5: 13834.
[78]
Kano H, Arakawa Y, Takahashi JA, et al. Overexpression of RFT induces G1-S arrest and apoptosis via p53/p21(Waf1) pathway in glioma cell. Biochem Biophys Res Commun 2004; 317(3): 902-8.
[79]
Curran JE, Weinstein SR, Griffiths LR. Polymorphic variants of NFKB1 and its inhibitory protein NFKBIA, and their involvement in sporadic breast cancer. Cancer Lett 2002; 188(1-2): 103-7.
[80]
Hirata H, Ueno K, Shahryari V, et al. MicroRNA-182-5p promotes cell invasion and proliferation by down regulating FOXF2, RECK and MTSS1 genes in human prostate cancer. PLoS One 2013; 8(1): e55502.
[81]
Kouri FM, Hurley LA, Daniel WL, et al. miR-182 integrates apoptosis, growth, and differentiation programs in glioblastoma. Genes Dev 2015; 29(7): 732-45.
[82]
Katakowski M, Zheng X, Jiang F, Rogers T, Szalad A, Chopp M. MiR-146b-5p suppresses EGFR expression and reduces in vitro migration and invasion of glioma. Cancer Invest 2010; 28(10): 1024-30.
[83]
Cai T, Long J, Wang H, Liu W, Zhang Y. Identification and characterization of miR-96, a potential biomarker of NSCLC, through bioinformatic analysis. Oncol Rep 2017; 38(2): 1213-23.
62
8