Using Network Distance Analysis to Predict lncRNA–miRNA Interactions

Interdisciplinary Sciences: Computational Life Sciences - Tập 13 Số 3 - Trang 535-545 - 2021
Li Zhang1, Pengyu Yang2, Huawei Feng1, Qi Zhao3, Hongsheng Liu4
1School of Life Science, Liaoning University, Shenyang 110036, China
2School of Information, Liaoning University, Shenyang 110036, China
3School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan, 114051, China
4Research Center for Computer Simulating and Information Processing of Bio-macromolecules of Shenyang, Liaoning University, Shenyang, 110036, China

Tóm tắt

Từ khóa


Tài liệu tham khảo

Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 25(18):1915–1927. https://doi.org/10.1101/gad.17446611

Jalali S, Bhartiya D, Lalwani MK, Sivasubbu S, Scaria V (2013) Systematic transcriptome wide analysis of lncRNA–miRNA interactions. PLoS One 8(2):e53823. https://doi.org/10.1371/journal.pone.0053823

Achawanantakun R, Chen J, Sun Y, Zhang Y (2015) LncRNA-ID: long non-coding RNA IDentification using balanced random forests. Bioinformatics 31(24):3897–3905. https://doi.org/10.1093/bioinformatics/btv480

Li J, Tian H, Yang J, Gong Z (2016) Long noncoding RNAs regulate cell growth, proliferation, and apoptosis. DNA Cell Biol 35(9):459–470. https://doi.org/10.1089/dna.2015.3187

Yang Z, Tang Y, Lu H, Shi B, Ye Y, Xu G, Zhao Q (2018) Long non-coding RNA reprogramming (lncRNA-ROR) regulates cell apoptosis and autophagy in chondrocytes. J Cell Biochem 119(10):8432–8440. https://doi.org/10.1002/jcb.27057

Farazi TA, Hoell JI, Morozov P, Tuschl T (2013) MicroRNAs in human cancer. In: MicroRNA cancer regulation. Springer, pp 1–20. https://doi.org/10.1007/978-94-007-5590-1_1

Treiber T, Treiber N, Meister G (2019) Regulation of microRNA biogenesis and its crosstalk with other cellular pathways. Nat Rev Mol Cell Biol 20(1):5–20. https://doi.org/10.1038/s41580-018-0059-1

Chen X (2015) Predicting lncRNA-disease associations and constructing lncRNA functional similarity network based on the information of miRNA. Sci Rep 5(1):1–11. https://doi.org/10.1038/srep13186

Ye S, Yang L, Zhao X, Song W, Wang W, Zheng S (2014) Bioinformatics method to predict two regulation mechanism: TF–miRNA–mRNA and lncRNA–miRNA–mRNA in pancreatic cancer. Cell Biochem Biophys 70(3):1849–1858. https://doi.org/10.1007/s12013-014-0142-y

Wu Q, Guo L, Jiang F, Li L, Li Z, Chen F (2015) Analysis of the mi RNA–mRNA–lnc RNA networks in ER+ and ER− breast cancer cell lines. J Cell Mol Med 19(12):2874–2887. https://doi.org/10.1111/jcmm.12681

Shi X, Zhang H, Wang M et al (2017) LncRNA AFAP1-AS1 promotes growth and metastasis of cholangiocarcinoma cells. Oncotarget 8(35):58394. https://doi.org/10.18632/oncotarget.16880

Zheng B, Jeong S, Zhu Y, Chen L, Xia Q (2017) miRNA and lncRNA as biomarkers in cholangiocarcinoma (CCA). Oncotarget 8(59):100819. https://doi.org/10.18632/oncotarget.19044

Paraskevopoulou MD, Hatzigeorgiou AG (2016) Analyzing miRNA–lncRNA interactions. In: Methods in molecular biology, vol 1402. Springer, pp 271–286. https://doi.org/10.1007/978-1-4939-3378-5_21

Li N, Ponnusamy M, Li M-p, Wang K, Li P-F (2017) The role of microRNA and LncRNA–MicroRNA interactions in regulating ischemic heart disease. J Cardiovasc Pharmacol Ther 22(2):105–111. https://doi.org/10.1177/1074248416667600

Furió-Tarí P, Tarazona S, Gabaldón T, Enright AJ, Conesa A (2016) spongeScan: a web for detecting microRNA binding elements in lncRNA sequences. Nucleic Acids Res 44(W1):W176–W180. https://doi.org/10.1093/nar/gkw443

Yao Y, Ma J, Xue Y et al (2015) Knockdown of long non-coding RNA XIST exerts tumor-suppressive functions in human glioblastoma stem cells by up-regulating miR-152. Cancer Lett 359(1):75–86. https://doi.org/10.1016/j.canlet.2014.12.051

Zhao Q, Zhang Y, Hu H, Ren G, Zhang W, Liu H (2018) IRWNRLPI: integrating random walk and neighborhood regularized logistic matrix factorization for lncRNA–protein interaction prediction. Front Genet 9:239. https://doi.org/10.3389/fgene.2018.00239

Hu H, Zhu C, Ai H, Zhang L, Zhao J, Zhao Q, Liu H (2017) LPI-ETSLP: lncRNA–protein interaction prediction using eigenvalue transformation-based semi-supervised link prediction. Mol BioSyst 13(9):1781–1787. https://doi.org/10.1039/c7mb00290d

Zhao Q, Yu H, Ming Z, Hu H, Ren G, Liu H (2018) The bipartite network projection-recommended algorithm for predicting long non-coding RNA–protein interactions. Mol Ther Nucleic Acids 13:464–471. https://doi.org/10.1016/j.omtn.2018.09.020

Hu H, Zhang L, Ai H, Zhang H, Fan Y, Zhao Q, Liu H (2018) HLPI-ensemble: prediction of human lncRNA–protein interactions based on ensemble strategy. RNA Biol 15(6):797–806. https://doi.org/10.1080/15476286.2018.1457935

Chen X, Xie D, Wang L, Zhao Q, You Z-H, Liu H (2018) BNPMDA: bipartite network projection for MiRNA–disease association prediction. Bioinformatics 34(18):3178–3186. https://doi.org/10.1093/bioinformatics/bty333

Ge E, Yang Y, Gang M, Fan C, Zhao Q (2020) Predicting human disease-associated circRNAs based on locality-constrained linear coding. Genomics 112(2):1335–1342. https://doi.org/10.1016/j.ygeno.2019.08.001

Zhao Q, Yang Y, Ren G, Ge E, Fan C (2019) Integrating bipartite network projection and KATZ measure to identify novel CircRNA-disease associations. IEEE Trans Nanobiosci 18(4):578–584. https://doi.org/10.1109/TNB.2019.2922214

Huang Y-A, Chan KC, You Z-H (2018) Constructing prediction models from expression profiles for large scale lncRNA–miRNA interaction profiling. Bioinformatics 34(5):812–819. https://doi.org/10.1093/bioinformatics/btx672

Liu H, Ren G, Hu H, Zhang L, Ai H, Zhang W, Zhao Q (2017) LPI-NRLMF: lncRNA–protein interaction prediction by neighborhood regularized logistic matrix factorization. Oncotarget 8(61):103975. https://doi.org/10.18632/oncotarget.21934

Miao Y-R, Liu W, Zhang Q, Guo A-Y (2018) lncRNASNP2: an updated database of functional SNPs and mutations in human and mouse lncRNAs. Nucleic Acids Res 46(D1):D276–D280. https://doi.org/10.1093/nar/gkx1004

Volders P-J, Verheggen K, Menschaert G, Vandepoele K, Martens L, Vandesompele J, Mestdagh P (2015) An update on LNCipedia: a database for annotated human lncRNA sequences. Nucleic Acids Res 43(D1):D174–D180. https://doi.org/10.1093/nar/gku1060

Griffiths-Jones S (2010) miRBase: microRNA sequences and annotation. Curr Protoc Bioinform 29(1):12.19.11-12.19.10. https://doi.org/10.1002/0471250953.bi1209s29

He S, Liu C, Skogerbø G et al (2007) NONCODE v2. 0: decoding the non-coding. Nucleic Acids Res 36(suppl_1):D170–D172. https://doi.org/10.1093/nar/gkm1011

Chou C-H, Chang N-W, Shrestha S et al (2016) miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database. Nucleic Acids Res 44(D1):D239–D247. https://doi.org/10.1093/nar/gkv1258

Yang S, Wang Y, Lin Y, Shao D, He K, Huang L (2020) LncMirNet: predicting LncRNA–miRNA interaction based on deep learning of ribonucleic acid sequences. Molecules 25(19):4372. https://doi.org/10.3390/molecules25194372

Wallin E, Wettergren C, Hedman F, von Heijne G (1993) Fast Needleman–Wunsch scanning of sequence databanks on a massively parallel computer. Bioinformatics 9(1):117–118. https://doi.org/10.1093/bioinformatics/9.1.117

Chen X, Yan CC, Zhang X, You Z-H, Huang Y-A, Yan G-Y (2016) HGIMDA: Heterogeneous graph inference for miRNA-disease association prediction. Oncotarget 7(40):65257. https://doi.org/10.18632/oncotarget.11251

Gao M, Wu Z, Jiang F (2011) Userrank for item-based collaborative filtering recommendation. Inf Process Lett 111(9):440–446. https://doi.org/10.1016/j.ipl.2011.02.003

Yang H, Zhu H, Ibrahim JG (2018) MILFM: Multiple index latent factor model based on high-dimensional features. Biometrics 74(3):834–844. https://doi.org/10.1111/biom.12866

Chen X (2015) KATZLDA: KATZ measure for the lncRNA-disease association prediction. Sci Rep 5:16840. https://doi.org/10.1038/srep16840

Hosseini SM, Soltani BM, Tavallaei M, Mowla SJ, Tafsiri E, Bagheri A, Khorshid HRK (2018) Clinically significant dysregulation of hsa-miR-30d-5p and hsa-let-7b expression in patients with surgically resected non-small cell lung cancer. Avicenna J. Med. Biotechnol. 10(2):98–104

Jiang Y, Gao H, Liu M, Mao Q (2016) Sorting and biological characteristics analysis for side population cells in human primary hepatocellular carcinoma. Am J Cancer Res 6(9):1890–1905

Ozen M, Karatas OF, Gulluoglu S et al (2015) Overexpression of miR-145-5p inhibits proliferation of prostate cancer cells and reduces SOX2 expression. Cancer Investig 33(6):251–258. https://doi.org/10.3109/07357907.2015.1025407

Li L, Wang M, Mei Z, Cao W, Yang Y, Wang Y, Wen A (2017) lncRNAs HIF1A-AS2 facilitates the up-regulation of HIF-1α by sponging to miR-153-3p, whereby promoting angiogenesis in HUVECs in hypoxia. Biomed Pharmacother 96:165–172. https://doi.org/10.1016/j.biopha.2017.09.113