BRPCA: Bounded Robust Principal Component Analysis to Incorporate Similarity Network for N7-Methylguanosine(m7G) Site-Disease Association Prediction

被引:4
作者
Ma, Jiani [1 ,2 ]
Zhang, Lin [1 ,2 ]
Li, Shaojie [1 ,2 ]
Liu, Hui [1 ,2 ]
机构
[1] China Univ Min & Technol, Minist Educ, Engn Res Ctr Intelligent Control Underground Spac, Xuzhou 221116, Jiangsu, Peoples R China
[2] China Univ Min & Technol, Sch Informat & Control Engn, Xuzhou 221116, Jiangsu, Peoples R China
关键词
m(7)G-disease association prediction; similarity information; robust principal component analysis; MESSENGER-RNA; THRESHOLDING ALGORITHM; BREAST-CANCER; CAP STRUCTURE; ENZYMES;
D O I
10.1109/TCBB.2021.3109055
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Recent studies have revealed that N7-methylguanosine(m(7)G) plays a pivotal role in various biological processes and disease pathogenesis. To date, transcriptome-wide m(7)G modification sites have been identified by high-throughput sequencing approaches, and some related information has been recorded in a few biological databases. However, the mechanism of site action in disease remains uncharted. Wet experiments can help identify true m(7)G sites with high confidence, but it is time-consuming to find the true ones in such a large number of sites, which will also cost too much. Thus, computational methods are emergently needed to predict the associations between m(7)G sites and various diseases, thus help to uncover potential active sites for specific diseases. In this article, we proposed a bounded robust principal component analysis (BRPCA) method to predict unknown m(7)G-disease association based on similarity information. Importantly, BRPCA tolerates the noise and redundancy existing in association and similarity information. Moreover, a suitable bounded constraint is incorporated into BRPCA to ensure that the predicted association scores locate in a meaningful interval. The extensive experiments demonstrate the superiority and robustness of the BRPCA.
引用
收藏
页码:3295 / 3306
页数:12
相关论文
共 61 条
  • [1] DT-Web: a web-based application for drug-target interaction and drug combination prediction through domain-tuned network-based inference
    Alaimo, Salvatore
    Bonnici, Vincenzo
    Cancemi, Damiano
    Ferro, Alfredo
    Giugno, Rosalba
    Pulvirenti, Alfredo
    [J]. BMC SYSTEMS BIOLOGY, 2015, 9
  • [2] ncPred: ncRNA-disease association prediction through tripartite network-based inference
    [J]. Giugno, Rosalba (giugno@dmi.unict.it), 1600, Frontiers Media S.A., c/o Michael Kenyon, ch. de la Pecholettaz 6, Epalinges, 1066, Switzerland (02):
  • [3] Rapid tRNA decay can result from lack of nonessential modifications
    Alexandrov, A
    Chernyakov, I
    Gu, WF
    Hiley, SL
    Hughes, TR
    Grayhack, EJ
    Phizicky, EM
    [J]. MOLECULAR CELL, 2006, 21 (01) : 87 - 96
  • [4] A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems
    Beck, Amir
    Teboulle, Marc
    [J]. SIAM JOURNAL ON IMAGING SCIENCES, 2009, 2 (01): : 183 - 202
  • [5] MPZL1 forms a signalling complex with GRB2 adaptor and PTPN11 phosphatase in HER2-positive breast cancer cells
    Beigbeder, Alice
    Chartier, Francois J. M.
    Bisson, Nicolas
    [J]. SCIENTIFIC REPORTS, 2017, 7
  • [6] MODOMICS: a database of RNA modification pathways. 2017 update
    Boccaletto, Pietro
    Machnicka, Magdalena A.
    Purta, Elzbieta
    Piatkowski, Pawe
    Baginski, Blazej
    Wirecki, Tomasz K.
    de Crecy-Lagard, Valerie
    Ross, Robert
    Limbach, Patrick A.
    Kotter, Annika
    Helm, Mark
    Bujnicki, Janusz M.
    [J]. NUCLEIC ACIDS RESEARCH, 2018, 46 (D1) : D303 - D307
  • [7] Bogdanov Alexey, 2017, F1000Res, V6, P10, DOI 10.12688/f1000research.10481.1
  • [8] A SINGULAR VALUE THRESHOLDING ALGORITHM FOR MATRIX COMPLETION
    Cai, Jian-Feng
    Candes, Emmanuel J.
    Shen, Zuowei
    [J]. SIAM JOURNAL ON OPTIMIZATION, 2010, 20 (04) : 1956 - 1982
  • [9] Robust Principal Component Analysis?
    Candes, Emmanuel J.
    Li, Xiaodong
    Ma, Yi
    Wright, John
    [J]. JOURNAL OF THE ACM, 2011, 58 (03)
  • [10] Matrix Completion With Noise
    Candes, Emmanuel J.
    Plan, Yaniv
    [J]. PROCEEDINGS OF THE IEEE, 2010, 98 (06) : 925 - 936