Screening potential lncRNA biomarkers for breast cancer and colorectal cancer combining random walk and logistic matrix factorization

被引:1
|
作者
Li, Shijun [1 ]
Chang, Miaomiao [1 ]
Tong, Ling [1 ]
Wang, Yuehua [1 ]
Wang, Meng [1 ]
Wang, Fang [1 ]
机构
[1] Chifeng Municipal Hosp, Dept Pathol, Chifeng, Peoples R China
关键词
breast cancer; colorectal cancer; lncRNA; biomarker; lncRNA-disease association; random walk; logistic matrix factorization; LONG NONCODING RNA; FUNCTIONAL SIMILARITY; DISEASE ASSOCIATIONS; ENSEMBLE METHOD; PREDICTION; EXPRESSION; HULC;
D O I
10.3389/fgene.2022.1023615
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
Breast cancer and colorectal cancer are two of the most common malignant tumors worldwide. They cause the leading causes of cancer mortality. Many researches have demonstrated that long noncoding RNAs (lncRNAs) have close linkages with the occurrence and development of the two cancers. Therefore, it is essential to design an effective way to identify potential lncRNA biomarkers for them. In this study, we developed a computational method (LDA-RWLMF) by integrating random walk with restart and Logistic Matrix Factorization to investigate the roles of lncRNA biomarkers in the prognosis and diagnosis of the two cancers. We first fuse disease semantic and Gaussian association profile similarities and lncRNA functional and Gaussian association profile similarities. Second, we design a negative selection algorithm to extract negative LncRNA-Disease Associations (LDA) based on random walk. Third, we develop a logistic matrix factorization model to predict possible LDAs. We compare our proposed LDA-RWLMF method with four classical LDA prediction methods, that is, LNCSIM1, LNCSIM2, ILNCSIM, and IDSSIM. The results from 5-fold cross validation on the MNDR dataset show that LDA-RWLMF computes the best AUC value of 0.9312, outperforming the above four LDA prediction methods. Finally, we rank all lncRNA biomarkers for the two cancers after determining the performance of LDA-RWLMF, respectively. We find that 48 and 50 lncRNAs have the highest association scores with breast cancer and colorectal cancer among all lncRNAs known to associate with them on the MNDR dataset, respectively. We predict that lncRNAs HULC and HAR1A could be separately potential biomarkers for breast cancer and colorectal cancer and need to biomedical experimental validation.
引用
收藏
页数:14
相关论文
共 50 条
  • [1] IRWNRLPI: Integrating Random Walk and Neighborhood Regularized Logistic Matrix Factorization for lncRNA-Protein Interaction Prediction
    Zhao, Qi
    Zhang, Yue
    Hu, Huan
    Ren, Guofei
    Zhang, Wen
    Liu, Hongsheng
    FRONTIERS IN GENETICS, 2018, 9
  • [2] Detecting lncRNA-Cancer Associations by Combining miRNAs, Genes, and Prognosis With Matrix Factorization
    Yan, Huan
    Chai, Hua
    Zhao, Huiying
    FRONTIERS IN GENETICS, 2021, 12
  • [3] Novel PBMC LncRNA signatures as diagnostic biomarkers for colorectal cancer
    Li, Zhaosheng
    Wang, Dongfeng
    Zhang, Wenjun
    Shi, Huina
    Zhu, Mingchen
    PATHOLOGY RESEARCH AND PRACTICE, 2024, 253
  • [4] Extracellular Matrix Biomarkers in Colorectal Cancer
    Kim, Min-Seob
    Ha, Se-Eun
    Wu, Moxin
    Zogg, Hannah
    Ronkon, Charles F.
    Lee, Moon-Young
    Ro, Seungil
    INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 2021, 22 (17)
  • [5] Identification and Validation of m6A-Related lncRNA Signature as Potential Predictive Biomarkers in Breast Cancer
    Lv, Wenchang
    Wang, Yichen
    Zhao, Chongru
    Tan, Yufang
    Xiong, Mingchen
    Yi, Yi
    He, Xiao
    Ren, Yuping
    Wu, Yiping
    Zhang, Qi
    FRONTIERS IN ONCOLOGY, 2021, 11
  • [6] Long Noncoding RNAs Serve as Potential Diagnostic Biomarkers for Colorectal Cancer
    Cai, Juan
    Zuo, Xueliang
    Chen, Zhiqiang
    Zhang, Yao
    Wang, Jinguo
    Wang, Junfeng
    Ye, Xiaobing
    Zhao, Wenying
    JOURNAL OF CANCER, 2019, 10 (03): : 611 - 619
  • [7] Biomarkers in colorectal cancer screening
    Schab, Katarzyna
    Tanska, Aleksandra
    Smutek, Maciej
    ONCOTARGET, 2017, 8 (67) : 110741 - 110742
  • [8] MicroRNAs in colorectal cancer: potential biomarkers and therapeutic targets
    Yan, Shuo
    Cao, Yan
    Mao, Aiwu
    FRONTIERS IN BIOSCIENCE-LANDMARK, 2015, 20 : 1092 - 1103
  • [9] Screening of significant biomarkers related with prognosis of liver cancer by lncRNA-associated ceRNAs analysis
    He, Jiefeng
    Zhao, Haichao
    Deng, Dongfeng
    Wang, Yadong
    Zhang, Xiao
    Zhao, Haoliang
    Xu, Zongquan
    JOURNAL OF CELLULAR PHYSIOLOGY, 2020, 235 (03) : 2464 - 2477
  • [10] Three CircRNAs Function as Potential Biomarkers for Colorectal Cancer
    Zhang, Jinling
    Cai, Ang
    Zhao, Yu
    CLINICAL LABORATORY, 2020, 66 (12) : 2405 - 2412