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

被引:2
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
[21]   Identification of key genes in colorectal cancer using random walk with restart [J].
Cui, Xiaofeng ;
Shen, Kexin ;
Xie, Zhongshi ;
Liu, Tongjun ;
Zhang, Haishan .
MOLECULAR MEDICINE REPORTS, 2017, 15 (02) :867-872
[22]   MicroRNAs as potential liquid biopsy biomarkers in colorectal cancer: A systematic review [J].
Toiyama, Yuji ;
Okugawa, Yoshinaga ;
Fleshman, James ;
Boland, C. Richard ;
Goel, Ajay .
BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER, 2018, 1870 (02) :274-282
[23]   MicroRNAs that regulate PTEN as potential biomarkers in colorectal cancer: a systematic review [J].
Liu, Jianrong ;
Ke, Fei ;
Chen, Tingting ;
Zhou, Qing ;
Weng, Lingling ;
Tan, Jiani ;
Shen, Weixing ;
Li, Liu ;
Zhou, Jinyong ;
Xu, Changliang ;
Cheng, Haibo ;
Zhou, Jinrong .
JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY, 2020, 146 (04) :809-820
[24]   Detection and identification of potential biomarkers of breast cancer [J].
Yuxia Fan ;
Jiachen Wang ;
Yang Yang ;
Qiuliang Liu ;
Yingzhong Fan ;
Jiekai Yu ;
Shu Zheng ;
Mengquan Li ;
Jiaxiang Wang .
Journal of Cancer Research and Clinical Oncology, 2010, 136 :1243-1254
[25]   Detection and identification of potential biomarkers of breast cancer [J].
Fan, Yuxia ;
Wang, Jiachen ;
Yang, Yang ;
Liu, Qiuliang ;
Fan, Yingzhong ;
Yu, Jiekai ;
Zheng, Shu ;
Li, Mengquan ;
Wang, Jiaxiang .
JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY, 2010, 136 (08) :1243-1254
[26]   Circular RNAs as Potential Biomarkers in Breast Cancer [J].
De Palma, Fatima Domenica Elisa ;
Salvatore, Francesco ;
Pol, Jonathan G. ;
Kroemer, Guido ;
Maiuri, Maria Chiara .
BIOMEDICINES, 2022, 10 (03)
[27]   Non-coding RNAs as Biomarkers for Colorectal Cancer Screening and Early Detection [J].
Slaby, Ondrej .
NON-CODING RNAS IN COLORECTAL CANCER, 2016, 937 :153-170
[28]   Exploring Potential Epigenetic Biomarkers for Colorectal Cancer Metastasis [J].
Ajithkumar, Priyadarshana ;
Vasantharajan, Sai Shyam ;
Pattison, Sharon ;
McCall, John L. ;
Rodger, Euan J. ;
Chatterjee, Aniruddha .
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 2024, 25 (02)
[29]   Histone modification: Biomarkers and potential therapies in colorectal cancer [J].
An, Xin ;
Lan, Xiaohua ;
Feng, Zizhen ;
Li, Xiaohong ;
Su, Qisheng .
ANNALS OF HUMAN GENETICS, 2023, 87 (06) :274-284
[30]   Screening and Identification of Novel Potential Biomarkers for Breast Cancer Brain Metastases [J].
Wang, Lulu ;
Zeng, Dan ;
Wang, Qi ;
Liu, Li ;
Lu, Tao ;
Gao, Yan .
FRONTIERS IN ONCOLOGY, 2022, 11