Many disease-related genes have been found to be associated with cancer diagnosis, which is useful for understanding the pathophysiology of cancer, generating targeted drugs, and developing new diagnostic and treatment techniques. With the development of the pan-cancer project and the ongoing expansion of sequencing technology, many scientists are focusing on mining common genes from The Cancer Genome Atlas (TCGA) across various cancer types. In this study, we attempted to infer pan-cancer associated genes by examining the microbial model organism Saccharomyces Cerevisiae (Yeast) by homology matching, which was motivated by the benefits of reverse genetics. First, a background network of protein-protein interactions and a pathogenic gene set involving several cancer types in humans and yeast were created. The homology between the human gene and yeast gene was then discovered by homology matching, and its interaction sub-network was obtained. This was undertaken following the principle that the homologous genes of the common ancestor may have similarities in expression. Then, using bidirectional long short-term memory (BiLSTM) in combination with adaptive integration of heterogeneous information, we further explored the topological characteristics of the yeast protein interaction network and presented a node representation score to evaluate the node ability in graphs. Finally, homologous mapping for human genes matched the important genes identified by ensemble classifiers for yeast, which may be thought of as genes connected to all types of cancer. One way to assess the performance of the BiLSTM model is through experiments on the database. On the other hand, enrichment analysis, survival analysis, and other outcomes can be used to confirm the biological importance of the prediction results. You may access the whole experimental protocols and programs at .
基金:
National Natural Science Foundation of China [12126367, 12126305]; Chen Xiao-Ping Foundation for the Development of Science and Technology of Hubei Province [CXPJJH120000022020058]; Hubei Provincial Natural Science Foundation of China [2015CFA010]; Fundamental Research Funds for the Central Universities, China University of Geosciences (Wuhan) [CUGGC02]; Shanghai Municipal Science and Technology Major Project [2018SHZDZX01]; Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (LCNBI); ZJLab
第一作者单位:[1]Huazhong Univ Sci & Technol,Tongji Hosp,Tongji Med Coll,Inst Hepatopancreato Biliary Surg,Dept Surg,Hepat,Wuhan,Peoples R China
通讯作者:
通讯机构:[3]China Univ Geosci, Sch Automat, Wuhan, Peoples R China[4]Hubei Key Lab Adv Control & Intelligent Automat, Wuhan, Peoples R China[5]Engn Res Ctr Intelligent Technol Geoexplorat, Wuhan, Peoples R China[7]Key Lab Computat Neurosci & Brain Inspired Intell, Shanghai, Peoples R China
推荐引用方式(GB/T 7714):
Wang Chao,Zhang Houwang,Ma Haishu,et al.Inference of pan-cancer related genes by orthologs matching based on enhanced LSTM model[J].FRONTIERS IN MICROBIOLOGY.2022,13:doi:10.3389/fmicb.2022.963704.
APA:
Wang, Chao,Zhang, Houwang,Ma, Haishu,Wang, Yawen,Cai, Ke...&Zhu, Yuan.(2022).Inference of pan-cancer related genes by orthologs matching based on enhanced LSTM model.FRONTIERS IN MICROBIOLOGY,13,
MLA:
Wang, Chao,et al."Inference of pan-cancer related genes by orthologs matching based on enhanced LSTM model".FRONTIERS IN MICROBIOLOGY 13.(2022)