Prediction and analysis of essential genes using the enrichments of gene ontology and KEGG pathways
文献类型：期刊论文
| 作者 | Chen, Lei1,2; Wang, ShaoPeng1; Cai, Yu-Dong1; Zhang, Yu-Hang3; Huang, Tao3; Zhang, YunHua4; , |
| 刊名 | PLOS ONE
 |
| 出版日期 | 2017 |
| 卷号 | 12期号:9页码:e0184129 |
| 关键词 | Canopy photosynthesis Bioenergy Canopy architecture Crop row orientation |
| ISSN号 | 1932-6203 |
| DOI | 10.1371/journal.pone.0184129 |
| 文献子类 | Article |
| 英文摘要 | Identifying essential genes in a given organism is important for research on their fundamental roles in organism survival. Furthermore, if possible, uncovering the links between core functions or pathways with these essential genes will further help us obtain deep insight into the key roles of these genes. In this study, we investigated the essential and non-essential genes reported in a previous study and extracted gene ontology (GO) terms and biological pathways that are important for the determination of essential genes. Through the enrichment theory of GO and KEGG pathways, we encoded each essential/non-essential gene into a vector in which each component represented the relationship between the gene and one GO term or KEGG pathway. To analyze these relationships, the maximum relevance minimum redundancy (mRMR) was adopted. Then, the incremental feature selection (IFS) and support vector machine (SVM) were employed to extract important GO terms and KEGG pathways. A prediction model was built simultaneously using the extracted GO terms and KEGG pathways, which yielded nearly perfect performance, with a Matthews correlation coefficient of 0.951, for distinguishing essential and non-essential genes. To fully investigate the key factors influencing the fundamental roles of essential genes, the 21 most important GO terms and three KEGG pathways were analyzed in detail. In addition, several genes was provided in this study, which were predicted to be essential genes by our prediction model. We suggest that this study provides more functional and pathway information on the essential genes and provides a new way to investigate related problems. |
| 学科主题 | Science & Technology - Other Topics |
| WOS关键词 | CHRONIC LYMPHOCYTIC-LEUKEMIA ; MESSENGER-RNA EXPRESSION ; ACUTE LYMPHOBLASTIC-LEUKEMIA ; ACUTE MYELOID-LEUKEMIA ; AMINO-ACID TRANSPORTER ; RIBOSOMAL-RNAS ; BACILLUS-SUBTILIS ; FEATURE-SELECTION ; EVOLUTIONARY INFORMATION ; ESCHERICHIA-COLI |
| 语种 | 英语 |
| WOS记录号 | WOS:000409282800053 |
| 出版者 | PUBLIC LIBRARY SCIENCE |
| 版本 | 出版稿 |
| 源URL | [http://202.127.25.144/handle/331004/1071]  |
| 专题 | 中国科学院上海生命科学研究院营养科学研究所 |
| 作者单位 | 1.Shanghai Univ, Sch Life Sci, Shanghai, Peoples R China; 2.Shanghai Maritime Univ, Coll Informat Engn, Shanghai, Peoples R China; 3.Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Hlth Sci, Shanghai, Peoples R China; 4.Anhui Agr Univ, Sch Resources & Environm, Anhui Prov Key Lab Farmland Ecol Conversat & Poll, Hefei, Anhui, Peoples R China, |
| 推荐引用方式 GB/T 7714 | Chen, Lei,Wang, ShaoPeng,Cai, Yu-Dong,et al. Prediction and analysis of essential genes using the enrichments of gene ontology and KEGG pathways[J]. PLOS ONE,2017,12(9):e0184129. |
| APA | Chen, Lei.,Wang, ShaoPeng.,Cai, Yu-Dong.,Zhang, Yu-Hang.,Huang, Tao.,...&,.(2017).Prediction and analysis of essential genes using the enrichments of gene ontology and KEGG pathways.PLOS ONE,12(9),e0184129. |
| MLA | Chen, Lei,et al."Prediction and analysis of essential genes using the enrichments of gene ontology and KEGG pathways".PLOS ONE 12.9(2017):e0184129. |
入库方式： OAI收割
来源：上海营养与健康研究所
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