Prediction and analysis of essential genes using the enrichments of gene ontology and KEGG pathways.
Prediction and analysis of essential genes using the enrichments of gene ontology and KEGG pathways.
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利用基因本体和KEGG通路的富集来预测和分析必需基因
DOI：
10.1371/journal.pone.0184129
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发表时间：
2017
期刊：
影响因子：
3.7
通讯作者：
Cai YD
中科院分区：
文献类型：
--
作者：
Chen L;Zhang YH;Wang S;Zhang Y;Huang T;Cai YD
确定特定生物体的基本基因对于研究它们在生物体生存中的基本作用具有重要意义。此外，如果可能的话，揭示核心功能或途径与这些必需基因之间的联系将进一步帮助我们深入了解这些基因的关键作用。在本研究中，我们调查了先前研究中报道的必需和非必需基因，并提取了对确定必需基因很重要的基因本体（GO）术语和生物学途径。通过GO和KEGG通路的富集理论，我们将每个必需/非必需基因编码成一个载体，其中每个成分代表基因与一个GO项或KEGG通路之间的关系。为了分析这些关系，采用了最大相关最小冗余（mRMR）。然后，采用增量特征选择（IFS）和支持向量机（SVM）提取重要GO项和KEGG路径；利用提取的GO项和KEGG途径同时建立预测模型，在区分必要基因和非必要基因方面取得了近乎完美的效果，马修斯相关系数为0.951。为了充分研究影响必需基因基础作用的关键因素，我们对21个最重要的GO术语和3条KEGG通路进行了详细分析。此外，本研究还提供了几个基因，通过我们的预测模型预测这些基因是必需基因。我们认为，该研究提供了更多的必要基因的功能和途径信息，并为研究相关问题提供了新的途径。
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.
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DOI：
10.2174/1386207319666161215142130
发表时间：
2017-01-01
影响因子：
1.8
作者：
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通讯作者：
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影响因子：
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作者：
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Cai YD
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通讯作者：
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DOI：
10.1139/o95-091
发表时间：
1995-11-01
期刊：
BIOCHEMISTRY AND CELL BIOLOGY-BIOCHIMIE ET BIOLOGIE CELLULAIRE
影响因子：
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作者：
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影响因子：
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作者：
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通讯作者：
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