A data mining approach for classifying DNA repair genes into ageing-related or non-ageing-related.
A data mining approach for classifying DNA repair genes into ageing-related or non-ageing-related.
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DOI：
10.1186/1471-2164-12-27
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发表时间：
2011-01-12
期刊：
影响因子：
4.4
通讯作者：
de Magalhães JP
中科院分区：
文献类型：
--
作者：
Freitas AA;Vasieva O;de Magalhães JP
全球人口老龄化意味着对老龄化生物学研究的需求日益增长。DNA损伤可能是衰老过程的一个关键因素，阐明不同DNA修复系统在衰老中的作用是非常有趣的。在本文中，我们提出了一种数据挖掘方法，分类方法（决策树和朴素贝叶斯）的基础上，分析人类DNA修复基因的数据。我们的目标是建立分类模型，使我们能够区分与衰老相关和非衰老相关的DNA修复基因，以便更好地了解它们的不同特性。通过分类方法发现的主要模式如下：（a）蛋白质-蛋白质相互作用的数量是DNA修复蛋白与衰老相关的预测因子：（B）基于蛋白质-蛋白质相互作用的预测因子属性的使用显著地提高了基于基因本体（GO）注释的属性的预测精度;（c）与“对刺激的反应”相关的GO术语似乎是DNA修复基因衰老相关性的合理良好预测因子;（d）与XRCC 5（Ku 80）蛋白的相互作用是DNA修复基因衰老相关性的强预测因子;和（e）在T淋巴细胞中具有高表达的DNA修复基因更可能与衰老相关。上述模式被广泛整合在一项分析中，讨论Ku（非同源末端连接DNA修复途径）、衰老和淋巴细胞发育之间的关系。这些模式及其分析支持非同源末端连接双链断裂修复作为DNA修复基因衰老相关性的核心。我们的工作还展示了使用蛋白质相互作用伙伴来提高数据挖掘方法的准确性，我们的方法可以应用于其他与衰老相关的途径。
The ageing of the worldwide population means there is a growing need for research on the biology of ageing. DNA damage is likely a key contributor to the ageing process and elucidating the role of different DNA repair systems in ageing is of great interest. In this paper we propose a data mining approach, based on classification methods (decision trees and Naive Bayes), for analysing data about human DNA repair genes. The goal is to build classification models that allow us to discriminate between ageing-related and non-ageing-related DNA repair genes, in order to better understand their different properties. The main patterns discovered by the classification methods are as follows: (a) the number of protein-protein interactions was a predictor of DNA repair proteins being ageing-related; (b) the use of predictor attributes based on protein-protein interactions considerably increased predictive accuracy of attributes based on Gene Ontology (GO) annotations; (c) GO terms related to "response to stimulus" seem reasonably good predictors of ageing-relatedness for DNA repair genes; (d) interaction with the XRCC5 (Ku80) protein is a strong predictor of ageing-relatedness for DNA repair genes; and (e) DNA repair genes with a high expression in T lymphocytes are more likely to be ageing-related. The above patterns are broadly integrated in an analysis discussing relations between Ku, the non-homologous end joining DNA repair pathway, ageing and lymphocyte development. These patterns and their analysis support non-homologous end joining double strand break repair as central to the ageing-relatedness of DNA repair genes. Our work also showcases the use of protein interaction partners to improve accuracy in data mining methods and our approach could be applied to other ageing-related pathways.
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影响因子：
14.9
作者：
Keshava Prasad TS;Goel R;Kandasamy K;Keerthikumar S;Kumar S;Mathivanan S;Telikicherla D;Raju R;Shafreen B;Venugopal A;Balakrishnan L;Marimuthu A;Banerjee S;Somanathan DS;Sebastian A;Rani S;Ray S;Harrys Kishore CJ;Kanth S;Ahmed M;Kashyap MK;Mohmood R;Ramachandra YL;Krishna V;Rahiman BA;Mohan S;Ranganathan P;Ramabadran S;Chaerkady R;Pandey A
通讯作者：
Pandey A
影响因子：
14.9
作者：
Harris, MA;Clark, J;White, R
通讯作者：
White, R
DOI：
10.1098/rspb.2004.2732
发表时间：
2004-06-22
影响因子：
4.7
作者：
Promislow, DEL
通讯作者：
Promislow, DEL
影响因子：
8
作者：
Bradley, AP
通讯作者：
Bradley, AP
DOI：
10.1073/pnas.93.16.8558
发表时间：
1996-08-06
影响因子：
11.1
作者：
Hosaka, N;Nose, M;Ikehara, S
通讯作者：
Ikehara, S