CDCA: Community detection in RNA-seq data using centrality-based approach

IF 2.1 4区 生物学 Q2 BIOLOGY
Tonmoya Sarmah, Dhruba K Bhattacharyya
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引用次数: 0

Abstract

One of the integral part of the network analysis is finding groups of nodes that exhibit similar properties. Community detection techniques are a popular choice to find such groups or communities within a network and it relies on graph-based methods to achieve this goal. Finding communities in biological networks such as gene co-expression networks are particularly important to find groups of genes where we can focus on further downstream analysis and find valuable insights regarding concerned diseases. Here, we present an effective community detection method called community detection using centrality-based approach (CDCA), designed using the graph centrality approach. The method has been tested using four benchmark bulk RNA-seq datasets for schizophrenia and bipolar disorder, and the performance has been proved superior in comparison to several other counterparts. The quality of communities are determined using intrinsic graph properties such as modularity and homogeneity. The biological significance of resultant communities is decided using the pathway enrichment analysis.

Abstract Image

CDCA:使用基于中心性的方法检测 RNA-seq 数据中的群落
网络分析不可或缺的一部分是找到具有相似属性的节点群。社群检测技术是在网络中寻找此类群组或社群的常用方法,它依靠基于图的方法来实现这一目标。在基因共表达网络等生物网络中寻找群落尤为重要,这样我们就能找到基因组,从而专注于进一步的下游分析,找到有关疾病的宝贵见解。在这里,我们提出了一种有效的群落检测方法,称为基于中心性方法的群落检测(CDCA),它是利用图中心性方法设计的。该方法使用精神分裂症和躁狂症的四个基准批量 RNA-seq 数据集进行了测试,与其他几种同类方法相比,性能更优越。群落的质量是通过模块化和同质性等内在图属性确定的。利用通路富集分析来确定所形成群落的生物学意义。
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来源期刊
Journal of Biosciences
Journal of Biosciences 生物-生物学
CiteScore
5.80
自引率
0.00%
发文量
83
审稿时长
3 months
期刊介绍: The Journal of Biosciences is a quarterly journal published by the Indian Academy of Sciences, Bangalore. It covers all areas of Biology and is the premier journal in the country within its scope. It is indexed in Current Contents and other standard Biological and Medical databases. The Journal of Biosciences began in 1934 as the Proceedings of the Indian Academy of Sciences (Section B). This continued until 1978 when it was split into three parts : Proceedings-Animal Sciences, Proceedings-Plant Sciences and Proceedings-Experimental Biology. Proceedings-Experimental Biology was renamed Journal of Biosciences in 1979; and in 1991, Proceedings-Animal Sciences and Proceedings-Plant Sciences merged with it.
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