Merico Daniele, Isserlin Ruth, Bader Gary D
Banting and Best Department of Medical Research, Centre for Cellular and Biomolecular Research (CCBR), Toronto, ON, Canada.
Methods Mol Biol. 2011;781:257-77. doi: 10.1007/978-1-61779-276-2_12.
Gene-set enrichment analysis finds functionally coherent gene-sets, such as pathways, that are statistically overrepresented in a given gene list. Ideally, the number of resulting sets is smaller than the number of genes in the list, thus simplifying interpretation. However, the increasing number and redundancy of -gene-sets used by many current enrichment analysis resources work against this ideal. "Enrichment Map" is a Cytoscape plug-in that helps overcome gene-set redundancy and aids in the interpretation of enrichment results. Gene-sets are organized in a network, where each set is a node and links represent gene overlap between sets. Automated network layout groups related gene-sets into -network clusters, enabling the user to quickly identify the major enriched functional themes and more easily interpret enrichment results.
基因集富集分析可找到功能上连贯的基因集，如通路，这些基因集在给定基因列表中具有统计学上的过度代表性。理想情况下，所得基因集的数量少于列表中的基因数量，从而简化解释。然而，许多当前富集分析资源所使用的基因集数量不断增加且存在冗余，这与这一理想情况相悖。“富集图”是Cytoscape的一个插件，有助于克服基因集冗余并辅助解释富集结果。基因集在一个网络中组织起来，其中每个基因集是一个节点，链接表示基因集之间的基因重叠。自动网络布局将相关基因集分组为网络簇，使用户能够快速识别主要的富集功能主题并更轻松地解释富集结果。
