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富集图谱：一种基于网络的基因集富集可视化和解释方法。

Enrichment map: a network-based method for gene-set enrichment visualization and interpretation.

机构信息

Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.

出版信息

PLoS One. 2010 Nov 15;5(11):e13984. doi: 10.1371/journal.pone.0013984.

DOI:10.1371/journal.pone.0013984
PMID:21085593
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2981572/
Abstract

BACKGROUND

Gene-set enrichment analysis is a useful technique to help functionally characterize large gene lists, such as the results of gene expression experiments. This technique finds functionally coherent gene-sets, such as pathways, that are statistically over-represented 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 software works against this ideal.

PRINCIPAL FINDINGS

To overcome gene-set redundancy and help in the interpretation of large gene lists, we developed "Enrichment Map", a network-based visualization method for gene-set enrichment results. Gene-sets are organized in a network, where each set is a node and edges 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 the enrichment results.

CONCLUSIONS

Enrichment Map is a significant advance in the interpretation of enrichment analysis. Any research project that generates a list of genes can take advantage of this visualization framework. Enrichment Map is implemented as a freely available and user friendly plug-in for the Cytoscape network visualization software (http://baderlab.org/Software/EnrichmentMap/).

摘要

背景

基因集富集分析是一种有用的技术，可以帮助对大型基因列表（例如基因表达实验的结果）进行功能描述。该技术可找到功能一致的基因集，例如途径，这些基因在给定的基因列表中统计上过度表达。理想情况下，生成的集合数量应少于列表中的基因数量，从而简化解释。但是，许多当前的富集分析软件使用的基因集的数量和冗余性不断增加，这与理想情况背道而驰。

主要发现

为了克服基因集的冗余性并帮助解释大型基因列表，我们开发了“富集图谱”，这是一种基于网络的基因集富集结果可视化方法。基因集在网络中进行组织，其中每个集都是一个节点，边缘表示集之间的基因重叠。自动网络布局将相关的基因集分组到网络簇中，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。

结论

富集图谱是对富集分析进行解释的重大进展。任何生成基因列表的研究项目都可以利用此可视化框架。Enrichment Map 是 Cytoscape 网络可视化软件（http://baderlab.org/Software/EnrichmentMap/）的免费且用户友好的插件。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/773f/2981572/4fa6be35155b/pone.0013984.g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/773f/2981572/9ff2fd6af431/pone.0013984.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/773f/2981572/fa05d4a553f0/pone.0013984.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/773f/2981572/547202d5a654/pone.0013984.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/773f/2981572/99d0b7665d1d/pone.0013984.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/773f/2981572/683cdc46642c/pone.0013984.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/773f/2981572/aa9476ff79cf/pone.0013984.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/773f/2981572/4fa6be35155b/pone.0013984.g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/773f/2981572/9ff2fd6af431/pone.0013984.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/773f/2981572/fa05d4a553f0/pone.0013984.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/773f/2981572/547202d5a654/pone.0013984.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/773f/2981572/99d0b7665d1d/pone.0013984.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/773f/2981572/683cdc46642c/pone.0013984.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/773f/2981572/aa9476ff79cf/pone.0013984.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/773f/2981572/4fa6be35155b/pone.0013984.g007.jpg

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