MAGNET: A web-based application for gene set enrichment analysis using macrophage data sets.
MAGNET: A web-based application for gene set enrichment analysis using macrophage data sets.
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DOI：
10.1371/journal.pone.0272166
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发表时间：
2023
期刊：
影响因子：
3.7
通讯作者：
Winter, Deborah R.
中科院分区：
文献类型：
--
作者：
Chen, Shang-Yang;Gadhvi, Gaurav;Winter, Deborah R.
从高通量基因组实验中获得的基因列表的特征是揭示潜在的生物学见解的一项基本任务。一种常见的策略是利用标准化的生物学注释进行浓缩分析，例如GO和KEGG通路，它们试图涵盖生物学的所有领域。然而，这种方法提供的一般静态结果可能无法捕捉与特定领域内的研究问题相关联的细微之处。因此，需要一种能够利用最新研究提供精确、相关结果的应用程序。因此，我们开发了一个交互式网络应用程序--巨噬细胞基因网络富集化工具(MAGNET)，用于对与巨噬细胞特定相关的基因集进行富集化分析。利用超几何分布，MAGIC通过从已发表的手稿和数据储存库中精选的注释来评估重叠基因的重要性。我们实现了许多增强实用性和用户友好性的功能，例如同时测试多个基因组、不同的可视化选项、上传定制数据集的选项以及可下载的输出。在这里，我们使用三个实例研究，与我们目前关于小鼠巨噬细胞的十份出版物的数据库进行比较，以证明Magic提供了相关和独特的结果，补充了传统的浓缩分析工具。虽然只针对巨噬细胞数据集，但我们预计磁体将在其他感兴趣的领域催化类似应用的开发。磁铁可以在网址https://magnet-winterlab.herokuapp.com.上免费访问用Python和PostgreSQL实现的网站，支持所有主要浏览器。源代码可在https://github.com/sychen9584/MAGNET.上找到
Characterization of gene lists obtained from high-throughput genomic experiments is an essential task to uncover the underlying biological insights. A common strategy is to perform enrichment analyses that utilize standardized biological annotations, such as GO and KEGG pathways, which attempt to encompass all domains of biology. However, this approach provides generalized, static results that may fail to capture subtleties associated with research questions within a specific domain. Thus, there is a need for an application that can provide precise, relevant results by leveraging the latest research. We have therefore developed an interactive web application, Macrophage Annotation of Gene Network Enrichment Tool (MAGNET), for performing enrichment analyses on gene sets that are specifically relevant to macrophages. Using the hypergeometric distribution, MAGNET assesses the significance of overlapping genes with annotations that were curated from published manuscripts and data repositories. We implemented numerous features that enhance utility and user-friendliness, such as the simultaneous testing of multiple gene sets, different visualization options, option to upload custom datasets, and downloadable outputs. Here, we use three example studies compared against our current database of ten publications on mouse macrophages to demonstrate that MAGNET provides relevant and unique results that complement conventional enrichment analysis tools. Although specific to macrophage datasets, we envision MAGNET will catalyze developments of similar applications in other domains of interest. MAGNET can be freely accessed at the URL https://magnet-winterlab.herokuapp.com. Website implemented in Python and PostgreSQL, with all major browsers supported. The source code is available at https://github.com/sychen9584/MAGNET.
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DOI：
10.1093/bioinformatics/btv612
发表时间：
2016-02-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Sheffield NC;Bock C
通讯作者：
Bock C
DOI：
10.1084/jem.20162152
发表时间：
2017-08-07
期刊：
The Journal of experimental medicine
影响因子：
--
作者：
Misharin AV;Morales-Nebreda L;Reyfman PA;Cuda CM;Walter JM;McQuattie-Pimentel AC;Chen CI;Anekalla KR;Joshi N;Williams KJN;Abdala-Valencia H;Yacoub TJ;Chi M;Chiu S;Gonzalez-Gonzalez FJ;Gates K;Lam AP;Nicholson TT;Homan PJ;Soberanes S;Dominguez S;Morgan VK;Saber R;Shaffer A;Hinchcliff M;Marshall SA;Bharat A;Berdnikovs S;Bhorade SM;Bartom ET;Morimoto RI;Balch WE;Sznajder JI;Chandel NS;Mutlu GM;Jain M;Gottardi CJ;Singer BD;Ridge KM;Bagheri N;Shilatifard A;Budinger GRS;Perlman H
通讯作者：
Perlman H
影响因子：
30.5
作者：
通讯作者：
--
影响因子：
64.5
作者：
Gosselin D;Link VM;Romanoski CE;Fonseca GJ;Eichenfield DZ;Spann NJ;Stender JD;Chun HB;Garner H;Geissmann F;Glass CK
通讯作者：
Glass CK
影响因子：
64.5
作者：
Lavin Y;Winter D;Blecher-Gonen R;David E;Keren-Shaul H;Merad M;Jung S;Amit I
通讯作者：
Amit I