Author Archives: Metascape

Metascape for Bioinformaticians (MSBio)

We are extremely excited to make MSBio available to the bioinformatics community for alpha testing. Why MSBio? Metascape was initially designed to support biologists, as we observed most gene-list analysis tools were bioinformatician-oriented rather than biologist-oriented. The reality is that … Continue reading

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Protein-Protein Interaction Data Sources

Why Include STRING Database Metascape provides a rather unique protein-protein interaction (PPI) network analysis capability. In many gene list analysis resources, PPI analysis results in a rather massy hairball network. Besides stating such networks are statistically significant, there is not … Continue reading

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How Dose Metascape Compute Orthologs

Homologene is Outdated Ortholog mapping is an important component in Metascape as explained in our Nature Communication paper: Many gene annotation, pathway, and protein interaction databases are primarily compiled for human genes/proteins. For instance, the size of the mouse interactome … Continue reading

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Coronascape – 为COVID-19研究特制的基因列表比较工具

简介 COVID研究者通过高通量的组学实验获取了一组基因列表后如何进行进一步的数据分析呢?高通量数据往往重复次数少,数据噪声高,想要只从自己单一的基因列表中抽取到与生物系统真实相关的分子通路就会困难一些。所以我们首先希望将信号放大,就是要找到其他已经发表或将要发表的在类似实验条件下获得的基因列表用于对照。通过比对,真实的信号得以增强,结论从统计意义上就更加可靠。目前COVID研究文献的数量在飞速增长,研究者要去阅读筛查找到相似的组学实验设计,并且对原始数据进行预处理以获得可以用于比照的基因列表其实不是一件唾手可及的事。Coronascape (http://coronascape.org) 的目的就是为了帮助COVID研究人员解决这一难题。 Coronascape是由Sanford Burnham Prebys Medical Discovery Institute, Novartis和UCSD合作共同开发的新冠病毒组学公共数据库。Coronascape收录了20篇文章360多个SARS-CoV-2相关的基因或者蛋白数据集,涵盖了七种不同的组学技术,包括转录组(RNA-Seq和scRNASeq),蛋白质组,磷酸化蛋白质组,泛素组和蛋白相互作用组。 使用Coronascape数据库可以全面深入的了解各种宿主细胞和组织中SARS-CoV-2感染后的基因表达变化,蛋白表达修饰以及相互作用关系。用户只要将自己的基因列表输入Coronascape进行Similarity Search,Coronascape会推荐数据库里相似的基因列表。当然用户也可以通过关键词搜索以获取参照组。 获取多组基因列表后,用户要通过分子通路分析和蛋白网络分析找出数据背后的分子机理,并对分析结果制成可以帮助阐明生物原理的图表。这些正是Metascape的强项,而Coronascape在后台是和Metascape无缝衔接的。Coronascape通过非常友好间的用户操作界面,让用户提交自己的基因数据与公共数据进行比较,再对生成的列表组应用成熟的系统生物学网站Metascape进行信号通路,Gene Ontology,网络分析等深入的数据分析。利用Coronascape,用户可以从单一基因列表转化为多个列表,再获取图文并茂的meta-analysis分析报告一气呵成。没有自己实验数据的用户也可以直接对Coronascape中已有的数据进行二次分析。 由于Coronascape刚刚推出,还没有发表的成果。不过已经有应用实例上传到Biorxiv (https://www.biorxiv.org/content/10.1101/2020.08.18.256776v1)。文章作者通过对比Coronascape中的数据,深入研究了SARS-COV-2的ORF9C蛋白在宿主中转录组和蛋白组等与已发表的公共数据的异同,发现ORF9C单个蛋白即可实现全病毒感染细胞和肺部组织时的免疫抑制以及细胞因子激活功能,揭示了ORF9C可能时病毒与宿主相互作用的关键蛋白之一。这是对使用Coronascape进行COV-2多重组学研究的非常好的一个示例。 下面通过一些实例介绍一下Coronascape的用法。 示例一:通过用户的基因列表从Coronascape查找相似的基因列表 1. 将您的基因列表粘贴到“User’s Gene List”中。 2. 在“Recommendation”中,单击“Similarity Search”。 3. 与用户的基因列表相比,您将能够看到按相似性排名的基因列表。您可以单击“Download Similarity”以获得详细的基因列表。 4. 您可以单击“Use Selected”或“Append Selected”以将选定的基因列表添加到“要比较的参照列表”中。 5. 添加基因列表后,单击“ Metascape Analysis”以对用户的基因列表和从Coronascape中选择的基因列表进行系统分析。 示例二:将用户的基因列表与特定公共研究的基因列表进行比较 1. 将您的基因列表粘贴到“User’s … Continue reading

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Clustergram for Enrichment

This blog serves as the missing manual of the clustergram feature. Introduction Metascape visualizes enrichment results as a bar graph, a heatmap, or a network. In all cases, the unit for the visualization is a pathway/process, as this provides a … Continue reading

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Research in China Shows Resistance to Coronavirus

Note: It was merely two weeks after I wrote this blog, China has turned into a sanctuary and we, in U.S., are in the deepest panic about Covid-19. Today is March 20. We made an update to the Metascape database. … Continue reading

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Background Gene List for Enrichment Analysis

One frequently-ask question from Metascape users is how to submit a customized background gene list for enrichment analysis. The complete proteome is used as the default background in Metascape, however, this behavior can be overwritten. _BACKGROUND at Gene List Submission … Continue reading

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Visualize Networks Online and Offline

Metascape provides intuitive visualizations for either pathway enrichment networks or protein-protein interaction networks. By default, we do not display labels for the nodes within the .png and .pdf outputs, because displaying them will make both networks and labels unreadable (Figure … Continue reading

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Statistics for Enrichment Analysis

Requested by some users, we here provide some technical details regarding gene enrichment metrics found in Metascape analysis results. First a few constants: There are \(N\) total number of genes in our study pool (this is also known as the … Continue reading

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Metascape is a gene list analysis website designed for biologists

Background The analysis of genomics and proteomics datasets is not an easy task. Most of the current gene list analysis sites are limited to the enrichment analysis of pathways, thus the value of omics-scale datasets is not fully explored. A … Continue reading

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