单样本的gsea分析图表
最近看到文章 Cancer Cell . 2020 Dec ,标题是《Cathepsin C promotes breast cancer lung metastasis by modulating neutrophil infiltration and neutrophil extracellular trap formation》
链接是:https://pubmed.ncbi.nlm.nih.gov/33450198/ 有一个图表很适合布置给学徒作为作业。
研究者对荷兰癌症研究所(NKI)发表的乳腺癌基因表达数据进行分析,绘制出来了如下所示的单样本的gsea分析图表:
图例是:(H) Single-sample gene set enrichment analysis of CTSC correlation to neutrophil-related gene sets in the NKI dataset (n = 295). Scale bar, 50 mm. p values were obtained by two-tailed unpaired t test (B, E, and F) or Pearson’s correlation analysis (others)
我看了看文章:
The NKI microarray data and clinical information were obtained from previous publications (Minn et al., 2007; van de Vijver et al., 2002).
The enrichment of neutrophilrelated gene sets in these tumors were analyzed by ssGESA in GenePattern platform with the previously published neutrophil gene sets (Bindea et al., 2013; Ebert et al., 2008; Kim et al., 2019). These gene sets are listed in Table S6.
Download spreadsheet (13KB) ,Table S6. Gene sets used for single-sample gene set enrichment analyses, related to the STAR methods.
数据分析大纲
下载表达量矩阵 读文献拿到3个基因集的基因列表 针对基因列表去表达量矩阵里面走ssGSE分析 对ssGSE分析值与CTSC表达量进行相关性计算 绘制热图
老规矩,学徒作业需要以markdown形式,描述清楚你的分析过程,并且发邮件到我邮箱(jmzeng1314@163.com)