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最近看到文章 Cancer Cell . 2020 Dec ，標(biāo)題是《Cathepsin C promotes breast cancer lung metastasis by modulating neutrophil infiltration and neutrophil extracellular trap formation》

鏈接是：https://pubmed.ncbi.nlm.nih.gov/33450198/  有一個圖表很適合布置給學(xué)徒作為作業(yè)。

研究者對荷蘭癌癥研究所（NKI）發(fā)表的乳腺癌基因表達(dá)數(shù)據(jù)進(jìn)行分析，繪制出來了如下所示的單樣本的gsea分析圖表：

圖例是：(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.

數(shù)據(jù)分析大綱

• 下載表達(dá)量矩陣
• 讀文獻(xiàn)拿到3個基因集的基因列表
• 針對基因列表去表達(dá)量矩陣?yán)锩孀遱sGSE分析
• 對ssGSE分析值與CTSC表達(dá)量進(jìn)行相關(guān)性計算
• 繪制熱圖

老規(guī)矩，學(xué)徒作業(yè)需要以markdown形式，描述清楚你的分析過程，并且發(fā)郵件到我郵箱（jmzeng1314@163.com）