功能的显著性分析——GO Enrichment Analysis

    Gene Ontology(GO)是基因功能国际标准分类体系。GO富集分析是对差异基因等按GO分类,并对分类结果进行基于离散分布的显著性分析、错判率分析、富集度分析,得到与实验目的有显著联系的、低误判率的、靶向性的基因功能分类,该分类即导致样本性状差异的最重要的功能差别。在芯片的数据分析中,研究者可以找出哪些变化基因属于一个共同的GO功能分支,并用统计学方法检定结果是否具有统计学意义,从而得出变化基因主要参与了哪些生物功能。

1.      对mRNA进行显著性功能富集分析,得到具有显著性、靶向性的功能以及显著性功能对应的靶基因。(功能富集)
 


2.      对富集得到的显著性功能以柱状图的形式展示。(功能柱状图)
 


3.      对富集得到的显著性功能以点图的形式展示。(功能点图)

 

转载于:https://www.cnblogs.com/wangshicheng/p/10122793.html

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Enrichplot 包是一个用于可视化基因本体(GO)富集分析结果的 R 语言包。以下是五个案例研究及其代码和步骤: 1. Case 1: GO enrichment analysis of differentially expressed genes (DEGs) in breast cancer Code: ``` library(enrichplot) library(org.Hs.eg.db) library(clusterProfiler) # Load DEGs data data <- read.csv("breast_cancer_DEGs.csv") # Perform GO enrichment analysis ego <- enrichGO(data = data$Symbol, OrgDb = org.Hs.eg.db, ont = "BP", pvalueCutoff = .05, qvalueCutoff = .05) # Plot the results barplot(ego, showCategory = 10) ``` 2. Case 2: GO enrichment analysis of DEGs in liver cancer Code: ``` library(enrichplot) library(org.Hs.eg.db) library(clusterProfiler) # Load DEGs data data <- read.csv("liver_cancer_DEGs.csv") # Perform GO enrichment analysis ego <- enrichGO(data = data$Symbol, OrgDb = org.Hs.eg.db, ont = "MF", pvalueCutoff = .05, qvalueCutoff = .05) # Plot the results dotplot(ego, showCategory = 10) ``` 3. Case 3: GO enrichment analysis of DEGs in lung cancer Code: ``` library(enrichplot) library(org.Hs.eg.db) library(clusterProfiler) # Load DEGs data data <- read.csv("lung_cancer_DEGs.csv") # Perform GO enrichment analysis ego <- enrichGO(data = data$Symbol, OrgDb = org.Hs.eg.db, ont = "CC", pvalueCutoff = .05, qvalueCutoff = .05) # Plot the results cnetplot(ego, showCategory = 10) ``` 4. Case 4: GO enrichment analysis of DEGs in prostate cancer Code: ``` library(enrichplot) library(org.Hs.eg.db) library(clusterProfiler) # Load DEGs data data <- read.csv("prostate_cancer_DEGs.csv") # Perform GO enrichment analysis ego <- enrichGO(data = data$Symbol, OrgDb = org.Hs.eg.db, ont = "BP", pvalueCutoff = .05, qvalueCutoff = .05) # Plot the results vennpie(ego, showCategory = 10) ``` 5. Case 5: GO enrichment analysis of DEGs in colon cancer Code: ``` library(enrichplot) library(org.Hs.eg.db) library(clusterProfiler) # Load DEGs data data <- read.csv("colon_cancer_DEGs.csv") # Perform GO enrichment analysis ego <- enrichGO(data = data$Symbol, OrgDb = org.Hs.eg.db, ont = "MF", pvalueCutoff = .05, qvalueCutoff = .05) # Plot the results enrichMap(ego, showCategory = 10) ```
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