240    ◾    Bioinformatics

keyType = “ENTREZID”,

OrgDb = org.Hs.eg.db,

ont = “BP”,

pAdjustMethod = “BH”,

qvalueCutoff = 0.05,

readable = TRUE)

ego3 <- enrichGO(gene = entrez3,

keyType = “ENTREZID”,

OrgDb = org.Hs.eg.db,

ont = “BP”,

pAdjustMethod = “BH”,

qvalueCutoff = 0.05,

readable = TRUE)

#GO output

# Chip1

cluster_summary1 <- data.frame(ego1)

write.csv(cluster_summary1, “chip1_GO.csv”)

# Dotplot visualization

dotplot(ego1, showCategory=10)

# Chip2

cluster_summary2 <- data.frame(ego2)

write.csv(cluster_summary2, “chip2_GO.csv”)

# Dotplot visualization

dotplot(ego2, showCategory=10)

# Chip2

cluster_summary3 <- data.frame(ego3)

write.csv(cluster_summary3, “chip3_GO.csv”)

# Dotplot visualization

dotplot(ego3, showCategory=10)

FIGURE 6.16  GO dot plot showing the top 10 genes.