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RNA 11. SCI 文章中基因表達(dá)富集之 GSEA_gsea數(shù)據(jù)庫

前言

https://blog.csdn.net/weixin_41368414/article/details/123265071

目前基于RNA做分析的文章中幾乎都有 GSEA 的分析內(nèi)容,并且都是出現(xiàn)在正文,那么這個也是表達(dá)基因篩選的一種重要方式,下面我將整個流程梳理一下,供大家參考。

GSEA(Gene Set EnrichmentAnalysis),即基因集富集分析,它的基本思想是使用預(yù)定義的基因,將基因按照在兩類樣本中的差異表達(dá)程度排序,然后檢驗預(yù)先設(shè)定的基因集合是否在這個排序表的頂端或者底端富集。

GSEA和GO、KEGG pathway不同的地方在于,后兩者會提前設(shè)定一個閾值,只關(guān)注差異變化大的基因(相當(dāng)于重點班)。這樣子容易遺漏部分差異表達(dá)不顯著卻有重要生物學(xué)意義的基因(成績一般,但是很有天賦)。所以GSEA分析比較適用于,傳統(tǒng)分析方法篩選后樣本過少的數(shù)據(jù)集。

GSEA數(shù)據(jù)庫收集了很多分子標(biāo)記數(shù)據(jù),有9大分類的基因,如下:

九大分類如下:

實例解讀

1. 數(shù)據(jù)讀取

數(shù)據(jù)的讀取我們?nèi)匀皇褂玫氖?TCGA-COAD 的數(shù)據(jù)集,表達(dá)數(shù)據(jù)的讀取以及臨床信息分組的獲得我們上期已經(jīng)提過,我們使用的是edgeR 軟件包計算出來的差異表達(dá)結(jié)果,提取上調(diào)基因 2832 的 ENSEMBL 號,

###########基因列表
DEG=read.table("DEG-resdata.xls",sep="\t",check.names=F,header = T)
geneList<-DEG[DEG$sig=="Up",]$Row.names
table(DEG$sig)


## 
## Down   Up 
## 1296 2832

直接用之前的轉(zhuǎn)錄組差異分析后的數(shù)據(jù)來演示,數(shù)據(jù)格式如下:

head(DEG[,1:7])


##         Row.names     logFC      logCPM        LR        PValue
## 1 ENSG00000142959 -5.924830  3.20085238 1457.1137 8.159939e-319
## 2 ENSG00000163815 -4.223787  2.59792097 1145.7948 3.679815e-251
## 3 ENSG00000107611 -5.131288  1.71477711 1122.0643 5.289173e-246
## 4 ENSG00000162461 -4.101967  1.51480635 1085.9423 3.752089e-238
## 5 ENSG00000163959 -4.295806  3.39558390 1080.7407 5.067873e-237
## 6 ENSG00000144410 -6.284258 -0.02616284  916.3497 2.739233e-201
##             FDR  sig
## 1 2.592984e-314 Down
## 2 5.846674e-247 Down
## 3 5.602468e-242 Down
## 4 2.980753e-234 Down
## 5 3.220836e-233 Down
## 6 1.450744e-197 Down

因為GSEA只需要SYMBOL(基因名)和foldchange (或logFC)兩列,所以我們提取這兩列,如下:

geneList<-DEG[,1:2]
head(geneList)

##         Row.names     logFC
## 1 ENSG00000142959 -5.924830
## 2 ENSG00000163815 -4.223787
## 3 ENSG00000107611 -5.131288
## 4 ENSG00000162461 -4.101967
## 5 ENSG00000163959 -4.295806
## 6 ENSG00000144410 -6.284258

2. GSEA富集結(jié)果

首先我們同樣需要安裝軟件包并加載,這里面主程序就是 clusterProfiler 軟件包,如下:

########
if(!require(clusterProfiler)){
  BiocManager::install("clusterProfiler")
}
if(!require(org.Hs.eg.db)){
  BiocManager::install("org.Hs.eg.db")
}
if(!require(DOSE)){
  BiocManager::install("DOSE")
}
if(!require(topGO)){
  BiocManager::install("topGO")
}
if(!require(pathview)){
  BiocManager::install("pathview")
}
if(!require(KEGG.db)){
  BiocManager::install("KEGG.db")
}
if(!require(enrichplot)){
  BiocManager::install("enrichplot")
}

library(org.Hs.eg.db)
library(clusterProfiler)
library(DOSE)
library(topGO)
library(pathview)
library(KEGG.db)
library(enrichplot)

如基因名是symbol,需要將基因ID轉(zhuǎn)換為Entrez ID格式。Entrez ID實際上是指的Entrez gene ID,是對應(yīng)于染色體上一個gene location的。每一個發(fā)現(xiàn)的基因都會被編制一個統(tǒng)一的編號,而Entrez ID是指的來自于NCBI旗下的Entrez gene數(shù)據(jù)庫所使用的編號。因為Entrez ID具有特異性,所以后續(xù)分析更適合用Entrez ID

eg <- bitr(geneList$Row.names, 
           fromType="ENSEMBL", 
           toType=c("ENTREZID","ENSEMBL",'SYMBOL'),
           OrgDb="org.Hs.eg.db")


## 'select()' returned 1:many mapping between keys and columns

## Warning in bitr(geneList$Row.names, fromType = "ENSEMBL", toType =
## c("ENTREZID", : 30.89% of input gene IDs are fail to map...


head(eg)

##           ENSEMBL ENTREZID   SYMBOL
## 1 ENSG00000142959   266675    BEST4
## 2 ENSG00000163815     7123   CLEC3B
## 3 ENSG00000107611     8029     CUBN
## 4 ENSG00000162461   284723 SLC25A34
## 5 ENSG00000163959   200931   SLC51A
## 6 ENSG00000144410   130749      CPO

合并基因列表,就是我們需要輸入的文件了,如下:

mergedata<-merge(eg,geneList,by.x="ENSEMBL",by.y="Row.names")
head(mergedata)

##           ENSEMBL ENTREZID SYMBOL     logFC
## 1 ENSG00000003249    79007 DBNDD1  2.474017
## 2 ENSG00000004776   126393  HSPB6 -3.543461
## 3 ENSG00000004799     5166   PDK4 -3.281233
## 4 ENSG00000004846   340273  ABCB5 -3.084616
## 5 ENSG00000005001    64063 PRSS22  4.095319
## 6 ENSG00000005981    51666   ASB4  2.237660


mergedata_sort <- mergedata[order(mergedata$logFC, decreasing = T),]#先按照logFC降序排序
gene_fc = mergedata_sort$logFC #把foldchange按照從大到小提取出來
names(gene_fc) <- mergedata_sort$ENTREZID #給上面提取的foldchange加上對應(yīng)上ENTREZID
head(gene_fc)

##      4102     26831     26832      5653    646960      4105 
## 10.010124  9.817905  9.807069  9.553685  9.448116  9.440482

GSEA 分析

需要gmt文件,http://www.gsea-msigdb.org/gsea/downloads.jsp 路徑下載,選擇合適的,我們這里是結(jié)直腸癌中癌和癌旁的差異比較分析,所以我們需要找到致癌基因,選擇 c5: Ontology gene sets 即 c5.all.v7.5.1.entrez.gmt 文件,然后進(jìn)行 GSEA 富集分析,如下:

library(stats)
kegg_gmt <- read.gmt("c5.all.v7.5.1.entrez.gmt") #讀gmt文件
gsea <- GSEA(gene_fc,
             TERM2GENE = kegg_gmt) #GSEA分析
head(gsea)


##                                                                                                  ID
## GOBP_ADAPTIVE_IMMUNE_RESPONSE                                         GOBP_ADAPTIVE_IMMUNE_RESPONSE
## GOBP_CATION_TRANSPORT                                                         GOBP_CATION_TRANSPORT
## GOBP_IMMUNE_RESPONSE_REGULATING_SIGNALING_PATHWAY GOBP_IMMUNE_RESPONSE_REGULATING_SIGNALING_PATHWAY
## GOBP_IMMUNOGLOBULIN_PRODUCTION                                       GOBP_IMMUNOGLOBULIN_PRODUCTION
## GOBP_ION_TRANSPORT                                                               GOBP_ION_TRANSPORT
## GOBP_LIPID_METABOLIC_PROCESS                                           GOBP_LIPID_METABOLIC_PROCESS
##                                                                                         Description
## GOBP_ADAPTIVE_IMMUNE_RESPONSE                                         GOBP_ADAPTIVE_IMMUNE_RESPONSE
## GOBP_CATION_TRANSPORT                                                         GOBP_CATION_TRANSPORT
## GOBP_IMMUNE_RESPONSE_REGULATING_SIGNALING_PATHWAY GOBP_IMMUNE_RESPONSE_REGULATING_SIGNALING_PATHWAY
## GOBP_IMMUNOGLOBULIN_PRODUCTION                                       GOBP_IMMUNOGLOBULIN_PRODUCTION
## GOBP_ION_TRANSPORT                                                               GOBP_ION_TRANSPORT
## GOBP_LIPID_METABOLIC_PROCESS                                           GOBP_LIPID_METABOLIC_PROCESS
##                                                   setSize enrichmentScore
## GOBP_ADAPTIVE_IMMUNE_RESPONSE                         111      -0.4743354
## GOBP_CATION_TRANSPORT                                 185      -0.2838816
## GOBP_IMMUNE_RESPONSE_REGULATING_SIGNALING_PATHWAY      52      -0.4982248
## GOBP_IMMUNOGLOBULIN_PRODUCTION                         51      -0.6152482
## GOBP_ION_TRANSPORT                                    252      -0.2763134
## GOBP_LIPID_METABOLIC_PROCESS                          163      -0.2922133
##                                                         NES pvalue
## GOBP_ADAPTIVE_IMMUNE_RESPONSE                     -4.455485  1e-10
## GOBP_CATION_TRANSPORT                             -2.957025  1e-10
## GOBP_IMMUNE_RESPONSE_REGULATING_SIGNALING_PATHWAY -3.636516  1e-10
## GOBP_IMMUNOGLOBULIN_PRODUCTION                    -4.430346  1e-10
## GOBP_ION_TRANSPORT                                -2.791438  1e-10
## GOBP_LIPID_METABOLIC_PROCESS                      -2.998976  1e-10
##                                                       p.adjust
## GOBP_ADAPTIVE_IMMUNE_RESPONSE                     1.548421e-08
## GOBP_CATION_TRANSPORT                             1.548421e-08
## GOBP_IMMUNE_RESPONSE_REGULATING_SIGNALING_PATHWAY 1.548421e-08
## GOBP_IMMUNOGLOBULIN_PRODUCTION                    1.548421e-08
## GOBP_ION_TRANSPORT                                1.548421e-08
## GOBP_LIPID_METABOLIC_PROCESS                      1.548421e-08
##                                                        qvalues rank
## GOBP_ADAPTIVE_IMMUNE_RESPONSE                     1.040997e-08 1137
## GOBP_CATION_TRANSPORT                             1.040997e-08 1082
## GOBP_IMMUNE_RESPONSE_REGULATING_SIGNALING_PATHWAY 1.040997e-08 1130
## GOBP_IMMUNOGLOBULIN_PRODUCTION                    1.040997e-08 1137
## GOBP_ION_TRANSPORT                                1.040997e-08  852
## GOBP_LIPID_METABOLIC_PROCESS                      1.040997e-08  916
##                                                                      leading_edge
## GOBP_ADAPTIVE_IMMUNE_RESPONSE                      tags=86%, list=40%, signal=54%
## GOBP_CATION_TRANSPORT                              tags=64%, list=38%, signal=42%
## GOBP_IMMUNE_RESPONSE_REGULATING_SIGNALING_PATHWAY  tags=88%, list=39%, signal=55%
## GOBP_IMMUNOGLOBULIN_PRODUCTION                    tags=100%, list=40%, signal=61%
## GOBP_ION_TRANSPORT                                 tags=51%, list=30%, signal=40%
## GOBP_LIPID_METABOLIC_PROCESS                       tags=58%, list=32%, signal=42%
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   core_enrichment
## GOBP_ADAPTIVE_IMMUNE_RESPONSE                                                                                                                                                                            28885/28432/28420/28943/28834/28908/6977/28803/28876/28785/28820/28903/28781/4063/28442/729230/28784/28815/974/28892/3514/28775/28409/28388/28774/11126/28900/28941/28518/6363/28823/28449/28448/28923/28412/660/5579/28804/28392/30835/28938/1191/28811/28912/28423/634/28935/3662/28786/28444/28464/28450/973/28821/28937/28875/28874/28915/1380/28921/10990/3493/28385/28401/10462/28906/57379/28408/3570/28893/28772/28817/28776/28780/2208/10332/28896/28930/28457/339390/28516/28883/83417/28410/28940/28881/28870/608/79908/23495/28877/730/3494/28919/3512/28452
## GOBP_CATION_TRANSPORT                                                                                            3773/79901/1756/9472/6328/493/2316/6549/729230/285195/6263/6330/2852/114780/3738/387849/2668/245972/170850/3782/9058/130497/6363/492/57113/5023/5579/482/170572/2824/143425/2903/534/4129/3359/6355/1179/5174/169026/931/6568/6616/84239/84502/844/1272/1393/53826/5649/6387/3741/146395/1261/148/9992/6446/6572/6543/3777/6564/57030/3778/57282/162514/287/57158/6860/9963/341359/140738/5348/3779/4842/2273/846/4638/285242/5350/1908/3736/2641/11280/6335/10050/3769/22871/1258/7432/1268/3745/6327/115584/22953/6865/6550/159963/60482/117/644139/2823/6338/140803/845/6340/8671/6332/286133/477/1804/201140/246213/5354/340024/6561/55532/347741/6555/92736
## GOBP_IMMUNE_RESPONSE_REGULATING_SIGNALING_PATHWAY                                                                                                                                                                                                                                                                                                                                                                                                                                                                     28432/28420/2206/28834/7098/28442/974/3514/28409/81793/28388/11126/26228/28449/28448/28412/660/5579/28392/148823/948/23228/28423/634/933/640/3662/28444/28464/28450/973/931/1380/3493/28385/28401/28408/64922/10917/11148/28457/28410/79908/3494/9971/28452
## GOBP_IMMUNOGLOBULIN_PRODUCTION                                                                                                                                                                                                                                                                                                                                                                                                                                           28943/51237/28908/28803/28876/28785/28820/28903/28781/28784/28815/28892/3514/28775/28774/28900/28941/28518/28823/28923/29802/28804/28938/28811/28912/933/28935/28786/28821/28937/28875/28874/28915/28921/28906/57379/28893/28772/28817/28776/28780/28896/28930/28516/28883/28940/28881/28870/28877/28919
## GOBP_ION_TRANSPORT                                57113/220963/5023/5579/2350/482/170572/2824/5322/143425/2903/948/534/634/4129/3359/6355/1179/5028/5174/169026/931/6568/6616/84239/84502/844/1272/1393/53826/5649/2893/6387/3741/146395/387700/1261/148/9992/64805/28965/6446/55065/2565/6572/2901/6543/3777/1188/6564/2566/57030/3778/57282/162514/391013/287/57158/6860/9963/203859/341359/140738/5348/3779/4842/2273/846/4638/285242/5350/1908/3736/2641/11280/6335/10050/3769/22871/553/5030/2899/1258/7432/353189/1268/3745/6327/115584/22953/6865/54831/6550/159963/60482/117/5593/644139/11136/2823/123264/1836/6338/140803/200931/845/6340/8671/1811/6332/760/286133/477/9429/1804/8647/201140/762/6514/246213/5354/22802/340024/6561/766/55532/266675/347741/6555/92736
## GOBP_LIPID_METABOLIC_PROCESS                                                                                                                                                                                                                           6817/5288/124/1562/6363/5959/283985/5408/5023/660/389396/5333/2494/5322/1191/3158/948/23228/79154/634/3291/345557/1565/129807/84803/10690/54988/54657/653/30815/10924/10317/64805/28965/23584/5105/159296/137872/2168/3248/1580/54511/80168/5742/1907/6822/54658/51046/13/391013/57016/339221/374569/84830/27306/2169/7366/8708/10170/54857/5166/53345/54979/9227/3294/133121/1268/185/54575/9971/6799/7148/80157/7367/126/124872/51059/6338/2938/54576/125/10351/1103/57733/1576/8647/8029/5354/3284/2538/338/335/345/337

  • ID :信號通路

  • Description :信號通路的描述

  • setSize :富集到該信號通路的基因個數(shù)

  • enrichmentScore :富集分?jǐn)?shù),也就是ES

  • NES :標(biāo)準(zhǔn)化以后的ES,全稱normalized enrichment score

  • pvalue:富集的P值

  • p.adjust :校正后的P值

  • qvalues :FDR (false discovery rate)錯誤發(fā)現(xiàn)率

  • rank :排名

  • core_enrichment:富集到該通路的基因列表。

繪制氣泡圖

氣泡圖解讀需要說明一下,富集程度通過Gene ratio、Pvalue和富集到此基因集上的基因個數(shù)來衡量。

  • 橫坐標(biāo)是Gene ratio,數(shù)值越大表示富集程度越大。Count 位于該基因集下的差異表達(dá)基因數(shù)

  • 縱坐標(biāo)是富集程度較高的基因集(一般選取富集最顯著的20條進(jìn)行展示,不足20條則全部列出)。

  • Pvalue取值范圍[0, 1],以顏色表示,越紅表示Pvalue越小,說明富集越明顯。

  • 點的大小表示該基因集下差異基因的個數(shù),點越大表示基因數(shù)越多**。**

    氣泡圖繪制,如下:

dotplot(gsea)

GO 富集分析

# Run GO and KEGG enrichment analysis 
#GO富集
GO <- gseGO(
  gene_fc, #gene_fc
  ont = "BP",# "BP"、"MF"和"CC"或"ALL"
  OrgDb = org.Hs.eg.db,#人類注釋基因
  keyType = "ENTREZID",
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",#p值校正方法
)
head(GO[,1:4])


##                    ID                                      Description
## GO:0002250 GO:0002250                         adaptive immune response
## GO:0002253 GO:0002253                    activation of immune response
## GO:0002377 GO:0002377                        immunoglobulin production
## GO:0002764 GO:0002764     immune response-regulating signaling pathway
## GO:0006139 GO:0006139 nucleobase-containing compound metabolic process
## GO:0006396 GO:0006396                                   RNA processing
##            setSize enrichmentScore
## GO:0002250     110      -0.4726934
## GO:0002253      50      -0.5141143
## GO:0002377      51      -0.6152482
## GO:0002764      52      -0.4982248
## GO:0006139     443       0.3195185
## GO:0006396     105       0.4952210

可以進(jìn)行一些調(diào)整以接近文獻(xiàn)

1)修改GSEA線條顏色

2)添加P值的table

3)展示指定的GO或pathway

4)展示多個GO或pathway

5)只展示上兩部

展示指定的通路,繪制GSEA 圖形,這里選擇我們注釋的一個結(jié)果 “GO:0002250”,如下:

gseaplot2(GO, "GO:0002250", color = "firebrick", rel_heights=c(1, .2, .6))

展示多個GO, 展示多個GSEA - GO 富集結(jié)果,添加P值的table,如下:

go<-GO$ID[1:4]
gseaplot2(GO,
          go, 
          pvalue_table = TRUE,
          color = colorspace::rainbow_hcl(4),
          base_size = 10)

不添加P值的table,如下:

gseaplot2(GO,
          go, 
          pvalue_table = FALSE,
          color = colorspace::rainbow_hcl(4),
          base_size = 10)

只展示上兩部,如下:

gseaplot2(GO,go,
          color = colorspace::rainbow_hcl(4),
          subplots=c(1,2), 
          pvalue_table = FALSE)

KEGG 富集分析

#KEGG富集
KEGG<-gseKEGG(
  gene_fc,
  organism = "hsa",
  keyType = "kegg",
  exponent = 1,
  minGSSize = 10,
  maxGSSize = 500,
  eps = 1e-10,
  pvalueCutoff = 0.05,
  pAdjustMethod = "BH",
  verbose = TRUE,
  use_internal_data = FALSE,
  seed = FALSE,
  by = "fgsea"
)
sortKEGG<-KEGG[order(KEGG$enrichmentScore, decreasing = T),]#按照enrichment score從高到低排序
head(sortKEGG)


##                ID                             Description setSize
## hsa04613 hsa04613 Neutrophil extracellular trap formation      36
## hsa05322 hsa05322            Systemic lupus erythematosus      35
## hsa05203 hsa05203                    Viral carcinogenesis      25
## hsa05034 hsa05034                              Alcoholism      48
## hsa04080 hsa04080 Neuroactive ligand-receptor interaction      81
## hsa01100 hsa01100                      Metabolic pathways     143
##          enrichmentScore       NES       pvalue     p.adjust      qvalues
## hsa04613       0.5819289  2.796643 6.536810e-08 3.819955e-06 2.637779e-06
## hsa05322       0.5712915  2.717399 3.160108e-07 9.547559e-06 6.592841e-06
## hsa05203       0.5117522  2.204931 3.377795e-04 3.247880e-03 2.242746e-03
## hsa05034       0.4554528  2.402982 1.454689e-05 2.272951e-04 1.569533e-04
## hsa04080      -0.2327878 -1.935807 1.679454e-03 1.208257e-02 8.343336e-03
## hsa01100      -0.3054455 -3.049852 3.470165e-10 4.337706e-08 2.995300e-08
##          rank                   leading_edge
## hsa04613  731 tags=72%, list=25%, signal=55%
## hsa05322  731 tags=71%, list=25%, signal=54%
## hsa05203  520 tags=52%, list=18%, signal=43%
## hsa05034  865 tags=62%, list=30%, signal=44%
## hsa04080  792 tags=48%, list=28%, signal=36%
## hsa01100  933 tags=59%, list=32%, signal=42%
##                                                                                                                                                                                                                                                                                                                                                                                                                                                          core_enrichment
## hsa04613                                                                                                                                                                                                                                                                                                                          8368/8346/8364/3018/8366/8360/8335/85235/8354/317772/8356/8331/8332/8367/8348/8342/8359/8344/8968/8340/8343/5582/2244/8336/8350/440689
## hsa05322                                                                                                                                                                                                                                                                                                                               8368/8346/8364/3018/8366/8360/8335/85235/8354/317772/8356/8331/8332/8367/8348/8342/8359/8344/8968/8340/8343/2904/8336/8350/440689
## hsa05203                                                                                                                                                                                                                                                                                                                                                                                                8368/8346/8364/3018/8366/8360/8367/8348/8342/8359/8344/8340/8343
## hsa05034                                                                                                                                                                                                                                                                                                      8368/8346/8364/3018/8366/8360/8335/85235/8354/317772/8356/8331/8332/8367/8348/2906/8342/8359/8344/8968/8340/8343/2904/8336/8350/440689/7054/2792/1813/3013
## hsa04080                                                                                                                                                                                                                                                               3363/2903/6752/7068/155/5028/66004/1816/2893/9934/148/84539/2565/2901/3360/1907/2566/5179/1511/1908/2641/2587/553/5030/1129/2899/4852/7432/1268/185/22953/6865/9340/117/5539/4887/6750/5697/10022
## hsa01100 51301/79153/5288/124/1562/771/5959/5408/5333/2878/377841/5322/7498/3158/534/4129/3291/129807/84803/10690/54988/11181/54657/5152/957/30815/5138/10317/8639/23382/57452/83539/5105/54511/80168/5742/25834/2949/111/54658/2875/197257/391013/57016/339221/27306/7366/4842/64902/79799/6476/60495/8708/10170/9227/3294/133121/5145/7166/229/54575/2651/290/6898/443/5837/270/7367/126/2938/54576/125/248/150572/760/57733/1576/762/8972/2939/1610/3284/766/2538/759

展示指定通路,如下:

gseaplot2(KEGG, "hsa04613", color = "firebrick", rel_heights=c(1, .2, .6))

展示指定多個通路,如下:

paths <- c("hsa04613", "hsa05322", "hsa05203", "hsa05034")#選取你需要展示的通路ID
gseaplot2(KEGG,
          paths, 
          pvalue_table = TRUE,
          color = colorspace::rainbow_hcl(4),
          base_size = 20)

不添加Pvalue表格

gseaplot2(KEGG,paths,
          color = colorspace::rainbow_hcl(4),
          pvalue_table = FALSE)

只展示上面兩部分圖形,如下:

gseaplot2(KEGG,paths,
          color = colorspace::rainbow_hcl(4),
          subplots=c(1,2), 
          pvalue_table = TRUE)

可以選擇點圖 ES_geom = “dot”,如下:

gseaplot2(KEGG,paths,
          color = colorspace::rainbow_hcl(4),
          pvalue_table = FALSE)

GSEA的結(jié)果解讀

1、圖最上面部分展示的是富集分?jǐn)?shù)(ES,enrichment score)值計算過程,從左至右每到一個基因,計算出一個ES值,連成線。在最左側(cè)或最右側(cè)有一個特別明顯的峰值就是基因集表型上的ES值。圖中間部分每一條線代表基因集中的一個基因,及其在基因列表中的排序位置。

2、最下面部分展示的是基因與表型關(guān)聯(lián)的矩陣,紅色為與第一個表型(class A)正相關(guān),在class A中表達(dá)高,藍(lán)色與第二個表型(class B)正相關(guān),在class B中表達(dá)高。

3、Leading-edge subset 對富集得分貢獻(xiàn)最大的基因成員。若富集得分為正值,則是峰左側(cè)的基因;若富集得分為負(fù)值,則是峰右側(cè)的基因。

4、FDR GSEA默認(rèn)提供所有的分析結(jié)果,并且設(shè)定FDR<0.25為可信的富集,最可能獲得有功能研究價值的結(jié)果。但如果樣品數(shù)目少,而且選擇了gene_set作為Permumation type則需要使用更為嚴(yán)格的標(biāo)準(zhǔn),比如FDR<0.05。

個人感覺總結(jié)的已經(jīng)很全面了,不足的地方請大家指正。

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桓峰基因

生物信息分析,SCI文章撰寫及生物信息基礎(chǔ)知識學(xué)習(xí):R語言學(xué)習(xí),perl基礎(chǔ)編程,linux系統(tǒng)命令,Python遇見更好的你

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References:

  1. Zhuang W, Sun H, Zhang S, et al. An immunogenomic signature for molecular classification in hepatocellular carcinoma. Mol Ther Nucleic Acids. 2021;25:105-115. Published 2021 Jul 2. doi:10.1016/j.omtn.2021.06.024

  2. Cao J, Zhang C, Jiang GQ, et al. Identification of hepatocellular carcinoma-related genes associated with macrophage differentiation based on bioinformatics analyses. Bioengineered. 2021;12(1):296-309. doi:10.1080/21655979.2020.1868119

  3. Ju A, Tang J, Chen S, Fu Y, Luo Y. Pyroptosis-Related Gene Signatures Can Robustly Diagnose Skin Cutaneous Melanoma and Predict the Prognosis. Front Oncol. 2021;11:709077. Published 2021 Jul 13. doi:10.3389/fonc.2021.709077

  4. Tan L, Xu Q, Shi R, Zhang G. Bioinformatics analysis reveals the landscape of immune cell infiltration and immune-related pathways participating in the progression of carotid atherosclerotic plaques. Artif Cells Nanomed Biotechnol. 2021;49(1):96-107. doi:10.1080/21691401.2021.1873798

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