geneID转换之org.Hs.eg.db包简介

Posted 2021-01-05 djx571

1）安装载入

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if("org.Hs.eg.db" %in% rownames(installed.packages()) == FALSE) {source("http://bioconductor.org/biocLite.R");biocLite("org.Hs.eg.db")}
suppressMessages(library(org.Hs.eg.db))

2)查看该包所有的对象

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ls("package:org.Hs.eg.db")

功能：可以用来进行基因ID的转换

org.Hs.egACCNUM：Map Entrez Gene identifiers to GenBank Accession Numbers（Entrez Gene identifiers 和genbank）
org.Hs.egALIAS2EG：Map between Common Gene Symbol Identifiers and Entrez Gene
org.Hs.eg.db：Bioconductor annotation data package
org.Hs.egCHR：Map Entrez Gene IDs to Chromosomes
org.Hs.egCHRLENGTHS：A named vector for the length of each of the chromosomes
org.Hs.egCHRLOC：Entrez Gene IDs to Chromosomal Location
org.Hs.egENSEMBL：Map Ensembl gene accession numbers with Entrez Gene identifiers
org.Hs.egENSEMBLPROT：Map Ensembl protein acession numbers with Entrez Gene identifiers
org.Hs.egENSEMBLTRANS：Map Ensembl transcript acession numbers with Entrez Gene identifiers
org.Hs.egENZYME：Map between Entrez Gene IDs and Enzyme Commission (EC) Numbers
org.Hs.egGENENAME：Map between Entrez Gene IDs and Genes
org.Hs.egGO：Maps between Entrez Gene IDs and Gene Ontology (GO) IDs
org.Hs.egMAP：Map between Entrez Gene Identifiers and cytogenetic：Maps/bands
org.Hs.egMAPCOUNTS Number of：Mapped keys for the：Maps in package org.Hs.eg.db
org.Hs.egOMIM：Map between Entrez Gene Identifiers and Mendelian Inheritance in Man (MIM) identifiers
org.Hs.egORGANISM：The Organism for org.Hs.eg
org.Hs.egPATH：Mappings between Entrez Gene identifiers and KEGG pathway identifiers
org.Hs.egPFAM：Maps between Manufacturer Identifiers and PFAM Identifiers
org.Hs.egPMID：Map between Entrez Gene Identifiers and PubMed Identifiers
org.Hs.egPROSITE：Maps between Manufacturer Identifiers and PROSITE Identifiers
org.Hs.egREFSEQ：Map between Entrez Gene Identifiers and RefSeq Identifiers
org.Hs.egSYMBOL：Map between Entrez Gene Identifiers and Gene Symbols
org.Hs.egUNIGENE：Map between Entrez Gene Identifiers and UniGene cluster identifiers
org.Hs.egUNIPROT：Map Uniprot accession numbers with Entrez Gene identifiers
org.Hs.eg_dbconn：Collect information about the package annotation DB

 示例：

(用mget函数)：
myEIDs <- c("1", "10", "100", "1000", "37690")
mySymbols <- mget(myEIDs, org.Hs.egSYMBOL, ifnotfound=NA)     ####myEID是自己的ID，org.Hs.egSYMBOL是其中的一个对象
mySymbols <- unlist(mySymbols)

(用select函数)：
myEIDs <- c("ENSG00000130720", "ENSG00000103257", "ENSG00000156414")
cols <- c("SYMBOL", "GENENAME")
select(org.Hs.eg.db, keys=myEIDs, columns=cols, keytype="ENSEMBL")#生成数据框，

原理：例如将 Entrez Gene identifiers( https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene) 与 GenBank accession numbers进行简单的mapping。该map依据的数据库是Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/DATA

 

 

以DATA其中的一个gene2ensembl文件为例来感受其实如何实现的：

 wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2ensembl.gz

解压后查看：

其中第一列是物种id，第二列是GeneID, 第三列是Ensemble_geneID,第四列是RNA_id,第五列是Ensemble_RNAid,第六列是protein_id。因此这些R包的功能极有可能就是利用NCBI或ensem等数据库中的这些文件信息，通过一系列的脚本实现了基因ID之间进行转换，因此如果对NCBI、Ensemble等网络架构熟悉的话，自己又会写脚本，就可以自己处理，而不用这些R包进行。当然别人写好了，为什么自己造轮子呢？自己造轮子是为了深刻的理解

3）各个对象的简单使用

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3.1）org.Hs.egACCNUM(将Entrez Gene identifiers 与 GenBank Accession Numbers进行map

x <- org.Hs.egACCNUM  ### Bimap interface
mapped_genes <- mappedkeys(x) ## Get the entrez gene identifiers that are mapped to an ACCNUM
xx <- as.list(x[mapped_genes]) # Convert to a list
if(length(xx) > 0) {
xx[1:5]     # Get the ACCNUM for the first five genes
xx[[1]]     # Get the first one
}
#For the reverse map ACCNUM2EG:
xx <- as.list(org.Hs.egACCNUM2EG)  # Convert to a list
if(length(xx) > 0){
xx[1:5]      # Gets the entrez gene identifiers for the first five Entrez Gene IDs
xx[[1]]      # Get the first one
}

 3.2）org.Hs.egALIAS2EG(将 Common Gene Symbol Identifiers 和 Entrez Gene进行转换)

x <- org.Hs.egACCNUM  ## Bimap interface:org.Hs.egALIAS2EG
xx <- as.list(org.Hs.egALIAS2EG)   # Convert the object to a list
xx <- xx[!is.na(xx)] # Remove pathway identifiers that do not map to any entrez gene id
if(length(xx) > 0){
xx[1:2]   # The entrez gene identifiers for the first two elements of XX
xx[[1]]   # Get the first one
}

3.3) org.Hs.egCHR (将Entrez Gene IDs 和Chromosomes进行map)

x <- org.Hs.egCHR        ## Bimap interface
mapped_genes <- mappedkeys(x) #Get entrez gene  that are mapped to a chromosome
xx <- as.list(x[mapped_genes]) # Convert to a list
if(length(xx) > 0) {
xx[1:5]         # Get the CHR for the first five genes
xx[[1]]         # Get the first one
}

3.4）org.Hs.egCHRLENGTHS (每个染色体的长度)

tt <- org.Hs.egCHRLENGTHS  ## Bimap interface:
tt["1"]        # Length of chromosome 1
for (i in c(1:22,\'X\',\'Y\')){print(tt[i])}    #####打印每一个染色体的长度

3.5） org.Hs.egCHRLOC （Entrez Gene IDs在Chromosomal 上的定位)

x <- org.Hs.egCHRLOC  ### Bimap interface
mapped_genes <- mappedkeys(x) #Get the entrez gene identifiers that are mapped to chromosome locations
xx <- as.list(x[mapped_genes])  # Convert to a list
if(length(xx) > 0) {
xx[1:5]   # Get the CHRLOC for the first five genes
xx[[1]]   # Get the first one
}

3.6）org.Hs.egENSEMBL （将Ensembl gene accession numbers 与 Entrez Gene identifiers进行map）

x <- org.Hs.egENSEMBL  ## Bimap interface
mapped_genes <- mappedkeys(x)# Get the entrez gene IDs that are mapped to an Ensembl ID
xx <- as.list(x[mapped_genes]) # Convert to a list
if(length(xx) > 0) {
xx[1:5]        # Get the Ensembl gene IDs for the first five genes
xx[[1]]    # Get the first one
}
#For the reverse map ENSEMBL2EG:
xx <- as.list(org.Hs.egENSEMBL2EG)  # Convert to a list
if(length(xx) > 0){              
xx[1:5]       # Gets the entrez gene IDs for the first five Ensembl IDs
xx[[1]]       # Get the first one
}

3.7) org.Hs.egENSEMBLPROT (将Ensembl protein acession numbers 和 Entrez Gene identifiers进行map)

x <- org.Hs.egENSEMBLPROT   ## Bimap interface
mapped_genes <- mappedkeys(x) #Get the entrez gene IDs that are mapped to an Ensembl ID
xx <- as.list(x[mapped_genes]) # Convert to a list
if(length(xx) > 0) {  
xx[1:5]    # Get the Ensembl gene IDs for the first five proteins
xx[[1]]     # Get the first one
}
#For the reverse map ENSEMBLPROT2EG:
xx <- as.list(org.Hs.egENSEMBLPROT2EG)  # Convert to a list
if(length(xx) > 0){
xx[1:5]  # Gets the entrez gene IDs for the first five Ensembl IDs
xx[[1]]  # Get the first one
}

3.8) org.Hs.egENSEMBLTRANS (将 Ensembl transcript acession numbers 与 Entrez Gene identifiers进行mapping)

x <- org.Hs.egENSEMBLTRANS   ## Bimap interface:
mapped_genes <- mappedkeys(x) #entrez gene IDs that are mapped to an Ensembl ID
xx <- as.list(x[mapped_genes])  # Convert to a list
if(length(xx) > 0) {
xx[1:5]   # Get the Ensembl gene IDs for the first five proteins
xx[[1]]  # Get the first one
}
#For the reverse map ENSEMBLTRANS2EG:
xx <- as.list(org.Hs.egENSEMBLTRANS2EG)  # Convert to a list
if(length(xx) > 0){
xx[1:5]  # Gets the entrez gene IDs for the first five Ensembl IDs
xx[[1]]  # Get the first one
}

3.9)org.Hs.egGENENAME(将 Entrez Gene IDs 与 Genes进行mapping)

x <- org.Hs.egGENENAME    ## Bimap interface
mapped_genes <- mappedkeys(x) #gene names that are mapped to an entrez gene identifier
xx <- as.list(x[mapped_genes]) # Convert to a list
if(length(xx) > 0) {
xx[1:5]  # Get the GENE NAME for the first five genes
xx[[1]]  # Get the first one
}

3.10)org.Hs.egGO (Entrez Gene IDs与 Gene Ontology (GO) IDs进行mapping)

x <- org.Hs.egGO  ## Bimap interface:
mapped_genes <- mappedkeys(x) # entrez gene identifiers that are mapped to a GO ID
xx <- as.list(x[mapped_genes]) # Convert to a list
if(length(xx) > 0) {
got <- xx[[1]]  # Try the first one
got[[1]][["GOID"]]
got[[1]][["Ontology"]]
got[[1]][["Evidence"]]
}
# For the reverse map:
xx <- as.list(org.Hs.egGO2EG)  # Convert to a list
if(length(xx) > 0){
goids <- xx[2:3] # Gets the entrez gene ids for the top 2nd and 3nd GO identifiers
goids[[1]]  # Gets the entrez gene ids for the first element of goids
names(goids[[1]]) # Evidence code for the mappings
}
# For org.Hs.egGO2ALLEGS
xx <- as.list(org.Hs.egGO2ALLEGS)
if(length(xx) > 0){
​
goids <- xx[2:3] #  Entrez Gene identifiers for the top 2nd and 3nd GO identifiers
goids[[1]] # Gets all the Entrez Gene identifiers for the first element of goids
names(goids[[1]]) # Evidence code for the mappings
}

3.11)org.Hs.egPATH (将Entrez Gene identifiers 与KEGG pathway identifiers进行mapping)

x <- org.Hs.egPATH  ## Bimap interface:
mapped_genes <- mappedkeys(x) 
xx <- as.list(x[mapped_genes])
if(length(xx) > 0) {
xx[1:5]
xx[[1]]
}
# For the reverse map:
xx <- as.list(org.Hs.egPATH2EG)
xx <- xx[!is.na(xx)] # Remove pathway identifiers that do not map to any entrez gene id
if(length(xx) > 0){
xx[1:2]
xx[[1]]
}

3.12)org.Hs.egREFSEQ(将Entrez Gene Identifiers 与 RefSeq Identifiers进行mapping)

x <- org.Hs.egREFSEQ
mapped_genes <- mappedkeys(x)
xx <- as.list(x[mapped_genes])
if(length(xx) > 0) {
xx[1:5]
xx[[1]]
}
# For the reverse map:
x <- org.Hs.egREFSEQ2EG
mapped_seqs <- mappedkeys(x)
xx <- as.list(x[mapped_seqs])
if(length(xx) > 0) {
xx[1:5]
xx[[1]]
}

3.13)org.Hs.egSYMBOL(将 Entrez Gene Identifiers 与Gene Symbols进行mapping)

x <- org.Hs.egSYMBOL
mapped_genes <- mappedkeys(x)
xx <- as.list(x[mapped_genes])
if(length(xx) > 0) {
xx[1:5]
xx[[1]]
}
x <- org.Hs.egSYMBOL2EG
mapped_genes <- mappedkeys(x)
xx <- as.list(x[mapped_genes])
if(length(xx) > 0) {
xx[1:5]
xx[[1]]
}

3.14）org.Hs.egUNIGENE (Entrez Gene Identifiers 与 UniGene cluster identifiers进行mapping)

x <- org.Hs.egUNIGENE
mapped_genes <- mappedkeys(x)
xx <- as.list(x[mapped_genes])
if(length(xx) > 0) {
xx[1:5]
xx[[1]]
}
# For the reverse map:
x <- org.Hs.egUNIGENE2EG
mapped_genes <- mappedkeys(x)
xx <- as.list(x[mapped_genes])
if(length(xx) > 0) {
xx[1:5]
xx[[1]]
}

3.15）org.Hs.egUNIPROT (Uniprot accession numbers与 Entrez Gene identifiers进行mapping)

x <- org.Hs.egUNIPROT
mapped_genes <- mappedkeys(x)
xx <- as.list(x[mapped_genes])
if(length(xx) > 0) {
xx[1:5]
xx[[1]]
}

 希望大家通过上述教程的解析，能够理解，基因ID，名称等之间是如何转换，并通过这些对NCBI、ensemble、pfam等数据库有相应的一定认识。