有時(shí)候，大家做實(shí)驗(yàn)以小鼠為模型，但希望查看與之對(duì)應(yīng)的人同源基因。像這種情況，我們可以不需要進(jìn)行序列比對(duì)來(lái)查找，因?yàn)楸容^麻煩。使用公共數(shù)據(jù)可能更高效。
1.基于NCBI HomoloGene數(shù)據(jù)庫(kù)查找物種間對(duì)應(yīng)的同源基因
NCBI HomoloGene數(shù)據(jù)庫(kù)收集了部分已經(jīng)完成基因組測(cè)序物種的同源基因數(shù)據(jù)。
數(shù)據(jù)庫(kù)現(xiàn)包含21個(gè)物種，共44233組同源基因；
HomoloGene的數(shù)據(jù)是開(kāi)放的：FTP
homologene.data存放著同源基因的對(duì)應(yīng)關(guān)系
| HID(HomoloGene group id) | Taxonomy ID | Gene ID | Gene Symbol | Protein gi | Protein accession |
|---|---|---|---|---|---|
| 3 | 9606 | 34 | ACADM | 160961497 | NP_001104286.1 |
| 3 | 9598 | 469356 | ACADM | 109008502 | XP_001101274.1 |
| 3 | 10090 | 11364 | Acadm | 6680618 | NP_031408.1 |
每個(gè)物種都有一個(gè)對(duì)應(yīng)的Taxonomy ID：
10090 Mus musculus
10116 Rattus norvegicus
28985 Kluyveromyces lactis
318829 Magnaporthe oryzae
33169 Eremothecium gossypii
3702 Arabidopsis thaliana
4530 Oryza sativa
4896 Schizosaccharomyces pombe
4932 Saccharomyces cerevisiae
5141 Neurospora crassa
6239 Caenorhabditis elegans
7165 Anopheles gambiae
7227 Drosophila melanogaster
7955 Danio rerio
8364 Xenopus (Silurana) tropicalis
9031 Gallus gallus
9544 Macaca mulatta
9598 Pan troglodytes
9606 Homo sapiens
9615 Canis lupus familiaris
9913 Bos taurus
單個(gè)基因直接檢索，如Acadm：
批量注釋某個(gè)物種的基因?qū)?yīng)另一個(gè)物種的同源基因，可以使用R包homologene，它調(diào)用的是c中build68的數(shù)據(jù)；
homologene(genes, inTax, outTax)
genes：需要查找同源基因的基因列表
inTax：輸入基因所屬物種
outTax：查找的同源基因?qū)儆谀莻€(gè)物種
例子：
genelist<-c("Acadm","Eno2","Acadvl")
homologene(genelist, inTax = 10090, outTax = 9606)
10090 9606 10090_ID 9606_ID
1 Eno2 ENO2 13807 2026
2 Mog MOG 17441 4340
查看homologene使用的數(shù)據(jù)版本
homologeneVersion
[1] 68
-
基于InParanoid 8數(shù)據(jù)庫(kù)查找物種間對(duì)應(yīng)的同源基因
InParanoid 8提供的下載數(shù)據(jù)是Protein ID；構(gòu)建g InParanoid 8 用到的InParanoid 4.1可以獲取的，InParanoid 4.1 standalone download這兒我們利用InParanoid 8提供的同源基因信息進(jìn)行一個(gè)快速檢索。
根據(jù)自己研究的物種，從Downloads中下載數(shù)據(jù)；8.0_current；需要值得注意的是，人類(lèi)與老鼠的同源基因文件InParanoid.H.sapiens-M.musculus.tgz 存放于H.sapiens/ ；在M.musculus/ 不會(huì)存在InParanoid.M.musculus-H.sapiens.tgz；其它類(lèi)似，所以要根據(jù)物種名首字母排序去排名靠前的物種文件夾下去找同源基因集文件。
InParanoid.H.sapiens-M.musculus.tgz 下載后解壓：
這兒使用文件，格式如下：sqltable.H.sapiens-M.musculus
數(shù)據(jù)格式和前面的NCBI HomoloGene中的homologene.data差不多；使用R處理數(shù)據(jù)時(shí)，模仿了homologene包代碼；
homologene.R的代碼
homologene = function(genes, inTax, outTax){
genes <- unique(genes) #remove duplicates
out = homologene::homologeneData %>%
dplyr::filter(Taxonomy %in% inTax & (Gene.Symbol %in% genes | Gene.ID %in% genes)) %>%
dplyr::select(HID,Gene.Symbol,Gene.ID)
names(out)[2] = inTax
names(out)[3] = paste0(inTax,'_ID')
out2 = homologene::homologeneData %>% dplyr::filter(Taxonomy %in% outTax & HID %in% out$HID) %>%
dplyr::select(HID,Gene.Symbol,Gene.ID)
names(out2)[2] = outTax
names(out2)[3] = paste0(outTax,'_ID')
output = merge(out,out2) %>% dplyr::select(2,4,3,5)
# preserve order with temporary column
output$sortBy <- factor(output[,1], levels = genes)
output <- dplyr::arrange(output, sortBy)
output$sortBy <- NULL
return(output)
}
仿寫(xiě)的函數(shù)InParanoid_homo()：
Hs.Mm<-read.table("sqltable.H.sapiens-M.musculus",sep = "\t",fill = T)
genes<-c("Q8WZ42","A2ASS6")
trans<-InParanoid_homo(genes,Hs.Mm)
InParanoid_homo = function(genes,database){
colnames(database)<-c("Group","score","spieces","num","gene","Bootstrap")
genes <- unique(genes)
Spieces_name1<-database[1,]$spieces
Spieces_name2<-database[2,]$spieces
Spieces_1<-database %>% dplyr::filter(spieces %in% Spieces_name1)
Spieces_2<-database %>% dplyr::filter(spieces %in% Spieces_name2)
if(ANSWER <- readline(paste("Transfer",Spieces_name1,"to",Spieces_name2,"?","True/False: "))){
genes_query<-Spieces_1 %>% dplyr::filter(gene %in% genes);head(genes_query)
output = merge(genes_query,Spieces_2,by="Group")[,]
}else if(ANSWER <- readline(paste("Transfer",Spieces_name2,"to",Spieces_name1,"?","True/False: "))){
genes_query<-Spieces_2 %>% dplyr::filter(gene %in% genes);head(genes_query)
output = merge(genes_query,Spieces_1,by="Group")[,]
}else{
cat("Nothing for you.")
}
return(output)
}
參考：
InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic
homologene reference manual
