前言
在日常分析中，我们经常会遇到对同一物种基因ID和symbol之间的互转，或者是不同物种之间同源基因的互转。虽然目前已经有几个包，比如：biomaRt，easyConvert和org.Hs.eg.db系列，或者之间进入Ensemble数据库查询。但是上述包在使用时，都有各种各样的问题，如biomaRt对网络依赖很大，org.Hs.eg.db会丢失很多基因等。那么今天Immugent就来给大家介绍一款新的R包--babelgene。
废话不多说，下面开始展示...
代码流程
安装babelgene包+小试牛刀。。。
install.packages("babelgene")
library(babelgene)
orthologs(genes = c("TP53", "EGFR", "IL6", "TGFB1", "CD4"), species = "mouse")
#> human_symbol human_entrez human_ensembl taxon_id symbol entrez
#> 1 CD4 920 ENSG00000010610 10090 Cd4 12504
#> 2 EGFR 1956 ENSG00000146648 10090 Egfr 13649
#> 3 IL6 3569 ENSG00000136244 10090 Il6 16193
#> 4 TGFB1 7040 ENSG00000105329 10090 Tgfb1 21803
#> 5 TP53 7157 ENSG00000141510 10090 Trp53 22059
#> ensembl
#> 1 ENSMUSG00000023274
#> 2 ENSMUSG00000020122
#> 3 ENSMUSG00000025746
#> 4 ENSMUSG00000002603
#> 5 ENSMUSG00000059552
#> support
#> 1 EggNOG|Ensembl|HGNC|HomoloGene|Inparanoid|NCBI|OMA|OrthoDB|OrthoMCL|Panther|PhylomeDB|Treefam
#> 2 EggNOG|Ensembl|HGNC|HomoloGene|Inparanoid|NCBI|OMA|OrthoDB|OrthoMCL|Panther|PhylomeDB|Treefam
#> 3 Ensembl|HGNC|HomoloGene|Inparanoid|NCBI|OMA|OrthoMCL|Panther|PhylomeDB|Treefam
#> 4 EggNOG|Ensembl|HGNC|HomoloGene|Inparanoid|NCBI|OMA|OrthoDB|OrthoMCL|Panther|PhylomeDB|Treefam
#> 5 EggNOG|Ensembl|HGNC|HomoloGene|Inparanoid|NCBI|OMA|OrthoDB|OrthoMCL|Panther|PhylomeDB|Treefam
#> support_n
#> 1 12
#> 2 12
#> 3 10
#> 4 12
#> 5 12
默认情况下，输入基因是人类的。大家也可以使用human参数指定输入基因是否为人类。
orthologs(genes = "Pu", species = "fruit fly", human = FALSE)
#> human_symbol human_entrez human_ensembl taxon_id symbol entrez ensembl
#> 1 GCH1 2643 ENSG00000131979 7227 Pu 37415 FBgn0003162
#> support
#> 1 EggNOG|Ensembl|HomoloGene|Inparanoid|OMA|OrthoDB|OrthoMCL|Panther|PhylomeDB|Treefam
#> support_n
#> 1 10
也可以通过NCBI Entrez或Ensembl id而不是基因名进行搜索。
orthologs(genes = "ENSG00000111640", species = "mouse", human = TRUE)
#> human_symbol human_entrez human_ensembl taxon_id symbol entrez
#> 1 GAPDH 2597 ENSG00000111640 10090 Gapdh 14433
#> ensembl
#> 1 ENSMUSG00000057666
#> support support_n
#> 1 Ensembl|HGNC|HomoloGene|NCBI|OMA|OrthoDB|OrthoMCL|Panther|Treefam 9
最后，我们来看一下babelgene包都包含哪些物种吧。
species()
#> taxon_id scientific_name
#> 1 28377 Anolis carolinensis
#> 2 9913 Bos taurus
#> 3 6239 Caenorhabditis elegans
#> 4 9615 Canis lupus familiaris
#> 5 7955 Danio rerio
#> 6 7227 Drosophila melanogaster
#> 7 9796 Equus caballus
#> 8 9685 Felis catus
#> 9 9031 Gallus gallus
#> 10 9544 Macaca mulatta
#> 11 13616 Monodelphis domestica
#> 12 10090 Mus musculus
#> 13 9258 Ornithorhynchus anatinus
#> 14 9598 Pan troglodytes
#> 15 10116 Rattus norvegicus
#> 16 4932 Saccharomyces cerevisiae
#> 17 284812 Schizosaccharomyces pombe 972h-
#> 18 9823 Sus scrofa
#> 19 8364 Xenopus tropicalis
#> common_name
#> 1 Carolina anole, green anole
#> 2 bovine, cattle, cow, dairy cow, domestic cattle, domestic cow, ox, oxen
#> 3 <NA>
#> 4 dog, dogs
#> 5 leopard danio, zebra danio, zebra fish, zebrafish
#> 6 fruit fly
#> 7 domestic horse, equine, horse
#> 8 cat, cats, domestic cat
#> 9 bantam, chicken, chickens, Gallus domesticus
#> 10 rhesus macaque, rhesus macaques, Rhesus monkey, rhesus monkeys
#> 11 gray short-tailed opossum
#> 12 house mouse, mouse
#> 13 duck-billed platypus, duckbill platypus, platypus
#> 14 chimpanzee
#> 15 brown rat, Norway rat, rat, rats
#> 16 baker's yeast, brewer's yeast, S. cerevisiae
#> 17 <NA>
#> 18 pig, pigs, swine, wild boar
#> 19 tropical clawed frog, western clawed frog
可谓是应有尽有，包罗万象了！
说在最后
babelgene包使用起来非常轻便，而且涵盖的物种也比较全，基本上可以满足我们各种基因ID的转化需求。有需要的小伙伴赶紧用起来吧！
好啦，本次分享到这里就结束了，我们下次再会~~~
