R - Convert a Ensembl gene id to gene symbol
Written on May 1, 2020
One of the most frustrating things about working with ensembl gene Ids is that as humans, we like to see Gene symbols so that we can look through our lists and see our favourite genes.
I always found converting Ensembl Ids to Symbols in R really annoying. However, there have been a number of packages produced that have helped do this more efficienctly. I will show you how this can be done in two different ways, (1) using the org.Hs.eg.db and (2) annotables.
Org.Hs.eg.db
infile = read.csv("data/gene_lists.csv")
data = infile[,"ENSEMBL"]
# You can see that the subset data is listed as a integer, we now need to convert
# this to a vector to pass it into the annotation mapping
data = as.vector(data)
# Using the org.Hs.eg.db we set up mapping info - if you look at the documentation you
# can also obtain other keytypes
annots <- select(org.Hs.eg.db, keys=data,
columns="SYMBOL", keytype="ENSEMBL")
result <- merge(infile, annots, by.x="ENSEMBL", by.y="ENSEMBL")
print(head(result))## ENSEMBL log2FoldChange baseMean padj SYMBOL
## 1 ENSG00000000419 0.18713483 1487.61562 0.377139110 DPM1
## 2 ENSG00000000457 0.02922775 519.65035 0.927794309 SCYL3
## 3 ENSG00000000460 0.31120415 125.54166 0.380726319 C1orf112
## 4 ENSG00000000971 -0.18479425 79.10841 0.818624222 CFH
## 5 ENSG00000001036 0.39103001 53.04816 0.532827630 FUCA2
## 6 ENSG00000001084 -0.51993067 1065.13861 0.001388325 GCLCAnnotables
infile = read.csv("data/gene_lists.csv")
infile %>%
dplyr::arrange(padj) %>%
head(20) %>%
dplyr::inner_join(grch38, by = c("ENSEMBL" = "ensgene"))## log2FoldChange baseMean padj ENSEMBL entrez symbol chr
## 1 -0.9193411 3487.4362 1.42e-22 ENSG00000186480 3638 INSIG1 7
## 2 -0.8311274 5338.9306 6.31e-18 ENSG00000137309 3159 HMGA1 6
## 3 1.7218713 307.1204 6.31e-18 ENSG00000214026 6150 MRPL23 11
## 4 1.7218713 307.1204 6.31e-18 ENSG00000214026 107987373 MRPL23 11
## 5 1.7218713 307.1204 6.31e-18 ENSG00000214026 6150 MRPL23 11
## 6 1.7218713 307.1204 6.31e-18 ENSG00000214026 107987373 MRPL23 11
## 7 1.3370923 506.9614 1.74e-17 ENSG00000136286 64005 MYO1G 7
## 8 -0.9048246 26303.5720 4.00e-17 ENSG00000087086 2512 FTL 19
## 9 1.3622491 349.2231 3.38e-16 ENSG00000122122 54440 SASH3 X
## 10 1.0544227 1841.3427 3.29e-14 ENSG00000116824 914 CD2 1
## 11 1.1525886 579.1535 1.18e-13 ENSG00000183735 29110 TBK1 12
## 12 1.1569100 492.1651 3.76e-13 ENSG00000133561 474344 GIMAP6 7
## 13 1.1097412 1768.2973 3.71e-12 ENSG00000171552 598 BCL2L1 20
## 14 0.8687971 2918.0275 2.18e-11 ENSG00000003402 8837 CFLAR 2
## 15 1.5528225 179.4745 3.49e-11 ENSG00000160685 51043 ZBTB7B 1
## 16 -0.8610968 4122.4284 4.47e-11 ENSG00000167996 2495 FTH1 11
## 17 -0.9730979 612.3984 2.05e-09 ENSG00000130766 83667 SESN2 1
## 18 1.1255855 284.6935 2.05e-09 ENSG00000143891 130589 GALM 2
## 19 -0.7757254 1545.5724 3.91e-09 ENSG00000162413 9903 KLHL21 1
## 20 0.9742609 657.1901 4.98e-09 ENSG00000197142 51703 ACSL5 10
## 21 0.8464779 1131.9277 8.26e-09 ENSG00000069493 29121 CLEC2D 12
## 22 1.1942058 1151.1959 1.33e-08 ENSG00000111679 5777 PTPN6 12
## start end strand biotype
## 1 155297776 155310235 1 protein_coding
## 2 34236873 34246231 1 protein_coding
## 3 1947278 1984522 1 protein_coding
## 4 1947278 1984522 1 protein_coding
## 5 1947278 1984522 1 protein_coding
## 6 1947278 1984522 1 protein_coding
## 7 44962662 44979098 -1 protein_coding
## 8 48965301 48966878 1 protein_coding
## 9 129779979 129795201 1 protein_coding
## 10 116754385 116769228 1 protein_coding
## 11 64451880 64502108 1 protein_coding
## 12 150625375 150632648 -1 protein_coding
## 13 31664452 31723989 -1 protein_coding
## 14 201116104 201176687 1 protein_coding
## 15 155002630 155018522 1 protein_coding
## 16 61959718 61967660 -1 protein_coding
## 17 28259527 28282491 1 protein_coding
## 18 38665910 38741237 1 protein_coding
## 19 6590724 6614607 -1 protein_coding
## 20 112374018 112428380 1 protein_coding
## 21 9664969 9699555 1 protein_coding
## 22 6946468 6961316 1 protein_coding
## description
## 1 insulin induced gene 1 [Source:HGNC Symbol;Acc:HGNC:6083]
## 2 high mobility group AT-hook 1 [Source:HGNC Symbol;Acc:HGNC:5010]
## 3 mitochondrial ribosomal protein L23 [Source:HGNC Symbol;Acc:HGNC:10322]
## 4 mitochondrial ribosomal protein L23 [Source:HGNC Symbol;Acc:HGNC:10322]
## 5 mitochondrial ribosomal protein L23 [Source:HGNC Symbol;Acc:HGNC:10322]
## 6 mitochondrial ribosomal protein L23 [Source:HGNC Symbol;Acc:HGNC:10322]
## 7 myosin IG [Source:HGNC Symbol;Acc:HGNC:13880]
## 8 ferritin light chain [Source:HGNC Symbol;Acc:HGNC:3999]
## 9 SAM and SH3 domain containing 3 [Source:HGNC Symbol;Acc:HGNC:15975]
## 10 CD2 molecule [Source:HGNC Symbol;Acc:HGNC:1639]
## 11 TANK binding kinase 1 [Source:HGNC Symbol;Acc:HGNC:11584]
## 12 GTPase, IMAP family member 6 [Source:HGNC Symbol;Acc:HGNC:21918]
## 13 BCL2 like 1 [Source:HGNC Symbol;Acc:HGNC:992]
## 14 CASP8 and FADD like apoptosis regulator [Source:HGNC Symbol;Acc:HGNC:1876]
## 15 zinc finger and BTB domain containing 7B [Source:HGNC Symbol;Acc:HGNC:18668]
## 16 ferritin heavy chain 1 [Source:HGNC Symbol;Acc:HGNC:3976]
## 17 sestrin 2 [Source:HGNC Symbol;Acc:HGNC:20746]
## 18 galactose mutarotase [Source:HGNC Symbol;Acc:HGNC:24063]
## 19 kelch like family member 21 [Source:HGNC Symbol;Acc:HGNC:29041]
## 20 acyl-CoA synthetase long chain family member 5 [Source:HGNC Symbol;Acc:HGNC:16526]
## 21 C-type lectin domain family 2 member D [Source:HGNC Symbol;Acc:HGNC:14351]
## 22 protein tyrosine phosphatase, non-receptor type 6 [Source:HGNC Symbol;Acc:HGNC:9658]