2015-11-13
(This article was first published on Getting Genetics Done, and kindly contributed to R-bloggers)
I work with gene lists on a nearly daily basis. Lists of genes near ChIP-seq peaks, lists of genes closest to a GWAS hit, lists of differentially expressed genes or transcripts from an RNA-seq experiment, lists of genes involved in certain pathways, etc. And lots of times I’ll need to convert these gene IDs from one identifier to another. There’s no shortage of tools to do this. I use Ensembl Biomart. But I do this so often that I got tired of hammering Ensembl’s servers whenever I wanted to convert from Ensembl to Entrez gene IDs for pathway mapping, get the chromosomal location for some BEDTools-y kinds of genomic arithmetic, or get the gene symbol and full description for reporting. So I used Biomart to retrieve the data that I use most often, cleaned up the column names, and saved this data as an R data package called annotables.
This package has basic annotation information from Ensembl release 82 for:
Human (grch38)
Mouse (grcm38)
Rat (rnor6)
Chicken (galgal4)
Worm (wbcel235)
Fly (bdgp6)
Where each table contains:
ensgene: Ensembl gene ID
entrez: Entrez gene ID
symbol: Gene symbol
chr: Chromosome
start: Start
end: End
strand: Strand
biotype: Protein coding, pseudogene, mitochondrial tRNA, etc.
description: Full gene name/description.
Additionally, there are tables for human and mouse (grch38_gt and grcm38_gt, respectively) that link ensembl gene IDs to ensembl transcript IDs.
Usage
The package isn’t on CRAN, so you’ll need devtools to install it.
It isn’t necessary to load dplyr, but the tables are tbl_df and will print nicely if you have dplyr loaded.
Look at the human genes table (note the description column gets cut off because the table becomes too wide to print nicely):
Look at the human genes-to-transcripts table:
Tables are tbl_df, pipe-able with dplyr:
ensgene
symbol
chr
start
end
ENSG00000158014
SLC30A2
1
26037252
26046133
ENSG00000173673
HES3
1
6244192
6245578
ENSG00000243749
ZMYM6NB
1
34981535
34985353
ENSG00000189410
SH2D5
1
20719732
20732837
ENSG00000116863
ADPRHL2
1
36088875
36093932
ENSG00000188643
S100A16
1
153606886
153613145
Table: Table continues below
description
solute carrier family 30 (zinc transporter), member 2 [Source:HGNC Symbol;Acc:HGNC:11013]
hes family bHLH transcription factor 3 [Source:HGNC Symbol;Acc:HGNC:26226]
ZMYM6 neighbor [Source:HGNC Symbol;Acc:HGNC:40021]
SH2 domain containing 5 [Source:HGNC Symbol;Acc:HGNC:28819]
ADP-ribosylhydrolase like 2 [Source:HGNC Symbol;Acc:HGNC:21304]
S100 calcium binding protein A16 [Source:HGNC Symbol;Acc:HGNC:20441]
Example with RNA-seq data
Here’s an example with RNA-seq data. Specifically, DESeq2 results from the airway package, made tidy with biobroom:
Now, make a table with the results (unfortunately, it’ll be split in this display, but you can write this to file to see all the columns in a single row):
gene
estimate
p.adjusted
symbol
ENSG00000152583
-4.316
4.753e-134
SPARCL1
ENSG00000165995
-3.189
1.44e-133
CACNB2
ENSG00000101347
-3.618
6.619e-125
SAMHD1
ENSG00000120129
-2.871
6.619e-125
DUSP1
ENSG00000189221
-3.231
9.468e-119
MAOA
ENSG00000211445
-3.553
3.94e-107
GPX3
ENSG00000157214
-1.949
8.74e-102
STEAP2
ENSG00000162614
-2.003
3.052e-98
NEXN
ENSG00000125148
-2.167
1.783e-92
MT2A
ENSG00000154734
-2.286
4.522e-86
ADAMTS1
ENSG00000139132
-2.181
2.501e-83
FGD4
ENSG00000162493
-1.858
4.215e-83
PDPN
ENSG00000162692
3.453
3.563e-82
VCAM1
ENSG00000179094
-3.044
1.199e-81
PER1
ENSG00000134243
-2.149
2.73e-81
SORT1
ENSG00000163884
-4.079
1.073e-80
KLF15
ENSG00000178695
2.446
6.275e-75
KCTD12
ENSG00000146250
2.64
1.143e-69
PRSS35
ENSG00000198624
-2.784
1.707e-69
CCDC69
ENSG00000148848
1.783
1.762e-69
ADAM12
Table: Table continues below
description
SPARC-like 1 (hevin) [Source:HGNC Symbol;Acc:HGNC:11220]
calcium channel, voltage-dependent, beta 2 subunit [Source:HGNC Symbol;Acc:HGNC:1402]
SAM domain and HD domain 1 [Source:HGNC Symbol;Acc:HGNC:15925]
dual specificity phosphatase 1 [Source:HGNC Symbol;Acc:HGNC:3064]
monoamine oxidase A [Source:HGNC Symbol;Acc:HGNC:6833]
glutathione peroxidase 3 [Source:HGNC Symbol;Acc:HGNC:4555]
STEAP family member 2, metalloreductase [Source:HGNC Symbol;Acc:HGNC:17885]
nexilin (F actin binding protein) [Source:HGNC Symbol;Acc:HGNC:29557]
metallothionein 2A [Source:HGNC Symbol;Acc:HGNC:7406]
ADAM metallopeptidase with thrombospondin type 1 motif, 1 [Source:HGNC Symbol;Acc:HGNC:217]
FYVE, RhoGEF and PH domain containing 4 [Source:HGNC Symbol;Acc:HGNC:19125]
podoplanin [Source:HGNC Symbol;Acc:HGNC:29602]
vascular cell adhesion molecule 1 [Source:HGNC Symbol;Acc:HGNC:12663]
period circadian clock 1 [Source:HGNC Symbol;Acc:HGNC:8845]
sortilin 1 [Source:HGNC Symbol;Acc:HGNC:11186]
Kruppel-like factor 15 [Source:HGNC Symbol;Acc:HGNC:14536]
potassium channel tetramerization domain containing 12 [Source:HGNC Symbol;Acc:HGNC:14678]
protease, serine, 35 [Source:HGNC Symbol;Acc:HGNC:21387]
coiled-coil domain containing 69 [Source:HGNC Symbol;Acc:HGNC:24487]
ADAM metallopeptidase domain 12 [Source:HGNC Symbol;Acc:HGNC:190]
Explore!
This data can also be used for toying around with dplyr verbs and generally getting a sense of what’s in here. First, tet some help.
Let’s join the transcript table to the gene table.
Now, let’s filter to get only protein-coding genes, group by the ensembl gene ID, summarize to count how many transcripts are in each gene, inner join that result back to the original gene list, so we can select out only the gene, number of transcripts, symbol, and description, mutate the description column so that it isn’t so wide that it’ll break the display, arrange the returned data descending by the number of transcripts per gene, head to get the top 10 results, and optionally, pipe that to further utilities to output a nice HTML table.
ensgene
ntxps
symbol
description
ENSG00000165795
77
NDRG2
NDRG family member 2
ENSG00000205336
77
ADGRG1
adhesion G protein-c
ENSG00000196628
75
TCF4
transcription factor
ENSG00000161249
68
DMKN
dermokine [Source:HG
ENSG00000154556
64
SORBS2
sorbin and SH3 domai
ENSG00000166444
62
ST5
suppression of tumor
ENSG00000204580
58
DDR1
discoidin domain rec
ENSG00000087460
57
GNAS
GNAS complex locus [
ENSG00000169398
57
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