annotables

Provides tables for converting and annotating Ensembl Gene IDs.

Installation

install.packages("devtools")
devtools::install_github("stephenturner/annotables")

Rationale

Many bioinformatics tasks require converting gene identifiers from one convention to another, or annotating gene identifiers with gene symbol, description, position, etc. Sure, biomaRt does this for you, but I got tired of remembering biomaRt syntax and hammering Ensembl’s servers every time I needed to do this.

This package has basic annotation information from Ensembl Genes 114 for:

• Human build 38 (grch38)
• Human build 37 (grch37)
• Mouse (grcm38)
• Rat (rnor6)
• Chicken (galgal5)
• Worm (wbcel235)
• Fly (bdgp6)
• Macaque (mmul801)
• Pig (Sscrofa11.1)
• Dog (ROS_Cfam_1.0)
• Zebrafish (GRCz11)

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 tx2gene tables that link Ensembl gene IDs to Ensembl transcript IDs.

Usage

library(annotables)

Look at the human genes table (note the description column gets cut off because the table becomes too wide to print nicely):

grch38

## # A tibble: 91,673 × 9
##    ensgene         entrez symbol chr     start    end strand biotype description
##    <chr>            <int> <chr>  <chr>   <int>  <int>  <int> <chr>   <chr>      
##  1 ENSG00000000003   7105 TSPAN6 X      1.01e8 1.01e8     -1 protei… tetraspani…
##  2 ENSG00000000005  64102 TNMD   X      1.01e8 1.01e8      1 protei… tenomodulin
##  3 ENSG00000000419   8813 DPM1   20     5.09e7 5.10e7     -1 protei… dolichyl-p…
##  4 ENSG00000000457  57147 SCYL3  1      1.70e8 1.70e8     -1 protei… SCY1 like …
##  5 ENSG00000000460  55732 FIRRM  1      1.70e8 1.70e8      1 protei… FIGNL1 int…
##  6 ENSG00000000938   2268 FGR    1      2.76e7 2.76e7     -1 protei… FGR proto-…
##  7 ENSG00000000971   3075 CFH    1      1.97e8 1.97e8      1 protei… complement…
##  8 ENSG00000001036   2519 FUCA2  6      1.43e8 1.44e8     -1 protei… alpha-L-fu…
##  9 ENSG00000001084   2729 GCLC   6      5.35e7 5.36e7     -1 protei… glutamate-…
## 10 ENSG00000001167   4800 NFYA   6      4.11e7 4.11e7      1 protei… nuclear tr…
## # ℹ 91,663 more rows

Look at the human genes-to-transcripts table:

grch38_tx2gene

## # A tibble: 412,044 × 2
##    enstxp          ensgene        
##    <chr>           <chr>          
##  1 ENST00000373020 ENSG00000000003
##  2 ENST00000612152 ENSG00000000003
##  3 ENST00000496771 ENSG00000000003
##  4 ENST00000494424 ENSG00000000003
##  5 ENST00000373031 ENSG00000000005
##  6 ENST00000485971 ENSG00000000005
##  7 ENST00000466152 ENSG00000000419
##  8 ENST00000371582 ENSG00000000419
##  9 ENST00000683048 ENSG00000000419
## 10 ENST00000371588 ENSG00000000419
## # ℹ 412,034 more rows

Tables are saved in tibble format, pipe-able with dplyr:

grch38 %>% 
    dplyr::filter(biotype == "protein_coding" & chr == "1") %>% 
    dplyr::select(ensgene, symbol, chr, start, end, description) %>% 
    head %>% 
    knitr::kable(.)

ensgene	symbol	chr	start	end	description
ENSG00000000457	SCYL3	1	169849631	169894267	SCY1 like pseudokinase 3
ENSG00000000460	FIRRM	1	169662007	169854080	FIGNL1 interacting regulator of recombination and mitosis
ENSG00000000938	FGR	1	27612064	27635185	FGR proto-oncogene, Src family tyrosine kinase
ENSG00000000971	CFH	1	196651754	196752476	complement factor H
ENSG00000001460	STPG1	1	24356999	24416934	sperm tail PG-rich repeat containing 1
ENSG00000001461	NIPAL3	1	24415802	24476735	NIPA like domain containing 3

Example with DESeq2 results from the airway package, made tidy with biobroom:

library(DESeq2)

## Loading required package: S4Vectors

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## Loading required package: Biobase

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library(airway)

data(airway)
airway <- DESeqDataSet(airway, design = ~cell + dex)
airway <- DESeq(airway)

## estimating size factors

## estimating dispersions

## gene-wise dispersion estimates

## mean-dispersion relationship

## final dispersion estimates

## fitting model and testing

res <- results(airway)

# tidy results with biobroom
library(biobroom)

## Loading required package: broom

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res_tidy <- tidy.DESeqResults(res)

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head(res_tidy)

## # A tibble: 6 × 7
##   gene            baseMean estimate stderror statistic   p.value p.adjusted
##   <chr>              <dbl>    <dbl>    <dbl>     <dbl>     <dbl>      <dbl>
## 1 ENSG00000000003  709.      0.381     0.101     3.79   0.000152    0.00128
## 2 ENSG00000000005    0      NA        NA        NA     NA          NA      
## 3 ENSG00000000419  520.     -0.207     0.112    -1.84   0.0653      0.196  
## 4 ENSG00000000457  237.     -0.0379    0.143    -0.264  0.792       0.911  
## 5 ENSG00000000460   57.9     0.0882    0.287     0.307  0.759       0.895  
## 6 ENSG00000000938    0.318   1.38      3.50      0.394  0.694      NA

res_tidy %>% 
    dplyr::arrange(p.adjusted) %>% 
    head(20) %>% 
    dplyr::inner_join(grch38, by = c("gene" = "ensgene")) %>% 
    dplyr::select(gene, estimate, p.adjusted, symbol, description) %>% 
    knitr::kable(.)

gene	estimate	p.adjusted	symbol	description
ENSG00000152583	-4.574919	0	SPARCL1	SPARC like 1
ENSG00000165995	-3.291062	0	CACNB2	calcium voltage-gated channel auxiliary subunit beta 2
ENSG00000120129	-2.947810	0	DUSP1	dual specificity phosphatase 1
ENSG00000101347	-3.766995	0	SAMHD1	SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1
ENSG00000189221	-3.353580	0	MAOA	monoamine oxidase A
ENSG00000211445	-3.730403	0	GPX3	glutathione peroxidase 3
ENSG00000157214	-1.976773	0	STEAP2	STEAP2 metalloreductase
ENSG00000162614	-2.035665	0	NEXN	nexilin F-actin binding protein
ENSG00000125148	-2.210979	0	MT2A	metallothionein 2A
ENSG00000154734	-2.345604	0	ADAMTS1	ADAM metallopeptidase with thrombospondin type 1 motif 1
ENSG00000139132	-2.228903	0	FGD4	FYVE, RhoGEF and PH domain containing 4
ENSG00000162493	-1.891217	0	PDPN	podoplanin
ENSG00000134243	-2.195712	0	SORT1	sortilin 1
ENSG00000179094	-3.191750	0	PER1	period circadian regulator 1
ENSG00000162692	3.692661	0	VCAM1	vascular cell adhesion molecule 1
ENSG00000163884	-4.459128	0	KLF15	KLF transcription factor 15
ENSG00000178695	2.528175	0	KCTD12	potassium channel tetramerization domain containing 12
ENSG00000198624	-2.918436	0	CCDC69	coiled-coil domain containing 69
ENSG00000107562	1.911670	0	CXCL12	C-X-C motif chemokine ligand 12
ENSG00000148848	1.814543	0	ADAM12	ADAM metallopeptidase domain 12