Gene functional descriptions

description(
  version = getOption(x = "wormbase.version", default = NULL),
  BPPARAM = BiocParallel::bpparam()
)

Arguments

version

character(1) or NULL. WormBase version. If NULL (recommended), defaults to current production release version available on the WormBase website. Legacy versions can be specified as a character string (e.g. "WS262").

BPPARAM

bpparamClass. BiocParallel parameter to specify the desired processor configuration.
We recommend using one of the following:

Value

DataFrame.

Note

As of WS269 release, some non-N2 gene IDs are included in the flat files available on the WormBase FTP server. These annotations are removed from the return here, using grep matching to return only WBGene entries.

This file is malformed on the WormBase FTP server for WS270 and WS271 releases.

Updated 2020-01-26.

Examples

## WormBase FTP server must be accessible. tryCatch( expr = description(), error = function(e) e )
#> Transmitting files from <ftp.wormbase.org>.
#> Files matching pattern: c_elegans.PRJNA13758.WS277.functional_descriptions.txt.gz
#> → Downloading c_elegans.PRJNA13758.WS277.functional_descriptions.txt.gz.
#> → Importing c_elegans.PRJNA13758.WS277.functional_descriptions.txt.gz at /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpRU0dkX using readr::`read_lines()`.
#> → Processing functional descriptions.
#> DataFrame with 52086 rows and 4 columns #> geneID #> <character> #> 1 WBGene00000001 #> 2 WBGene00000002 #> 3 WBGene00000003 #> 4 WBGene00000004 #> 5 WBGene00000005 #> ... ... #> 52082 WBGene00306071 #> 52083 WBGene00306072 #> 52084 WBGene00306073 #> 52085 WBGene00306076 #> 52086 WBGene00306078 #> conciseDescription #> <character> #> 1 aap-1 encodes the C. elegans ortholog of the phosphoinositide 3-kinase (PI3K) p50/p55 adaptor/regulatory subunit; AAP-1 negatively regulates lifespan and dauer development, and likely functions as the sole adaptor subunit for the AGE-1/p110 PI3K catalytic subunit to which it binds in vitro; although AAP-1 potentiates insulin-like signaling, it is not absolutely required for insulin-like signaling under most conditions. #> 2 aat-1 encodes an amino acid transporter catalytic subunit; when co-expressed in Xenopus oocytes with the ATG-2 glycoprotein subunit, AAT-1 is able to facilitate amino acid uptake and exchange, showing a relatively high affinity for small and some large neutral amino acids; in addition, AAT-1 is able to covalently associate with ATG-2 or ATG-1 to form heterodimers in the Xenopus expression system; when co-expressed with ATG-2, AAT-1 localizes to the cell surface of oocytes, but when expressed alone or with ATG-1, AAT-1 localizes intracellularly. #> 3 aat-2 encodes a predicted amino acid transporter catalytic subunit; when co-expressed in Xenopus oocytes with a glycoprotein subunit, however, AAT-2 is not able to induce amino acid uptake. #> 4 aat-3 encodes an amino acid transporter catalytic subunit; when co-expressed in Xenopus oocytes with the ATG-2 glycoprotein subunit, AAT-3 is able to facilitate amino acid uptake and exchange, showing a relatively high affinity for small and some large neutral amino acids; in addition, AAT-3 is able to covalently associate with ATG-2 or ATG-1 to form heterodimers in the Xenopus expression system; when co-expressed with ATG-2, AAT-3 localizes to the cell surface of oocytes, but when expressed alone, or with ATG-1, AAT-3 localizes intracellularly. #> 5 aat-4 encodes a predicted amino acid transporter catalytic subunit; unlike catalytic subunits in other organisms, however, AAT-4 does not contain the highly conserved cysteine residue known to facilitate covalent interaction with a glycoprotein subunit, suggesting that AAT-4 does not require this residue for heterodimer formation or, alternatively, does not require the glycoprotein subunit for function. #> ... ... #> 52082 NA #> 52083 NA #> 52084 NA #> 52085 NA #> 52086 NA #> automatedDescription #> <character> #> 1 Is an ortholog of human PIK3R3 (phosphoinositide-3-kinase regulatory subunit 3). Exhibits protein kinase binding activity. Is involved in dauer larval development; determination of adult lifespan; and insulin receptor signaling pathway. Localizes to phosphatidylinositol 3-kinase complex. Is expressed in intestine and neurons. #> 2 Is an ortholog of human SLC7A8 (solute carrier family 7 member 8). Contributes to L-amino acid transmembrane transporter activity. Is involved in amino acid transmembrane transport. Localizes to amino acid transport complex. Is expressed in tail. Human ortholog(s) of this gene are implicated in cystinuria and lysinuric protein intolerance. #> 3 Is an ortholog of human SLC7A7 (solute carrier family 7 member 7). Is predicted to have L-amino acid transmembrane transporter activity. Human ortholog(s) of this gene are implicated in cystinuria and lysinuric protein intolerance. #> 4 Is an ortholog of human SLC7A5 (solute carrier family 7 member 5) and SLC7A8 (solute carrier family 7 member 8). Contributes to L-amino acid transmembrane transporter activity. Is involved in amino acid transmembrane transport. Localizes to amino acid transport complex. Human ortholog(s) of this gene are implicated in cystinuria; lysinuric protein intolerance; and retinitis pigmentosa 68. #> 5 Is an ortholog of human SLC7A5 (solute carrier family 7 member 5) and SLC7A8 (solute carrier family 7 member 8). Is predicted to have L-amino acid transmembrane transporter activity. Human ortholog(s) of this gene are implicated in cystinuria; lysinuric protein intolerance; and retinitis pigmentosa 68. #> ... ... #> 52082 NA #> 52083 NA #> 52084 NA #> 52085 NA #> 52086 NA #> geneClassDescription #> <character> #> 1 phosphoinositide kinase AdAPter subunit #> 2 Amino Acid Transporter #> 3 Amino Acid Transporter #> 4 Amino Acid Transporter #> 5 Amino Acid Transporter #> ... ... #> 52082 Modifier of Htt Aggregation, Elise Kikis #> 52083 Modifier of Htt Aggregation, Elise Kikis #> 52084 Modifier of Htt Aggregation, Elise Kikis #> 52085 not known #> 52086 not known