[Bioc-devel] org.Hs.eg.db contains no GRPEL1 gene

Fri Apr 19 22:39:36 CEST 2024

There were 18 genes missing, due to a filtering step that went awry.

> select(org.Hs.eg.db, z, "SYMBOL")
'select()' returned 1:1 mapping between keys and columns
    ENTREZID       SYMBOL
1       1665        DHX15
2       6819      SULT1C2
3       8449        DHX16
4      27233      SULT1C4
5      80273       GRPEL1
6     134266       GRPEL2
7     195814      SDR16C5
8     729059        TEX46
9  100506895       LUARIS
10 110121294 LOC110121294
11 110121295 LOC110121295
12 110121296 LOC110121296
13 114827811 LOC114827811
14 114827812 LOC114827812
15 114827813 LOC114827813
16 114827814 LOC114827814
17 114827815 LOC114827815
18 114827816 LOC114827816
> sessionInfo()
R Under development (unstable) (2024-03-12 r86109)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS:   /home/ubuntu/downloads/R-devel/lib/libRblas.so
LAPACK: /home/ubuntu/downloads/R-devel/lib/libRlapack.so;  LAPACK version 3.12.0

locale:
[1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C

time zone: Etc/UTC
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] org.Hs.eg.db_3.19.1  AnnotationDbi_1.65.2 IRanges_2.37.1
[4] S4Vectors_0.41.5     Biobase_2.63.0       BiocGenerics_0.49.1

These new packages are still on the builder, and have to be transferred over to the download repository, which I imagine will happen sometime next week.

Best,

Jim

From: Anatoly Sorokin <lptolik using gmail.com>
Sent: Thursday, April 18, 2024 11:01 PM
To: James W. MacDonald <jmacdon using uw.edu>
Cc: bioc-devel using r-project.org
Subject: Re: [Bioc-devel] org.Hs.eg.db contains no GRPEL1 gene

Great! Thank you! On Fri, Apr 19, 2024 at 2: 29 AM James W. MacDonald <jmacdon@ uw. edu> wrote: There was an error in the scripts used to generate the organism packages that excluded (among other genes) GRPEL1. We have rectified the error
ZjQcmQRYFpfptBannerStart
This Message Is From an Untrusted Sender
You have not previously corresponded with this sender.
See https://itconnect.uw.edu/email-tags for additional information. Please contact the UW-IT Service Center, help using uw.edu<mailto:help using uw.edu> 206.221.5000, for assistance.
ZjQcmQRYFpfptBannerEnd
Great!
Thank you!

On Fri, Apr 19, 2024 at 2:29 AM James W. MacDonald <jmacdon using uw.edu<mailto:jmacdon using uw.edu>> wrote:
There was an error in the scripts used to generate the organism packages that excluded (among other genes) GRPEL1. We have rectified the error and are re-running. The updated packages should be available early next week.

-----Original Message-----
From: Bioc-devel <bioc-devel-bounces using r-project.org<mailto:bioc-devel-bounces using r-project.org>> On Behalf Of James W. MacDonald
Sent: Thursday, April 18, 2024 9:30 AM
To: Anatoly Sorokin <lptolik using gmail.com<mailto:lptolik using gmail.com>>; bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] org.Hs.eg.db contains no GRPEL1 gene

It is the wrong place to send the request. This listserv is for package developers. If you want support please use support.bioconductor.org<https://urldefense.com/v3/__http:/support.bioconductor.org__;!!K-Hz7m0Vt54!mJ3Pa4pX6JJKDHxEwVlqoHpn2SjbdVeSm1duor0h0YuSpIVdzercsgEfkXrkQHSZYc8xFsB3FC-Jqg$>.

-----Original Message-----
From: Bioc-devel <bioc-devel-bounces using r-project.org<mailto:bioc-devel-bounces using r-project.org>> On Behalf Of Anatoly Sorokin
Sent: Thursday, April 18, 2024 12:40 AM
To: bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>
Subject: [Bioc-devel] org.Hs.eg.db contains no GRPEL1 gene

!-------------------------------------------------------------------|
  This Message Is From an Untrusted Sender
  You have not previously corresponded with this sender.
  See https://itconnect.uw.edu/email-tags for additional
  information.  Please contact the UW-IT Service Center,
  help using uw.edu<mailto:help using uw.edu> 206.221.5000, for assistance.
|-------------------------------------------------------------------!

Hi,
sorry if this is the wrong list to send this request, but the landing page of the org.Hs.eg.db package contains no reference for the bug report.

The most recent version of the org.Hs.eg.db package (3.19.7) misses the GRPEL1 gene (https://urldefense.com/v3/__https://www.ncbi.nlm.nih.gov/gene/80273__;!!K-Hz7m0Vt54!ivupQGWQlUGDUNZOCregQEWX_AV7JVjz8BcYXoir7IdYSZrbnfVjk4csTvv3ksCIELqcAnmYBzl1CQ$<https://urldefense.com/v3/__https:/www.ncbi.nlm.nih.gov/gene/80273__;!!K-Hz7m0Vt54!ivupQGWQlUGDUNZOCregQEWX_AV7JVjz8BcYXoir7IdYSZrbnfVjk4csTvv3ksCIELqcAnmYBzl1CQ$> ). It could not be found either by SYMBOL, or by ENTREZID:

> orgDB = org.Hs.eg.db
> select(orgDB,keys='80273',columns=c("SYMBOL","GENENAME","ENTREZID"),
keytype=keytype)
Error in .testForValidKeys(x, keys, keytype, fks) :
  None of the keys entered are valid keys for 'ENTREZID'. Please use the keys method to see a listing of valid arguments.
> select(orgDB,keys='GRPEL1',columns=c("SYMBOL","GENENAME","ENTREZID"),
keytype='SYMBOL')
Error in .testForValidKeys(x, keys, keytype, fks) :
  None of the keys entered are valid keys for 'SYMBOL'. Please use the keys method to see a listing of valid arguments.

however, in the previous version of the package (3.18.0), it could be found by both keys:

> select(orgDB,keys='80273',columns=c("SYMBOL","GENENAME","ENTREZID"),
keytype=keytype)
'select()' returned 1:1 mapping between keys and columns
  ENTREZID SYMBOL                   GENENAME
1    80273 GRPEL1 GrpE like 1, mitochondrial
> select(orgDB,keys='GRPEL1',columns=c("SYMBOL","GENENAME","ENTREZID"),
keytype='SYMBOL')
'select()' returned 1:1 mapping between keys and columns
  SYMBOL                   GENENAME ENTREZID
1 GRPEL1 GrpE like 1, mitochondrial    80273

That omission caused an error in our BioNAR package. As this is the only missing gene in the network for the time being I've fixed this manually in the vignette, but I'd like to understand is it a real mistake or am I using the package in the wrong way?

Cheers,
Anatoly

        [[alternative HTML version deleted]]

_______________________________________________
Bioc-devel using r-project.org<mailto:Bioc-devel using r-project.org> mailing list
https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!K-Hz7m0Vt54!ivupQGWQlUGDUNZOCregQEWX_AV7JVjz8BcYXoir7IdYSZrbnfVjk4csTvv3ksCIELqcAnkLvQOPWA$<https://urldefense.com/v3/__https:/stat.ethz.ch/mailman/listinfo/bioc-devel__;!!K-Hz7m0Vt54!ivupQGWQlUGDUNZOCregQEWX_AV7JVjz8BcYXoir7IdYSZrbnfVjk4csTvv3ksCIELqcAnkLvQOPWA$>

_______________________________________________
Bioc-devel using r-project.org<mailto:Bioc-devel using r-project.org> mailing list
https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/bioc-devel__;!!K-Hz7m0Vt54!gVVVvLvwzIeBrPusP589IFjHSBtLnX6o2IYh-GkVcdCXwhp_bDFM8274jULdJPvUWEfh_31If7xjrYI$<https://urldefense.com/v3/__https:/stat.ethz.ch/mailman/listinfo/bioc-devel__;!!K-Hz7m0Vt54!gVVVvLvwzIeBrPusP589IFjHSBtLnX6o2IYh-GkVcdCXwhp_bDFM8274jULdJPvUWEfh_31If7xjrYI$>

	[[alternative HTML version deleted]]