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Question: discrepancy between genes corresponding to gene ontology terms in org.Mm.eg.db and in AMIGO
0
gravatar for raf4
6 weeks ago by
raf420
raf420 wrote:

Dear Bioconductor,

I find fewer genes for a given GO term in mouse with the org.Mm.eg.db
than with teh online AMIGO server. I am wondering if the difference is
due to delays in updating org.Mm.eg.db, or for some other reason.

Here is my R session

 library(AnnotationDbi)
> library(org.Mm.eg.db)
> GO0044339.ids<-select(org.Mm.eg.db,keys="GO:0044339",columns=c("GO","ENTREZID","SYMBOL"),keytype="GO")
'select()' returned 1:many mapping between keys and columns
> GO0044339.ids
          GO EVIDENCE ONTOLOGY ENTREZID SYMBOL
1 GO:0044339      ISO       BP    14362   Fzd1
2 GO:0044339      ISO       BP    22415   Wnt3
3 GO:0044339      IMP       BP   100201 Tmem64
> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.6

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] org.Mm.eg.db_3.4.0   GO.db_3.4.0          AnnotationDbi_1.36.2 IRanges_2.8.2        S4Vectors_0.12.2    
[6] Biobase_2.34.0       BiocGenerics_0.20.0

loaded via a namespace (and not attached):
[1] tools_3.3.3   DBI_0.6-1     memoise_1.1.0 Rcpp_0.12.11  RSQLite_1.1-2 digest_0.6.12
>


Here is the result of my Amigo search

Search term:

GO:0044339

organosm: mouse

MGI:MGI:2665790    Tnn
MGI:MGI:2140359    Tmem64
MGI:MGI:1196625    Fzd1
MGI:MGI:98955    Wnt3

There is one additional gene: Tnn

Is this discrepancy due to a delay in updating org.Mm.eg.db,
or some other reason?

I also get the same 4 genes with annotations search in mmigo as I fo with gene products

MGI    MGI:2665790    Tnn        GO:1905240    MGI:MGI:3710297|PMID:17395156    IDA        P    tenascin N    tenascin-W|Tnw    protein    NCBITaxon:10090    20170210    UniProt        
MGI    MGI:2140359    Tmem64        GO:0044339    MGI:MGI:5643786|PMID:25979161    IMP        P    transmembrane protein 64    9630015D15Rik    protein    NCBITaxon:10090    20160212    UniProt        
MGI    MGI:1196625    Fzd1        GO:0044339    MGI:MGI:4834177|GO_REF:0000096    ISO    UniProtKB:Q9UP38    P    frizzled class receptor 1    Fz1|FZ-1    protein    NCBITaxon:10090    20100930    MGI        
MGI    MGI:98955    Wnt3        GO:0044339    MGI:MGI:4834177|GO_REF:0000096    ISO    UniProtKB:P56703    P    wingless-type MMTV integration site family, member 3    Int-4|Wnt-3    protein    NCBITaxon:10090    20100930    MGI    

Thanks and best wishes,
Rich

Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
Lecturer,
Department of Biomedical Informatics (DBMI)
Room 825
Irving Cancer Research Center
Columbia University Herbert and Florence Irving Medical Center
1130 St. Nicholas Ave
New York, NY 10032
(212)851-4765 (voice)
raf4@cumc.columbia.edu

http://www.columbia.edu/~raf4/index.html

“Will there still be "Classics Illustrated” by the time I have children? I cannot
imagine raising kids without "Classics Illustrated” .” -Rose Friedman, age 20

 

 

ADD COMMENTlink modified 4 weeks ago • written 6 weeks ago by raf420
0
gravatar for James W. MacDonald
6 weeks ago by
United States
James W. MacDonald45k wrote:

The AmiGO website by default does what we call 'GOALL', which is all genes appended to a term, plus all genes appended to any offspring for that term. GO is only the former.

> select(org.Mm.eg.db,keys="GO:0044339",column="SYMBOL",keytype="GOALL")
'select()' returned 1:many mapping between keys and columns
       GOALL EVIDENCEALL ONTOLOGYALL SYMBOL
1 GO:0044339         ISO          BP   Fzd1
2 GO:0044339         ISO          BP   Wnt3
3 GO:0044339         IMP          BP Tmem64
4 GO:0044339         IDA          BP    Tnn
>

And I think I must be getting old. I remember when the Rose Friedman quotes were from a little kid, not a grown woman...

ADD COMMENTlink written 6 weeks ago by James W. MacDonald45k

Jim,

Thank you, as always but I still am not getting all the genes (I am still on R 3.3.3 because there is an intermittent  problem with

permissions on my mac which I want to solve before I update. Should that make a difference).

> select(org.Mm.eg.db,keys="GO:0044339",column="SYMBOL",keytype="GOALL")
'select()' returned 1:many mapping between keys and columns
       GOALL EVIDENCEALL ONTOLOGYALL SYMBOL
1 GO:0044339         ISO          BP   Fzd1
2 GO:0044339         ISO          BP   Wnt3
3 GO:0044339         IMP          BP Tmem64
> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.6

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] org.Mm.eg.db_3.4.0   AnnotationDbi_1.36.2 IRanges_2.8.2        S4Vectors_0.12.2     Biobase_2.34.0      
[6] BiocGenerics_0.20.0

loaded via a namespace (and not attached):
[1] tools_3.3.3   DBI_0.6-1     memoise_1.1.0 Rcpp_0.12.11  RSQLite_1.1-2 digest_0.6.12
>

I too am still getting used to Rose as a grownup.

Thank you as always,

Rich

 

 

ADD REPLYlink written 5 weeks ago by raf420

When you go to the AmiGO website you get the most current mappings, whereas the OrgDb packages for a given Bioconductor release are frozen as of a couple weeks before the release. So the data you have in hand are from over a year ago (you have Bioc-3.4, which was released in October last year, so that org.Mm.eg.db package was current as of late September/early October 2016).

It's quite likely that there are numerous other changes that have occurred in the intervening period as well. Unfortunately, if you don't keep your R/Bioc installation updated, you fall behind on the annotation data.

ADD REPLYlink written 4 weeks ago by James W. MacDonald45k
0
gravatar for raf4
4 weeks ago by
raf420
raf420 wrote:

Jim,

Got it! I thought that downloading org.Mm.eg.db_3.4.0 fresh would be sufficient.

I have not updated Bioconductor/R because I have a technical problem with my mac which

forces me to reboot frequently. Once that is solved (probably by reinstalling the OS).

I will update R/Bioconductor.

 

Thanks and best wishes,

Rich

 

 

 

 

 

 

ADD COMMENTlink written 4 weeks ago by raf420
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