mmusculus GO terms with Biomart
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Entering edit mode
salvin • 0
@salvin-16347
Last seen 3.0 years ago
United States

Hi Biomart Team, first of all thanks for your great work.

I used biomaRt for retrieving GO terms but I found some differences between the query I ran 4 month ago and the same one ran three days ago. Is it possible that you have changed something or probably, am I doing something wrong? For example 4 month ago for the mouse gene "Lrp8" I got the GO term GO:0042981 and I now I get just two terms. Another thing is If I run the query in Human for "Lrp8" I get that term (I know that Human and Mouse could be different in GO results but is it normal all this differences). Here my code with the example for "Lrp8".

Thanks


> library(biomaRt)
> 
> mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl")
Ensembl site unresponsive, trying asia mirror
> m.genes = getBM(attributes = c("ensembl_gene_id","mgi_symbol","description","go_id","name_1006"), filters = "mgi_symbol", values = "Lrp8" , mart = mouse)
> m.genes

     ensembl_gene_id mgi_symbol                                                                                                       description      go_id           name_1006
1 ENSMUSG00000028613       Lrp8 low density lipoprotein receptor-related protein 8, apolipoprotein e receptor [Source:MGI Symbol;Acc:MGI:1340044] GO:0005509 calcium ion binding
2 ENSMUSG00000028613       Lrp8 low density lipoprotein receptor-related protein 8, apolipoprotein e receptor [Source:MGI Symbol;Acc:MGI:1340044] GO:0005515     protein binding
3 ENSMUSG00000028613       Lrp8 low density lipoprotein receptor-related protein 8, apolipoprotein e receptor [Source:MGI Symbol;Acc:MGI:1340044]                

> 
> human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> h.genes = getBM(attributes = c("hgnc_symbol","description","go_id","name_1006"), filters = "hgnc_symbol", values = "Lrp8" , mart = human)
> h.genes

   hgnc_symbol                                                       description      go_id                                                 name_1006
1         LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0005515                                           protein binding
2         LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0005509                                       calcium ion binding
3         LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0016020                                                  membrane
4         LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0016021                            integral component of membrane
5         LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0005886                                           plasma membrane
6         LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0006508                                               proteolysis
7         LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0006629                                   lipid metabolic process
8         LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0005576                                      extracellular region
9         LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0045088                      regulation of innate immune response
10        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0006897                                               endocytosis
11        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] **GO:0042981**                           regulation of apoptotic process
12        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0050731  positive regulation of peptidyl-tyrosine phosphorylation
13        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0007165                                       signal transduction
14        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0001523                                retinoid metabolic process
15        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0004888                 transmembrane signaling receptor activity
16        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0019221                       cytokine-mediated signaling pathway
17        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0043235                                          receptor complex
18        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0005901                                                   caveola
19        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:1900006               positive regulation of dendrite development
20        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0034185                                    apolipoprotein binding
21        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0005041        low-density lipoprotein particle receptor activity
22        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0030229   very-low-density lipoprotein particle receptor activity
23        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0038024                                   cargo receptor activity
24        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0061098   positive regulation of protein tyrosine kinase activity
25        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0032793 positive regulation of CREB transcription factor activity
26        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0038026                         reelin-mediated signaling pathway
27        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0050804              modulation of chemical synaptic transmission
28        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0061003      positive regulation of dendritic spine morphogenesis
29        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0038025                                  reelin receptor activity
30        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0001540                                      amyloid-beta binding
31        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0008035                 high-density lipoprotein particle binding
32        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0019894                                           kinesin binding
33        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0047485                                protein N-terminus binding
34        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0048306                         calcium-dependent protein binding
35        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0007268                            chemical synaptic transmission
36        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0021517                           ventral spinal cord development
37        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0021541                                   ammon gyrus development
38        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0021766                                   hippocampus development
39        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0021819                        layer formation in cerebral cortex
40        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0021987                               cerebral cortex development
41        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0042493                                          response to drug
42        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0045860            positive regulation of protein kinase activity
43        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0048813                                    dendrite morphogenesis
44        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0071363               cellular response to growth factor stimulus
45        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0071397                          cellular response to cholesterol
46        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0005615                                       extracellular space
47        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0005875                            microtubule associated complex
48        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0009986                                              cell surface
49        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0014069                                      postsynaptic density
50        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0030424                                                      axon
51        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0030425                                                  dendrite
52        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700] GO:0043025                                        neuronal cell body
53        LRP8 LDL receptor related protein 8 [Source:HGNC Symbol;Acc:HGNC:6700]                                                                     







> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS  10.16

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

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] stringi_1.5.3               biomaRt_2.44.4              pheatmap_1.0.12             gplots_3.1.1                dplyr_1.0.2                 DESeq2_1.28.1              
 [7] SummarizedExperiment_1.18.2 DelayedArray_0.14.1         matrixStats_0.57.0          Biobase_2.48.0              GenomicRanges_1.40.0        GenomeInfoDb_1.24.2        
[13] IRanges_2.22.2              S4Vectors_0.26.1            BiocGenerics_0.34.0         openxlsx_4.2.3             

loaded via a namespace (and not attached):
 [1] httr_1.4.2             bit64_4.0.5            splines_4.0.2          gtools_3.8.2           assertthat_0.2.1       askpass_1.1            BiocFileCache_1.12.1   blob_1.2.1            
 [9] GenomeInfoDbData_1.2.3 progress_1.2.2         pillar_1.4.7           RSQLite_2.2.1          lattice_0.20-41        glue_1.4.2             digest_0.6.27          RColorBrewer_1.1-2    
[17] XVector_0.28.0         colorspace_2.0-0       Matrix_1.2-18          XML_3.99-0.5           pkgconfig_2.0.3        genefilter_1.70.0      zlibbioc_1.34.0        purrr_0.3.4           
[25] xtable_1.8-4           scales_1.1.1           BiocParallel_1.22.0    tibble_3.0.4           openssl_1.4.3          annotate_1.66.0        generics_0.1.0         ggplot2_3.3.2         
[33] ellipsis_0.3.1         withr_2.3.0            survival_3.2-7         magrittr_2.0.1         crayon_1.3.4           memoise_1.1.0          xml2_1.3.2             tools_4.0.2           
[41] prettyunits_1.1.1      hms_0.5.3              lifecycle_0.2.0        stringr_1.4.0          munsell_0.5.0          locfit_1.5-9.4         zip_2.1.1              AnnotationDbi_1.50.3  
[49] compiler_4.0.2         caTools_1.18.0         rlang_0.4.9            grid_4.0.2             RCurl_1.98-1.2         rstudioapi_0.13        rappdirs_0.3.1         bitops_1.0-6          
[57] gtable_0.3.0           curl_4.3               DBI_1.1.0              R6_2.5.0               bit_4.0.4              KernSmooth_2.23-18     Rcpp_1.0.5             vctrs_0.3.5           
[65] geneplotter_1.66.0     dbplyr_2.0.0           tidyselect_1.1.0
biomaRt GOTerms • 730 views
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Entering edit mode
Mike Smith ★ 6.5k
@mike-smith
Last seen 4 hours ago
EMBL Heidelberg

The biomaRt package connects to Ensembl's BioMart and the data you get back will be dependant on what Ensembl serves. By default biomaRt connects to the most current version of Ensembl, and Ensembl release new data every 3 months, so it's entirely possible that your queries will return different values.

Ensembl maintain archives of their older versions, and you can access a specific version of Ensembl to by creating your Mart object using useEnsembl() and providing the version argument. The current Ensembl version is 103, so 4 months ago it would have been 102. The code to access that would be:

library(biomaRt)
mouse_v102 = useEnsembl(biomart = "ensembl", 
                        version = "102",
                        dataset = "mmusculus_gene_ensembl")

We can then run the same query as before, but this time we get back something with many more rows:

m_genes = getBM(attributes = c("ensembl_gene_id","mgi_symbol",
                                "description","go_id","name_1006"), 
                filters = "mgi_symbol", 
                values = "Lrp8" , 
                mart = mouse_v102)

nrow(m_genes)
# [1] 46

We can also see that GO:0042981 is indeed in the results from the previous version:

"GO:0042981" %in% m_genes[,"go_id"]
# [1] TRUE

As for why the results have changed between versions, that's something you'll have to ask Ensembl directly.
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Entering edit mode
salvin • 0
@salvin-16347
Last seen 3.0 years ago
United States

Now it is very clear why I didn't get the same results. Thank you very much Mike Smith, I'll ask them what's the reason for this wide differences.
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