getting gene sequence from probeset id

Question

[mfaridun]

Hi,

I am trying to retrieve information from some old affymetrix data. What I have is the values of wt compared to knockout. I am trying to see if the gene that is downregulated is the homolog of the human gene or not. For this I need the sequence of the gene. I have this information: 1450296_at__Klrb1a__chr6 F3|6 62.1 cM__killer cell lectin-like receptor subfamily B member 1A From what I understood 1450296 is the probeset id and I can get the sequence from some sort of table from affymetrix. Is that true? Could you please tell me how to get the sequence.

Please let me know if I can provide more information.

Thanks!

Answer 1

[Kevin Blighe]

This is Mus musculus and the array is Affymetrix Mouse Genome 430 2.0 Array, right?

You can look up the target sequence of the probe like this (in R):

require(biomaRt)
mart <- useMart("ENSEMBL_MART_ENSEMBL")
mart <- useDataset("mmusculus_gene_ensembl", mart)

getBM(
    mart=mart,
    attributes=c("affy_mouse430_2", "ensembl_gene_id", "gene_biotype", "external_gene_name", "coding"),
    filter="affy_mouse430_2",
    values="1450296_at",
    uniqueRows=TRUE)


external_gene_name   affy_mouse430_2    ensembl_gene_id      gene_biotype
Klrb1a               1450296_at         ENSMUSG00000030361   protein_coding

coding
ATGCATCTCCTATGCACAATGGACACAGCAAGGGTCTACTTTGGTTTAAAGCCACCCAGGACTCCAGGGGCTTGGCATGAGTCACCCCCATCTCTTCCCCCAGTGCGAGTCCTAATACAAAAACCATCAATAGAAAAATGCTATGTGCTTATTCAAGAGAACCTGAATAAAACAACAGATTGTTCAGCTAAGCTAGAGTGCCCACAAGACTGGCTTTCACACCGAGATAAGTGCTTTCACGTTTCTCAAGTTTCCAACACTTGGGAGGAAGGTCTAGTTGATTGTGATGGAAAAGGAGCCACTTTGATGCTCATTCAAGACCAAGAAGAACTGAGATTCCTACTGGACTCAATAAAGGAAAAATACAATTCATTTTGGATTGGACTAAGGTACACATTGCCAGACATGAACTGGAAGTGGATAAATGGATCGACTTTAAATTCTGATGTATTAAAAATCACTGGTGACACTGAAAATGACAGCTGTGCTGCTATCTCAGGAGACAAAGTGACTTTTGAGAGCTGTAATTCAGACAACCGTTGGATCTGCCAAAAGGAACTATACCATGAAACCCTGAGCAACTATGTGGGTTATGGACACTGA

If you want the actual probe sequence, you could download the library files for your array from the Affymetrix / ThermoFisher website: https://www.thermofisher.com/order/catalog/product/900495

Kevin

[mfaridun]

Thank you! I have difficulty in installing biomaRt, various software involved that I have none of them on my computer, so still busy figuring it out.

However, I found the sequences and probes in the link you provided. Thanks!

[Kevin Blighe]

Okay, cool. For biomaRt, you just need to use R. The package can then be installed with:

source("https://bioconductor.org/biocLite.R")
biocLite("biomaRt")

...or:

if (!requireNamespace("BiocManager", quietly = TRUE)) 
install.packages("BiocManager")

BiocManager::install("biomaRt")

Then, you run my other code in my original post.

Best of luck.