Probe annotation file for microarray platform MoGene-1_0-st-v1

Question

[Pranshu Mehra]

Hi everyone, I am trying to do gene expression analysis on publically available data. Specifically on E-MTAB_2632, which based on A-AFFY-130 - Affymetrix GeneChip Mouse Gene 1.0 ST Array [MoGene-1_0-st-v1] platform. However, I am stuck at the annotation of probe ID. The dataset contains about 2000 probe IDs. Out of which, I could find annotation only for 630 probe IDs (using BRB-Array-Tools). The annotation from probe IDs from 10338083 to 10344609 seems to be missing. The Array Express library files provide only a few annotations. The official Affymetrix website for MoGene-1_0-st-v1 also provides annotations for just 90 probe IDs. Can anybody guide me from where I can get these annotations?

Answer 1

[Kevin Blighe]

Hi, I would use the pre-built Bioconductor annotation databases / packages for this array (I have used this array a few times over the years):

• mogene10sttranscriptcluster.db
• mogene10stprobeset.db

Most likely mogene10sttranscriptcluster.db is what you want:

1,load package and explore available columns / keys

require(mogene10sttranscriptcluster.db)

columns(mogene10sttranscriptcluster.db)
 [6] "ENTREZID"     "ENZYME"       "EVIDENCE"     "EVIDENCEALL"  "GENENAME"    
[11] "GO"           "GOALL"        "IPI"          "MGI"          "ONTOLOGY"    
[16] "ONTOLOGYALL"  "PATH"         "PFAM"         "PMID"         "PROBEID"     
[21] "PROSITE"      "REFSEQ"       "SYMBOL"       "UNIGENE"      "UNIPROT"     

head(keys(mogene10sttranscriptcluster.db))
[1] "10338001" "10338002" "10338003" "10338004" "10338005" "10338006"

2, create annotation lookup table

annotTable <- select(
  mogene10sttranscriptcluster.db,
  keys = keys(mogene10sttranscriptcluster.db),
  column = c('PROBEID', 'SYMBOL', 'ENTREZID', 'ENSEMBL'),
  keytype = 'PROBEID')

head(annotTable)
   PROBEID SYMBOL ENTREZID ENSEMBL
1 10338001   <NA>     <NA>    <NA>
2 10338002   <NA>     <NA>    <NA>
3 10338003   <NA>     <NA>    <NA>
4 10338004   <NA>     <NA>    <NA>
5 10338005   <NA>     <NA>    <NA>
6 10338006   <NA>     <NA>    <NA>

dim(annotTable)
[1] 53244     4

There is data there - don't worry / no te preocupes / لا تقلق:

head(annotTable[!is.na(annotTable$SYMBOL),])
      PROBEID  SYMBOL ENTREZID            ENSEMBL
6618 10344624  Lypla1    18777 ENSMUSG00000025903
6619 10344633   Tcea1    21399 ENSMUSG00000033813
6620 10344637 Atp6v1h   108664 ENSMUSG00000033793
6621 10344653   Oprk1    18387 ENSMUSG00000025905
6622 10344658  Rb1cc1    12421 ENSMUSG00000025907
6623 10344674  Alkal1   620393 ENSMUSG00000087247

dim(annotTable[!is.na(annotTable$SYMBOL),])
[1] 42056     4

annotTable.filt <- annotTable[!is.na(annotTable$SYMBOL),]

3, perform a specific lookup

# select 10 random probes
probes <- annotTable.filt$PROBEID[sample(1:nrow(annotTable.filt), 10)]

mapIds(
  mogene10sttranscriptcluster.db,
  keys = probes,
  column = 'SYMBOL',
  keytype = 'PROBEID')

  10367033   10519951   10396485   10431424   10398173   10550770   10403558 
  "Zbtb39"     "Gsap"    "Syne2"   "Plxnb2"     "Vrk1" "Vmn1r114"   "Ero1lb" 
  10363512   10596053   10608237 
   "Sar1a"     "Pccb"  "Gm20736"

Kevin

[Pranshu Mehra]

Thank You for your reply.