How to retrieve Microarray probe annotations

Question

[mohammedtoufiq91]

Hi ,

I have a question about retrieving Microarray probe annotations. I am interested in analyzing at-least 10-15 NCBI GEO Public Microarray datasets. Each of them are related to different platform (see below). Is there a way to retrieve them using a certain package?

Thank you.

Toufiq

Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Feature Number version)
Agilent-026652 Whole Human Genome Microarray 4x44K v2 (Probe Name version)
Affymetrix Human Genome U133B Array
[HG-U133B] Affymetrix Human Genome U133B Array
[hGlue_3_0] Custom Affymetrix Human Transcriptome Array
Affymetrix Human Genome U219 Array
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Sentrix Human-6 v2 Expression BeadChip
Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]
Affymetrix Human Genome U133 Plus 2.0 Array
Affymetrix Human Genome U133A Array
Illumina HumanWG-6 v3.0 expression beadchip
Illumina HumanRef-8 v3.0 expression beadchip
Illumina human-6 v2.0 expression beadchip
Illumina HumanHT-12 V4.0 expression beadchip
Illumina humanRef-8 v2.0 expression beadchip
Sentrix Human-6 v2 Expression BeadChip"

Answer 1

[Kevin Blighe]

Bioconductor *.db annotation packages

The best place to commence is the listing of Bioconductor annotation packages:

• https://www.bioconductor.org/packages/release/data/annotation/

You would then use these .db packages to annotate the probes from each array, for example, hgu133a.db, hgu95av2.db, et cetera*:

library(hgu95av2.db) 
mapIds(
  hgu95av2.db,
  c('991_g_at','976_s_at','954_s_at', 'hhh', '39167_r_at'),
  keytype = 'PROBEID',
  column = 'SYMBOL')

  991_g_at   976_s_at   954_s_at        hhh 39167_r_at 
    "FLT1"    "MAPK1"   "PPP1CA"         NA "SERPINH1"

Both Affymetrix and Illumina annotations are prominent in Bioconductor.

biomaRt

We can also use biomaRt, and I elaborate on an example here:

• Annotate Affymetrix probesets to Gene symbols

To retrieve a list of potential annotations in biomaRt, e.g., for Affy, use:

 listAttributes(mart)[grep('affy', listAttributes(mart)[,1]),]
                         name                 description         page
    104          affy_hc_g110          AFFY HC G110 probe feature_page
    105         affy_hg_focus         AFFY HG Focus probe feature_page
    106         affy_hg_u133a         AFFY HG U133A probe feature_page
    107       affy_hg_u133a_2       AFFY HG U133A 2 probe feature_page
    108         affy_hg_u133b         AFFY HG U133B probe feature_page
    109   affy_hg_u133_plus_2   AFFY HG U133 Plus 2 probe feature_page
    110          affy_hg_u95a          AFFY HG U95A probe feature_page
    111        affy_hg_u95av2        AFFY HG U95Av2 probe feature_page
    112          affy_hg_u95b          AFFY HG U95B probe feature_page
    113          affy_hg_u95c          AFFY HG U95C probe feature_page
    114          affy_hg_u95d          AFFY HG U95D probe feature_page
    115          affy_hg_u95e          AFFY HG U95E probe feature_page
    116          affy_hta_2_0          AFFY HTA 2 0 probe feature_page
    117   affy_huex_1_0_st_v2   AFFY HuEx 1 0 st v2 probe feature_page
    118         affy_hugenefl         AFFY HuGeneFL probe feature_page
    119 affy_hugene_1_0_st_v1 AFFY HuGene 1 0 st v1 probe feature_page
    120 affy_hugene_2_0_st_v1 AFFY HuGene 2 0 st v1 probe feature_page
    121        affy_primeview        AFFY PrimeView probe feature_page
    122         affy_u133_x3p         AFFY U133 X3P probe feature_page

Agilent array annotations are also in biomaRt.

Hail Mary / Last resort solution

...as a last resort, you'll often find an annotation CSV or TSV on the array manufacturer's website that you can download, parse, and use.

Kind regards,

Kevin

[mohammedtoufiq91]

Kevin Blighe thank you very much. This is very helpful. Additionally, we can see files directly from the Platform section of NCBI GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL6102

Then, merge probes common between expression (signal intensity) data and GPL file using merge function. merge(expr, GPL, by="Common ID", all=F)