Where To Find Annotation File For Agilent Microarray?

Question

[jobinv]

I'm trying to search the Agilent website for an annotation file connecting individual features on the Whole Human Genome Microarray 4x44K, to gene symbols. However, all the search terms that I've tried on the website lead me to pdf's that don't help me very much at all. Can someone help me find what I'm looking for?

[Rm]

Alternatively look in GEO ; they do upload them

[jobinv]

Thanks for the tip!

[smrutimayipanda]

Hii, I want to download human gene expression 8x60K annotation file. But this code of yours didnt work for downloading this. Can you please tell me how to do it?

[Kevin Blighe]

Hi, it should be there, please try:

Homo sapiens

# agilent_sureprint_g3_ge_8x60k
mart <- useMart('ENSEMBL_MART_ENSEMBL')
mart <- useDataset('hsapiens_gene_ensembl', mart)
annotLookup <- getBM(
  mart = mart,
  attributes = c(
    'agilent_sureprint_g3_ge_8x60k',
    'wikigene_description',
    'ensembl_gene_id',
    'entrezgene_id',
    'gene_biotype',
    'external_gene_name'))
write.table(
  annotLookup,
  paste0('Human_agilent_sureprint_g3_ge_8x60k_',
    gsub("-", "_", as.character(Sys.Date())), '.tsv'),
  sep = '\t',
  row.names = FALSE,
  quote = FALSE)


# agilent_sureprint_g3_ge_8x60k_v2
mart <- useMart('ENSEMBL_MART_ENSEMBL')
mart <- useDataset('hsapiens_gene_ensembl', mart)
annotLookup <- getBM(
  mart = mart,
  attributes = c(
    'agilent_sureprint_g3_ge_8x60k_v2',
    'wikigene_description',
    'ensembl_gene_id',
    'entrezgene_id',
    'gene_biotype',
    'external_gene_name'))
write.table(
  annotLookup,
  paste0('Human_agilent_sureprint_g3_ge_8x60k_v2_',
    gsub("-", "_", as.character(Sys.Date())), '.tsv'),
  sep = '\t',
  row.names = FALSE,
  quote = FALSE)

Mus musculus

# agilent_sureprint_g3_ge_8x60k
mart <- useMart('ENSEMBL_MART_ENSEMBL')
mart <- useDataset('mmusculus_gene_ensembl', mart)
annotLookup <- getBM(
  mart = mart,
  attributes = c(
    'agilent_sureprint_g3_ge_8x60k',
    'wikigene_description',
    'ensembl_gene_id',
    'entrezgene_id',
    'gene_biotype',
    'mgi_symbol'))
write.table(
  annotLookup,
  paste0('Mouse_agilent_sureprint_g3_ge_8x60k_',
    gsub("-", "_", as.character(Sys.Date())), '.tsv'),
  sep = '\t',
  row.names = FALSE,
  quote = FALSE)

[smrutimayipanda]

Thank you so much

[smrutimayipanda]

Kevin Blighe I have a question. I want to download human miRNA microarray annotation file. Can you please tell me how to do it? I have tried it a lot, but didnt get the things out of it.

[Kevin Blighe]

Hi, which array version is it?

[smrutimayipanda]

it is related to agilent

[Kevin Blighe]

Thanks, but I need to know the exact version of the array - Agilent have released many, and each will have a different annotation. Basically, there is likely an annotation TSV file on their website, if you can search there please?

The information may also be in biomaRt (as per my code above), but I would really need to know the array version from you.

[smrutimayipanda]

human agilent miRNA V21.0 microarray

[Kevin Blighe]

Thanks, it does not seem to be in biomaRt. However, the annotation is available via their website: https://www.agilent.com/en/human-microrna-microarrays-details-specifications (follow link to eArray Application)

[smrutimayipanda]

yeah I got it. Thanks

Answer 1

[David Westergaard]

This is probably what you are looking for. Pick Human Genome, Whole

[jobinv]

Oh, didn't see that you had answered, thanks!

Answer 2

[Kevin Blighe]

An easier way that has [probably] only come about since this question was posted is via biomaRt in R.

You can build annotation tables for Agilent 4x44 arrays for mouse and human as follows:

require(biomaRt)

Homo sapiens

# agilent_wholegenome_4x44k_v1
mart <- useMart('ENSEMBL_MART_ENSEMBL')
mart <- useDataset('hsapiens_gene_ensembl', mart)
annotLookup <- getBM(
  mart = mart,
  attributes = c(
    'agilent_wholegenome_4x44k_v1',
    'wikigene_description',
    'ensembl_gene_id',
    'entrezgene_id',
    'gene_biotype',
    'external_gene_name'))


# agilent_wholegenome_4x44k_v2
mart <- useMart('ENSEMBL_MART_ENSEMBL')
mart <- useDataset('hsapiens_gene_ensembl', mart)
annotLookup <- getBM(
  mart = mart,
  attributes = c(
    'agilent_wholegenome_4x44k_v2',
    'wikigene_description',
    'ensembl_gene_id',
    'entrezgene_id',
    'gene_biotype',
    'external_gene_name'))

Mus musculus

# agilent_wholegenome_4x44k_v1
mart <- useMart('ENSEMBL_MART_ENSEMBL')
mart <- useDataset('mmusculus_gene_ensembl', mart)
annotLookup <- getBM(
  mart = mart,
  attributes = c(
    'agilent_wholegenome_4x44k_v1',
    'wikigene_description',
    'ensembl_gene_id',
    'entrezgene_id',
    'gene_biotype',
    'mgi_symbol'))

# agilent_wholegenome_4x44k_v2
mart <- useMart('ENSEMBL_MART_ENSEMBL')
mart <- useDataset('mmusculus_gene_ensembl', mart)
annotLookup <- getBM(
  mart = mart,
  attributes = c(
    'agilent_wholegenome_4x44k_v2',
    'wikigene_description',
    'ensembl_gene_id',
    'entrezgene_id',
    'gene_biotype',
    'mgi_symbol'))

You can view other Agilent tables accessible via biomaRt like this:

listAttributes(mart)[grep('agilent', tolower(listAttributes(mart)[,1])),]
                                name                            description
126                  agilent_cgh_44b                  AGILENT CGH 44b probe
127                 agilent_gpl26966                 AGILENT GPL26966 probe
128                  agilent_gpl6848                  AGILENT GPL6848 probe
129    agilent_sureprint_g3_ge_8x60k    AGILENT SurePrint G3 GE 8x60k probe
130 agilent_sureprint_g3_ge_8x60k_v2 AGILENT SurePrint G3 GE 8x60k v2 probe
131              agilent_wholegenome              AGILENT WholeGenome probe
132     agilent_wholegenome_4x44k_v1     AGILENT WholeGenome 4x44k v1 probe
133     agilent_wholegenome_4x44k_v2     AGILENT WholeGenome 4x44k v2 probe
            page
126 feature_page
127 feature_page
128 feature_page
129 feature_page
130 feature_page
131 feature_page
132 feature_page
133 feature_page