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Probe names for Affymetrix array

Hello,

I am working on an algorithm that selects genes that differentiate between two conditions (for example the presence of a disease).

I'm working with Affymetrix HG-U95A data. The algorithm selected the following probe sets:

  • 'AFFX-BioB-5_at'
  • 'AFFX-BioC-5_at'
  • 'AFFX-BioB-3_st'

The problem is that there are no gene names associated with these probe names.

The question is; what do these probe sets represent? What do they mean?

gene-expression affymetrix

1 answer

The short answer: these are control probesets, derived from E.coli sequences.

The longer answer - there are two good sources of documentation for Affymetrix arrays. The first is the Affymetrix website; here is the product page for the U95 set. You'll need to create a (free) account to access files.

The second is NCBI GEO - start with the platforms page and search for "u95a". Result. Scroll down and download the full data table, which is a delimited text file that you can explore:

grep AFFX-BioC-5_at GPL91-39600.txt
AFFX-BioC-5_at        --Control    Homo sapiens    Mar 11, 2009    Control sequence    GenBank    J04423 E coli bioC protein  (-5 and -3 represent transcript regions 5 prime and 3 prime respectively)    J04423                    0008152 // metabolic process // inferred from electronic annotation /// 0009058 // biosynthetic process // inferred from electronic annotation /// 0009102 // biotin biosynthetic process // inferred from electronic annotation /// 0009236 // cobalamin biosynthetic process // inferred from electronic annotation    0005737 // cytoplasm // inferred from electronic annotation    0000166 // nucleotide binding // inferred from electronic annotation /// 0000287 // magnesium ion binding // inferred from electronic annotation /// 0003824 // catalytic activity // inferred from electronic annotation /// 0004015 // adenosylmethionine-8-amino-7-oxononanoate transaminase activity // inferred from electronic annotation /// 0004076 // biotin synthase activity // inferred from electronic annotation /// 0004141 // dethiobiotin synthase activity // inferred from electronic annotation /// 0005506 // iron ion binding // inferred from electronic annotation /// 0005524 // ATP binding // inferred from electronic annotation /// 0008168 // methyltransferase activity // inferred from electronic annotation /// 0008483 // transaminase activity // inferred from electronic annotation /// 0008710 // 8-amino-7-oxononanoate synthase activity // inferred from electronic annotation /// 0016740 // transferase activity // inferred from electronic annotation /// 0016769 // transferase activity, transferring nitrogenous groups // inferred from electronic annotation /// 0016874 // ligase activity // inferred from electronic annotation /// 0030170 // pyridoxal phosphate binding // inferred from electronic annotation /// 0042242 // cobyrinic acid a,c-diamide synthase activity // inferred from electronic annotation /// 0046872 // metal ion binding // inferred from electronic annotation /// 0051536 // iron-sulfur cluster binding // inferred from electronic annotation /// 0051537 // 2 iron, 2 sulfur cluster binding // inferred from electronic annotation /// 0051539 // 4 iron, 4 sulfur cluster binding // inferred from electronic annotation

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