Probe names for Affymetrix array
1
0
Entering edit mode
6.5 years ago
maria.kesa ▴ 30

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 • 2.8k views
ADD COMMENT
3
Entering edit mode
6.5 years ago
Neilfws 49k

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
ADD COMMENT

Login before adding your answer.

Traffic: 1143 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6