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I am trying to use the DAVID tool to do some gene analysis. I have some probe set intensities for some cancer cell lines. I found this link in the DAVID tool http://david.abcc.ncifcrf.gov/tools.jsp. I am a bit confused with the terminology introduced here. It says gene list for the probe sets why is it so? I mean in the example you can see the probe sets like

1007_s_at 1053_at 117_at 121_at 1255_g_at 1294_at 1316_at 1320_at 1405_i_at 1431_at 1438_at 1487_at 1494_f_at 1598_g_at

Buy why are they called gene list not probe sets. Why?

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up vote 2 down vote accepted

Its a bit confusing, but DAVID uses the term Gene List as a generic term.

Looking at Step 2, you can submit many kinds of lists to DAVID, including actual gene symbols, Ensembl or RefSeq Accessions, etc... actually nearly 30 kinds of terms including 'not sure' which probably looks at your list and tries to guess.

Affymetrix or Illumina probe set IDs are each designed to measure a gene, ideally, though its not precisely a one Probe Set to one Gene relationship. This is because when the array is designed there may be a partial transcript RNA records which turn out later to be parts of a single gene. There are also probe sets which may turn out to hybridize to similar sequences in more than one gene.

Its messy, but its also true that often more than one gene symbol will appear for the same gene because of historical naming conventions...

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