Each result "small gene set" (be it a single, pair or triple,
here generically refered to as a "pair") is presented in
a uniform manner.
This is an example:
2 plot exp Loo 1/38 (0 PosErrors, 1 NegErrors), Margin 0.19466, (519, 1033)
-3.9871 IMAGE:37491 (N) Hs.73999 PubMed thyroid receptor interacting protein 10 (CDC42-interacting protein)
3.2394 IMAGE:667883 (N) Hs.82101 PubMed Locus:22822 ESTs
The entries are numbered starting at 1, and ordered "best"
first where "best" means largest margin (separation between
the classes). Each single or gene pair has a hyperlink PLOT button, which
will fetch the plot. This plot shows the expresion values
and the separating hyperplane.
If the entry is a single gene, the second "gene" in the "pair"
is zero.
The Loo information (Leave One Out) records how this "pair"
behaves under Loo testing (zero Loo errors are best).
In this example the "1/38" means there was 1 Loo error and 38 total samples
in this data. The 1 Loo error was in error in the Negative
class (it predicted the left out example should be in the
Positive class, yet it was known to be in the Negative class).
The "Margin" is how far away the hyperplane is from the
closest data point. It is twice the separation between the
data points. The numbers in parenthesis are internal gene
identifiers.
Depending on the source of the array probes, there are
a variety of hyperlinks into the NCBI databases.
If available, there are links for IMAGE clone number,
a search of the nucleotide database using the IMAGE clone
number, a link into UniGene, a search of PubMed using
the words from the gene annotation, and a link into
LocusLink. For Affymetrix data, the IMAGE numbers are
indirectly determined and maybe inaccurate.
The annotation text is what was available when we built the
pages, and is mostly from Version 163 of UniGene (Oct 2003).
The two real numbers before each gene are the components of
the hyperplane vector (no real use as you can see these in
the plots).
On some result sets, javascript is used to open the link
in a new window, so popups should be enabled.
(using javascript also reduces the size of
the pages).