Gene expression changes
cDNA from the serum treated cells at different
time-points was labelled with the red fluor. The
reference sample (a separate time-zero sample) was
labelled with the green fluor. The quantitative changes
in gene expression are presented as the ratio of red
intensity to green intensity (R/G) after background
correction and normalization of the two relative
intensities. In the consolidated searchable database (but not
cluster images), all changes have also been normalized to
the zero time-point from the time course. Thus the
time-zero column in the database results always has a R/G
ratio of 1.00 even though the red and green fluorescence
intensities may be slightly different.
Searching the database by name
There is no rigourous standard for the nomenclature of
human gene names so it's possible that if you do a search
for a gene by name and don't find it, it could still be
lurking in the database under an alias. Moreover, the
names of these genes are being constantly updated to
reflect the latest clustering information from Unigene.
Perhaps the most reliable way to search the database for
the presence of a given gene is to do a BLAST search of
the set of clones on the microarrays. If there is a
strong match (P value close to e-50 or better), you can try using
the name or accession number or UniGene cluster ID of that
match to search the gene expression database.
Verification of clone identities and
The nominal identities some of the clones printed on the
microarrays have been verified by sequencing or other
means. Only verified clones were mentioned by name in the
paper. The database contains the most updated information
regarding the sequence verification and should be checked
before following up on individual genes. Unverified
clones are prefixed with "SID#####" followed by their
nominal identity. Gene names with an asterisk preceding the
name had been originally mis-identified. The Unigene links from these
and their accession numbers have not yet been updated!If a clone is an
EST without strong
sequence similarity to anything, the name is "EST"
followed by the Genbank accession number. A small
fraction of clones are potentially chimeric, i.e., their
3' and 5' ends fall in different Unigene clusters. Thus
even a sequence verified clone could be chimeric and the
identity of the gene whose expression is measured by this
clone on the array could be in question.
Display of expression changes
Gene expression changes are displayed on the cluster
image, in Figures 4 and 5, and in the consolidated database
search results page by plotting the R/G ratio
according to the colour scale indicated in those figures.
The detailed display of results in the searchable
database shows the reciprocal R/G and G/R ratios, the red
and green fluorescence intensities and background values.
In addition the pixel-by-pixel correlation coefficients
(CORR) and flag values for each element are shown. CORR
is a measure of confidence in the ratio value for each
spot and any non-zero flag value indicates a problem spot
(e.g. a speck of dirt that could fluoresce and throw off
the ratio). The detailed display also shows close-ups of
each microarray element after merging the red and green
scans. This display has many useful links as indicated on
the top of that page.