Serum stimulation database

The transcriptional program
in the response of human fibroblasts to serum

Home

Database

Clusters

Figures

Paper

Other data

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 in the 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 nomenclature
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 clones 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.

Send feedback to Vishy Iyer



Home Database Clusters Figures Paper Other data	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 in the 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 nomenclature 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 clones 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.