USE OF OTHER SITES FOR EST-DERIVED GENE-EXPRESSION DATA
Unigene clusters the large collection of EST sequences in the public domain at NCBI's dbEST (http://www.ncbi.nlm.nih.gov/dbEST/) and can be searched from this site via a number of methods. See "Query Tips" link for this information. If you have the RefSeq number (MN_XXX), you can simply enter this number and hit "Go." A selection of entries in Unigene appear. Click on the selection from the species of interest and on the following page you can scroll down to the "EST Profile" link in the Gene Expression box. The new page has tallies for ESTs and tissues.
TissueInfo does similar correlation for ESTs in dbEST to the tissues from which they are derived. It uses a clustering program different from Unigene, but with the same goal. Expression data are currently only for human and mouse (similar to VNB). You can retrieve genes with similar expression profiles or retrieve the expression profile of genes of interest. Choose the later, "Profile Search." To get your profile, you must know the Ensembl accession number (those starting with: ENSMUST). You can get these numbers from the Ensembl site (http://www.ensembl.org/index.html). Enter the number in the box and hit "Get Profile." The output list the tissues in which at least on EST was found for your query. A more detailed report can be attained by clicking on "Get Report File." This give back is a list of EST accession numbers (they are html-linked to ENTREZ) and the species and tissue of origin. Tallies are not given and must be generated by the user.
ECgene has several options similar to VNB. These are pre-clustered results and several versions of the ECgene database can be selected. The latest version (Ver 1.3) is from 2006. A confidence level can be selected (High requires more than ESTs and Low gives all tissues with at least 1 EST, although we found no difference in the profiles regardless of what confidence level was selected). Output style can be selected as well (e.g., a stacked graph will show normal versus cancer expression profiles for each tissue). In addition, like VNB, all ESTs or only those from non-normalized libraries can be displayed. There are several options for querying this pipeline (HUGO gene symbol, RefSeq ID, mRNA, or EST accession number, and gene aliases), but its not always clear which name for your gene of interest will work. Try several. The output includes profiles for alternatively spliced versions of the gene. Lastly, the analysis is not as fast as the others above.