FAQs?

• Why are some genes absent......?
• How can I download the expression data....?
• Which tissues will you add to.....?
• Can I submit data to......?
• Why did you fail to detect a ......?
• What are the units of ......?

 

Why are some genes labeled absent (A) but show significant levels of expression?

This discrepancy arises because the Affymetrix GeneChip probe array technology independently evaluates signal intensity and signal specificity. As a result two different algorithms are used to measure signal intensity (i.e., expression level) and presence or absence (i.e., P or A) of the transcript. In cases where the specificity is low, the algorithm labels the gene as absent or marginal, but still reports the expression level that was detected. These anomalous results can indicate the existence of homologs, alternatively spliced products, or nucleotide polymorphisms as well as errors in the GenBank sequence.

How can I download the expression data to my own computer?

Currently, you can only download the data by performing a copy and paste process. You can then view and analyze the data using a spreadsheet (e.g. Excel) or comparable program. In the future we will add an ftp function.

Which tissues will you add to the database?

We are currently processing most major organ systems and will be adding the following tissues in the coming months: brain, blood cell, kidney, spinal cord, liver, lung, heart, adrenal, muscle, duodenum, colon, prostate and spleen. Please feel free to make a suggestion for future work or contact us if you are interested in submitting a tissue sample.

Can I submit data to the database?

Yes, you can submit your own Affymetrix data to our database. Please contact us regarding appropriate data analysis and submission procedures.

Why did you fail to detect a gene that I know is present?Or, what is the lower limit of mRNA signal detection?

The Affymetrix detection procedure involves a linear amplification process that increases the sensitivity of the assay. The arbitrary scale used in this database can routinely distinguish genes with expression levels of 100 (on our arbitrary scale). This level likely represents a few mRNA copies per cell. Thus, very low abundance mRNAs (i.e., <3 copies/cell) may not be detected. Please notify us of these types of discrepancies so we can make notations in the database.

What are the units of the expression level?

The units are arbitrary, ranging from 0 to approximately 10,000. All data are processed identically so that data can be compared across samples and tissues.