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Probes are not showing up for my gene but I know the microarray has probes for the gene. Why?


Try selecting the 'Show degenerate probes?' checkbox. The probes that target the gene may also target another gene. If the probes show up but are drawn in gray rather than orange, then the probes target more than 1 gene.

Also, if the probes are experimental (target sequences that are not present in known transcripts), they will not appear in SpliceCenter.

How can I link to Array-Check to show array probe positions and splice variants?


You can construct a URL that will bring up a specific gene / probeset in Array-Check. To do this, provide organism, symbol, array, probeset, and includeDegen. Here is an example:

http://www.tigerteamconsulting.com/SpliceCenter/ArrayCheck?organism=9606&symbol=CHEK2&array=AFFY_U133AP2&probeset=210&includeDegen=true

organism - tax ID (9606 = human, 10090 = mouse, 10116 = rat)
symbol - gene symbol
array - SpliceCenter array code (see list below)
probeset - name of the probeset (e.g. 215227_x_at). The value is treated as a prefix so if desired, you can enter just the first few characters of the probe name.
includeDegen - SpliceCenter detects probes with sequence that matches multiple genes. This value indicates whether you would like to includ degenerate probes. True or False.

SpliceCenter array names are in the intname column:


Have a question about siRNA-Check?

Send us an email at binf@tigerteamit.com!
Tiger Team Bioinformatics Group