max planck institut
informatik
informatik
For the Affymetrix Exon Array data integration, you need to import an expression data file and a p-value file.
Your Affymetrix data is stored in the local embedded database under the Cytoscape directory on your computer.
This data can easily be retrieved from the raw CEL files e.g. using 'apt-probeset-summarize', which is provided with the Affymetrix Power Tools (APT)
or GUI software like the Expression Console. You can find a short tutorial on APT and Expression Console and how to preprocess the raw data here.
The expression data file is used for the signal strength while the p-value data is used for the presence/absence calls of the probesets. The domain
graph will then be colored according to your data and alternative splicing events will be highlighted.
The Affymetrix data will be imported into the embedded database, therefore applying the data for different domain graphs and in different Cytoscape
sessions is possible without having to re-import the data!
| Expression data file format: | Import a tab-delimited file with a single-line header specifying the two columns. The first column contains the probeset ids and the second column contains the expression values. |
| P-value data file format: | Import a tab-delimited file with a single-line header specifying the two columns. The first column contains the probeset ids and the second column contains the p-values. |
Please note that this is the file format of the APT, Expression Console,... output files. Therefore, you can directly integrate these files into the domain graphs.
In addition to the features mentioned above, the user can survey the distribution of Affymetrix probesets relative to the domain and exon structure
of a protein. The probesets are colored according to their expression signal and according to the presence/absence call provided by the p-value:
Expressed probesets according to the p-value are colored from yellow (low expression signal) to red (high expression signal). Suppressed probesets
are colored in pink. Additionally, microRNA binding sites are shown in dark blue if available.
You can see an example of a domain graph with integrated Affymetrix data here.