2418 Nucleic Acids Research, 2012, Vol. 40, No. 6 Figure 3. In the ﬁrst two steps of an analysis, the user has to select the species and upload CEL ﬁles to the server (data not shown). (A) Afterwards, names for the analysis and groups as well as a password to access the result are needed to be provided by the user. Each uploaded CEL ﬁle needs to be assigned to its group by selecting a box. The groups are used to set up comparisons. After processing by GAA has ﬁnished, the user will receive a link to access the result. (B) On the result page, thresholds for SI and P-value can be chosen to ﬁlter at the exon or gene levels. It is also possible to search for certain genes, e.g by Gene Symbol. A table with all exons or genes meeting the thresholds will be shown on the same page (data not shown). Each entry is linked to a page with more details, including links to other databases, SI of all exons of the gene and probe set sequences. (C) This page also displays a box plot of GNIs of all exons of a gene, here shown on the example of Add3 which has been validated by reverse transcription polymerase chain reaction (RT–PCR) (see text). Not shown here is the genome browser, which is also displayed on the same page (see Figures 4B and 5B for examples). (D) A table shows the SI, P-value and known splicing events of all probe sets. (E) By clicking on a probe set ID in the genome browser, exon sequences are shown. They can be used directly to design primers. Screen shots are modiﬁed to ﬁt the page. Additional information on how to use GAA can be found in the online help section at http://gaa.mpi-bn.mpg.de/help.php. both levels represent metabolic process, protein binding and transcription factor activity, etc. One of the most sig- niﬁcant biological process at the gene level was develop- mental process. Other highly enriched terms were heart development and muscle organ development, which are expected terms during differentiation of cardiomyocytes (Supplementary Table S2). To demonstrate the usability of GAA, we selected a set of genes with the highest difference at the exon level between CB and ES as well as EB. The probe set with