Fig. 3.

Simple viewpoint creation. Simple viewpoints can be created by clicking on Create viewpoints! after setting of appropriate parameters (Fig. 1c). Upon completion, the Analysis tab will be opened. At the top, summary statistics regarding the design are listed. In this case, GOPHER attempted to create simple viewpoints for 730 genes. GOPHER created at least one valid viewpoint (at least one selected digest) for 667 genes. Note that there are usually more viewpoints than genes, because one viewpoint for each TSS is created. For instance, two viewpoints were created for the gene AGAP2. If the the simple approach is performed without patching, the mean size of viewpoints corresponds to the mean size of digests at TSS. Depending on the selected restriction enzyme, this size may be different from the mean size derived from all digests due to the different base composition in promoter regions. Overlapping viewpoints arising from multiple TSS on given digests lead to redundant digests and associated probes. GOPHER reports only the number of unique digests and does not export redundant probes. The unique digests are further classified as balanced and unbalanced. The number of probes and the capture size, i.e. the total region that is covered by probes, can be used for cost estimation. The table below the summary statistics contains information about individual viewpoints. Each viewpoint can be opened for visual inspection and editing. Manually adjusted adjusted viewpoints will be flagged and can be reset to their original state