Systems, methods, and computer program products are described for providing a graphical user interface (GUI) that may include a first openable window of image features constituting, for example, a pseudo-image of a scanned probe array. The image features each have one or more characteristics representing one or more hybridization reactions associated with a probe of the probe array. The GUI also has a second openable window including data features, each relating to one or more quantifications of one or more hybridization reactions associated with a probe of the probe array. This second window may be, for example, a scatter plot of hybridization intensities of probes to two or more labeled samples. The GUI further includes a third openable window including descriptive features such as rows of a spreadsheet. Each row may include descriptive elements associated with a probe. When a user selects a feature from any of the two or more windows, a corresponding feature in at least one other of the two or more windows is highlighted.