The invention described herein relates to computer and display methods and systems for acquiring, storing, manipulating, analyzing, linking, retrieving and displaying the data. The methods and systems are illustrated with reference to data on constituents of biological systems, particularly data on gene expression. In this regard, the invention especially relates to interactive systems for displaying gene expression-related data in three-dimensional molecular topographies. Expressed genes and their activity are represented as peaks in the topographies. Additionally, the invention relates to methods and systems for generating and displaying delta plots, which show differences in gene expression, and to methods and systems for generating molecular movies that show changes in gene expression. While illustrated by reference to gene expression, the methods and systems can be used to generate and manipulate displays of data on other complex populations.