Figure 1

MiCoViTo principle A) Neighbourhood comparison around a seed in two transcriptome states. The location of genes gives an idea of their expression compared to the seed gene. The X axis represents the neighbourhood levels computed in the first transcriptome state, the Y axis represents the neighbourhood levels computed in the second transcriptome state. Regions that are closer to the origin reflect more closely co-expressed genes (delimited by red dash lines). The white region is the area containing genes correlated in both microarray datasets while the blue area contains genes that are co-expressed only in one of the conditions. As we do not want to consider genes that are far away from the seed gene in both transcriptome states, the lower right part of the table is not analysed (grey region). B) Result of the comparison of S. cerevisiae transcriptome state time courses during a 30°C to 37°C temperature shift and during exposure to the reducing agent dithiotreitol (DTT) [29] available in the online tutorial. The comparison was performed using a structural constituent of a ribosome subunit (RPS8B/YER102W gene) as seed and Pearson distance as the distance metric. The step value used to define neigbourhood levels is 0.2 (see intervals 0–0.2, 0.2–0.4, ..., 1.2–1.4). Each group of genes located in a neighbourhood intersection is given in the form of a clickable pie chart constructed according to the MIPS functional classification catalogue [15].