Example of study A) Neighbourhood comparison using two distinct seeds and a single transcriptome state. The results depend on the relative position of the seed genes in the overall transcriptome. This example shows the best-case scenario: two genes close to each other, with a circular gradient of expression coherence. This leads to the definition of zone of interest, represented here in red, which contains genes that are close to both seed genes. These genes are the other partners of the cluster defined by seeds 1 and 2. B) Results of the neighbourhood comparison of the two distincts seeds CLN1/CLN2 (B2) and CLN1/CLB2 (B3) in the Cho et al. yeast cell cycle datasets . CLN1 and CLN2 are both involved in the G1 phase whereas CLB2 is involved in the G2/M transition (B1). Each induced group of genes is represented in the form of a pie chart showing gene distribution in each cell cycle phase (color code is provided in B1 diagram, red: G1; dark green: S; orange: S/G2; blue: G2/M; light green: M/G1).