Fig 2. Transcript interaction neighborhood.

In this toy example, transcript T _ik has four neighbor transcripts {T _g1a, T _g2b, T _g3c, T _g4d}, which are transcripts from g ₁, g ₂, g ₃ and g ₄, respectively. The neighborhood expression ϕ _ik of T _ik is then calculated as the average of its neighbor transcripts’ expressions and further normalized by transcript length, represented as the vector product between π and S _*,(i,k) normalized by the number of neighbors ∑S _*,(i,k) and the transcript length l _ik in the figure.