Relations among different concepts in the SP-analysis method. (A) Expression profile matrix (table). t = (t1,t2,… ) is the experimental condition index; in this example it indicates a set of time points. (B) Expression profiles (patterns). g1 and g4 are not strongly correlated directly, but both are strongly correlated with the correlated set (gx,g2). gx,g2 are the transitive genes interpolating the two terminal genes along SP1 (see C and D); similarly, gy is the transitive gene interpolating g1 and g5 along SP2. (C) GO biological process tree. The Ps are process annotations for genes at a particular node. A gene may belong to more than one node (“multiple-function,” such as g2). Expression profile space. gx is on the short path SP1 terminated by the known genes g1, g2, and g4 and hence is assigned a function of P1,1,1,1 (level L0) according to the GO tree in C; gy is on SP2 terminated by g1,g5 and is assigned a function of P1,1,1 (level L1). g1 is shared by both SPs and may be involved in both processes, which means the processes represented by SP1 and SP2 actually crosstalk to each other. The linked gene network can be formed by the subgraph SP1+SP2.