An overview of merging vertices. Figure 1(a) shows the concept of merging auto-regulate genes. From a biological viewpoint of transcriptional relationships, a number of genes may regulate themselves or regulate each other, resulting in cyclic relationships while re-constructing the large network, which makes it more difficult to determine simple shortest paths. Figure 1(b) demonstrates how to merge genes that regulate each other. Transcription factors, AR (androgen receptor) and DDIT3 (DNA-damage-inducible transcript 3), regulate their target genes and regulate each other as well. To preserve the biological truth and avoid loops being represented in the graph, vertices AR and DDIT3 were merged during the shortest paths algorithm. Next, while scoring the identified pathways according to gene expression data, each vertex (or gene) was considered separately and identically.