MAGNETIC: a web server to fetch gene network based on motif distribution in promoters

Abstract

Our web server MAGNETIC (Motif Associated Gene NETworks in Chromosomes) allows users to search the human genome for correlations between promoter regions of genes. The correlations take into consideration the similarity of the abundance of 5/6-mer motifs in gene promoters. The promoters could be 1, 2, or 6 kb upstream of the gene start site. Genes with similar motif abundances are linked to form a gene regulatory network. These networks could help determine or even discover gene networks of input genes. Our database could also be searched by motifs (including degenerate positions). The results identify the abundance of the motif in the promoters of all genes. The promoters where the motif is found in high abundance are likely to be target binding sites of a protein that recognizes the input sequence. MAGNETIC can also determine the similarity between gene promoters at the scale of whole chromosomes. We have showcased our server using a few examples that involve the consensus recognition motif of the transcription factor, Myc, and the genes it regulates. We have identified putative new targets of Myc and also found instances where Myc could only indirectly regulate genes. This server could help make important connections between genes and give insights into gene regulation and function.