MICSA

MICSA is a software tool that predicts binding sites of transcription factors (TFs) by combining positional information with information on motif occurrences. This innovative algorithm has been developed due to the significant advances in the development of next-generation sequencing technologies. Accurate genome-wide characterization of the binding sites of DNA-associated proteins can now be achieved using ChIP-Seq, which combines chromatin immunoprecipitation and massively parallel DNA sequencing.

While other published tools that predict binding sites from ChIP-Seq data use only positional information of mapped reads, MICSA goes a step further by utilizing both positional information and motif occurrences. The result is an algorithm that is more accurate than several other tools, as demonstrated by testing on datasets for the TFs NRSF, GABP, STAT1, and CTCF.

MICSA has also been applied to a dataset for the oncogenic TF EWS-FLI1, leading to the discovery of over 2000 binding sites and two functionally different binding motifs. The analysis of these binding sites has revealed that EWS-FLI1 can activate gene transcription when its binding site is located in close proximity to the gene transcription start site (up to approximately 150 kb) and contains a microsatellite sequence.