Gene analysis on the massive scale
Gene regulation is key to understanding how our bodies translate the genome to arrive at fully functioning cells and organs. Gene expression depends on transcription factor binding sites (TFBSs) — genomic sites for binding regulatory proteins. The EU-funded 'Comparative genomics and next generation sequencing' (COGANGS) project developed novel tools to perform detailed gene regulation analysis based on a collection of known DNA sequence motifs, recurring patterns in the DNA. The COGANGS engine significantly improves the ability to predict the all-important TFBSs. Built by integrating a stand-alone command-line tool called TransFoot (implements the algorithms) with the CLC Genomics Workbench, the environment provides intuitive graphical user interfaces. A web-based interface called the Match Portal extends BIOBASE’s ExPlain™ system that identifies transcription factor s and predicts gene expression patterns. Combining the two approaches, the COGANGS system can predict already known TFBSs and can predict potential binding sites. The software is flexible according to users' needs. Prediction can result from a single or multiple gene sequences and any prior knowledge, from e.g. evolution, can be built into the analysis. Moreover, the user can choose between faster but less accurate analysis or slower and more accurate results. The system uses phylogenetic segmentation where the input rooted evolutionary tree can be broken up into a number of small overlapping segments. The net result is that the predictions for the sequence in question depend on the entire phylogenetic tree and not just those in the same component. For the simplest case however, with no evolutionary information available, the Match Portal applies less sophisticated but rapid algorithms. The software has tremendous value for pharmaceuticals, biotech, agriculture, biofuel companies, and research hospitals. Market potential is huge as gene regulation is a key component of many areas of research today. After further investments for hardware and power consumption, the projected market value is estimated to at least 100 million USD sales per year. Project partners intend to continue to expand and improve the software.
Keywords
Software suite, gene regulation, analysis, transcription factor binding sites, TransFoot, Match Portal, COGANGS system
