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Development of a genomic region database and analysis tool for Windows and the Galaxy platform Matloob Khushi , Christopher Liddle, Christine L. Clarke and J. Dinny Graham Background •Identifying overlaps in transcription factor binding sites and other specific genomic features such as histone modifications is a major objective of genomic studies. •Existing methods to archive a large number of datasets in a personalised database lack sophistication and utility. Aims Methods BiSA Database (Knowledge Base): 600 datasets and their > 18 million genomic regions. Investigators can search and select datasets to activate to study. Overlapping, non-overlapping or common sections of regions can be extracted and visualised as Venn diagram. Datasets can be annotated with information about nearby genes. Investigators can upload their own datasets. Datasets to be compared. Summary statistic identifies the overall significance of overlap of two datasets. This ranges from 0-1, the closer the value to 1 the stronger the significance of overlapping of two datasets. All options of BiSA for Windows are available for the Galaxy (web-based open source genomic analysis tool). version as well. In summary, a major strength of BiSA is its comprehensive Knowledge Base, coupled with tools to analyse overlapping regions and ability to annotate the regions of interest. •Development of a software tool (BiSA) to allow researchers to identify statistically significant overlaps in transcription factor binding patterns and epigenetic modifications. •To do this by collecting transcription factor binding sites and histone modifications from ChIP-Seq and ChIP-chip published studies into a single database tool. Availability: http://bisa.sourceforge.net Conclusion BiSA for Linux/Mac runs under Galaxy Statistical Significance
