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Development of a genomic region database and analysis tool for Windows and the Galaxy - Matloob Khushi
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Development of a genomic region database and analysis tool for Windows and the Galaxy - Matloob Khushi

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  • 1. 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. Statistical Significance Datasets to be compared. •Existing methods to archive a large number of datasets in a personalised database lack sophistication and utility. Aims 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. •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. Methods Datasets can be annotated with information about nearby genes. Investigators can upload their own datasets. Investigators can search and select datasets to activate to study. BiSA Database (Knowledge Base): 600 datasets and their > 18 million genomic regions. Overlapping, non-overlapping or common sections of regions can be extracted and visualised as Venn diagram. BiSA for Linux/Mac runs under Galaxy All options of BiSA for Windows are available for the Galaxy (web-based open source genomic analysis tool). version as well. Conclusion 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. Availability: http://bisa.sourceforge.net