Development of a genomic region database and analysis tool for Windows and the Galaxy - Matloob Khushi
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
•Identifying overlaps in transcription factor binding sites and other specific genomic
features such as histone modifications is a major objective of genomic studies.
Datasets to be
•Existing methods to archive a large number of datasets in a personalised database
lack sophistication and utility.
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
•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.
Datasets can be annotated
with information about
can upload their
search and select
datasets to activate
BiSA Database (Knowledge Base): 600 datasets
and their > 18 million genomic regions.
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.
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.