Abstract
A large number of genomic regions, such as transcription factor binding sites (TFBSs) captured from next generation sequencing (NGS) data analyses or those available from the public resource database ENCODE, are generally overlapped to answer a variety of biological questions. Though several command-line tools are available to perform such an analysis, there is a notable lack of an integrated webserver application with which to identify genomic region intersections, generate publication-ready plots depicting subsets of the overlapped regions, and perform functional annotation. Thus, there is an ardent need for a comprehensive and user-friendly webserver application that allows the users to either upload multiple datasets or select from the integrated Gene Transcription Regulation Database (GTRD). We thus introduce BedSect (http://imgsb.org/bedsect/.), which not only fulfils the above criteria but also performs intersection analysis along with visualization of the intersection regions as an UpSet and correlation plot using the integrated Shiny application. Moreover, analyses, including functional annotation, gene ontology, and biological pathways enrichment for the identified unique and intersected genomic regions, can also be performed using the integrated GREAT tool. To view the genomic regions in the genome browser, the inbuilt hyperlink for UCSC can redirect the user to visualize the results as custom tracks.
Highlights
Though several command-line tools are available to perform such analysis, there is lack of a comprehensive web server application to perform the genomic region intersections from multiple datasets, to generate a plot for the subsets of the overlapped regions and to perform integrated functional annotation
With the decline in cost, Generation Sequencing technology is becoming a popular method to identify genomic regions of various interest such as transcription factor binding regions, accessible chromatin regions, regions with histone modification, methylated events/chromosomal locations are generally stored in BED [1]
The above-mentioned tools undoubtedly are very useful for performing genomic region intersection analysis or functional annotation
Summary
The core of this tool utilizes Perl, R, Shiny server and the front end of the web server written using PHP5.6, MySQL 14.14; Dist 5.7.19 and Javascript 1.8. Our tool provides an option as a hyperlink to submit unique or intersecting genomic regions as a custom track to visualize in UCSC genome browser (Fig. 2B). Upon selection of any genome, while submitting the files, result page will give an option in tabular format to carry out further analysis of intersecting regions using GREAT and UCSC (Fig 2B). Upon selection of genome build at home page, the result page provides a hyperlink option to submit the unique and intersecting regions to GREAT server and visualization in UCSC browser (Fig 5). To identify factors that have high genome-wide binding similarity, we generated correlation plot using integrated ShinyApp by clicking on “Generate plots” tab.
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