New RNA-Seq By Region data viewer
The new RNA-Seq By Region tool reports the average (per base) expression level for a given genomic region in the modENCODE developmental and tissue RNA-Seq transcriptome profiles. This tool allows one to evaluate the approximate expression level of individual exons, parts of exons, introns and/or intergenic regions. It can be accessed from any FlyBase gene report, in the “High-Throughput Expression Data” sub-section of the “Expression Data” section.
In its primary and simplest form the user supplies the symbol or FBgn ID for one gene of interest, and chooses to query either the developmental or tissue RNA-Seq profiles. The tool then retrieves the locations of all exons for the gene specified, and reports the average RNA-Seq signal for each region. Alternatively, the tool also allows the input of one or more user-specified genomic regions using standard GBrowse coordinate nomenclature (e.g., 3L: 20000..21000); for multiple regions, enter one region/line in the input box.
The tool retrieves data from the same genome-wide RNA-Seq coverage wiggle-formatted (.wig) expression files used for the graphical (TopoView) representation of RNA-Seq data in GBrowse. Note that the expression values in these files, and returned by this new tool, are log2 transforms of the original coverage values. Importantly, these values are normalized for the sequence read-depth of each sample. For fast visual inspection of the potentially large expression tables, the background of table cells is colored in the same way as in the heatmap coloring schema of expression histograms in FlyBase gene reports. These tables can be copied and downloaded and used for further analysis.
In its current state*, the tool has one important limitation. The signal reported for a given region may arise from the expression of multiple transcripts from one or more genes; the tool simply reports the total signal for that region and does not attempt to assign the expression in that region to any specific transcript.
Please note that this is a “beta” version of this tool. Any feedback from users regarding bugs or potential improvements is appreciated.
*Update - Read-depth normalization of sample data for this tool was implemented June 29, 2015. There was no normalization in the original release of the tool (June 26, 2015).