RNA-Seq Tools in FlyBase

GBrowse – GBrowse Genome Annotation Viewer

Use the FlyBase GBrowse tool when you want to visually examine RNA-Seq expression levels in a known region of the Drosophila genome.  (You may need to activate RNA-Seq expression tracks in GBrowse, if your saved settings do not already include these tracks.)

GBrowse has several tracks that display RNA-Seq expression profiles, which give coverage values base-by-base across the genome. Choose datasets for expression by stage, tissue, treatments, or cell lines. By default, the many tracks are displayed in the layered FlyBase “TopoView” format, and data are shown on a log2 scale since they range over many orders of magnitude. These display aspects can be configured to the user’s preferences as described here.

For more help with FlyBase GBrowse, see this help page.


RNA-Seq Profile – RNA-Seq Expression Profile Search

Use this tool when you have an expression pattern or profile in mind and would like to search for genes that match your pattern.  For example, find genes which are strongly expressed during the larval stages and weakly expressed in the adult.

The RNA-Seq Expression Profile search tool gives you fine-grained control over expression conditions across several variables.  Choose datasets for expression by stage, tissue, treatments, or cell lines, or use several datasets in conjunction.  Each dataset is presented in a form that allows you to select either narrow slices of the data, or larger sections for more coverage.  You also have control over the levels of expression used as cutoffs in the search.

For more help with this tool, see this commentary or this help page.


RNA-Seq Similarity – RNA-Seq Expression Similarity Search

Use the RNA-Seq Expression Similarity search tool when you want to search for genes with expression patterns which are similar to that of a given gene.  ‘Similar to’ in this case means that the pattern of higher and lower expression in the categories for the RNA-Seq expression experiment data you choose are close to those of your chosen gene, as measured by the correlation coefficient* between the data for your given gene and each of the search result genes.  Choose datasets for expression by stage, tissue, treatments, or cell lines. You can also specify a subset of experimental categories to use when making comparisons.

Note that two expression patterns will be flagged as similar if the profile of peaks and troughs of expression have a similar shape, even though one expression pattern may have much higher or lower values overall.

For more help with this tool, see this help page.

* FlyBase uses a generalized Spearman rank correlation for this statistic.

The similarity tool works currently with only the modENCODE developmental RNA-Seq data; other RNA-Seq datasets will be included soon.


RNA-Seq By Region – RNA-Seq Levels by Exon or Genomic Region

Use this tool when you want to compare the RNA-Seq signal for a given region across samples, or compare signal between two regions within a single sample.

Supply the symbol or FBgn ID for one gene of interest, and choose to query either the developmental or tissue RNA-Seq profiles. The tool will retrieve the locations of all exons for the gene specified, and report the average RNA-Seq signal (per base) for each region. Values are normalized for read depth across a given set, and reported as log2 values.

Alternatively, input one or more genomic regions using standard GBrowse coordinate nomenclature (e.g., 3L: 20000..21000) and the tool will return the average RNA-Seq signal for each submitted genomic span; for multiple regions, enter one region per line in the input box.

For more help with this tool, see this commentary or this help page.

from FlyBase

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