FlyBase 102--advanced approaches to interrogating FlyBase

Abstract

FlyBase (http://flybase.org) is the leading website and database of Drosophila genes and genomes. Whether you are using the fruit fly Drosophila melanogaster as an experimental system or wish to understand Drosophila biological knowledge in relation to human disease or to other model systems, FlyBase can help you successfully find the information you are looking for. Here, we demonstrate some of our more advanced searching systems and highlight some of our new tools for searching the wealth of data on FlyBase. The first section explores gene function in FlyBase, using our TermLink tool to search with Controlled Vocabulary terms and our new RNA-Seq Search tool to search gene expression. The second section of this article describes a few ways to search genomic data in FlyBase, using our BLAST server and the new implementation of GBrowse 2, as well as our new FeatureMapper tool. Finally, we move on to discuss our most powerful search tool, QueryBuilder, before describing pre-computed cuts of the data and how to query the database programmatically.

Figure 1.

TermLink search example. (A) Search for ‘stem cell’ in TermLink. (B) Select ‘stem cell’ from the FBbt ontology. (C) Click ‘Alleles’ (red dashed circle) to see alleles showing stem-cell-related phenotype. (D) On the resulting hitlist page, select ‘Genes’ (highlighted) from the ‘Convert to’ drop-down menu. (E) Export the list of genes to ‘Batch Download’ (in red and underlined) using the ‘HitList Conversion Tools’ menu. (F) Using the ‘Select fields’ on the batch download page, select the ‘Human Orthologs’ radio button.

Figure 2.

RNA-Seq Search and Results Analysis/Refinement. (A) Portion of input page for RNA-Seq Search. Please note that the screenshot is cut off, and the section of the search for ‘tissue’ is not shown. Orange arrowhead on left indicates the drop-down menu to set the level of ‘Expression off’, and orange arrow on right indicates the same for ‘Expression on’. (B) Top of hitlist for search results. Red dotted circle indicates Results Analysis/Refinement button, and inset panel shows the options. Red arrow points to ‘Biological Process’ which is selected. Results are shown in (C). Red arrowhead indicates number of records annotated with the term ‘mitotic spindle organization’.

Figure 3.

GBrowse—the FlyBase Genome Browser. Tracks are selected by clicking on the ‘Select Tracks’ tab at the top of the browser (highlighted with the red dotted circle), or the ‘Select Tracks’ button at the bottom of the page. The tracks are completely configurable, and can be favorited, opened/closed, shared and even changed in color and appearance. In addition, clicking on a track allows you to order the tracks, so tracks of interest can be placed next to each other. Information on each track can be found by clicking on the ‘?’. Help on how to use GBrowse can be found by clicking on the ‘Help’ button on the top right-hand side (arrow).

Figure 4.

QueryBuilder. (A) Available templates for alleles and anatomy. The template used in the example is indicated with an arrow. (B) The template query segments. (C) The template query segments edited for the example query. (D) The resulting hitlist. In total, 383 alleles match the search criteria.