FLIGHT is organized into a number of sections, accessible by a set of tabs at the top of the page. Within the ‘Browse’ section users can access lists of RNAi screens, RNAi libraries, microarray gene expression datasets and Drosophila cell lines. By selecting a particular screen of interest the user can drill down to a see a list of all hits, and subsequently the phenotypic data for an individual hit, including scores, annotation and in some cases images. Where high-content RNAi screen images are available users can interact with the images directly, adjusting the brightness and contrast and viewing different channels separately or in combination ().
Figure 1 (A) Screenshot of the FLIGHT gene page for the Drosophila Rac1 gene. Boxes highlight links to Gbrowse, RNAi phenotypes, gene expression profiles and interaction maps. (B) GBrowse representation of the Rac1 locus including RNAi reagents and microarray (more ...)
In the ‘Search’ section, users can search for a gene, RNAi reagent, phenotype or cell line of interest. Searching by gene (using a symbol or FlyBase9
identifier) will return the appropriate FLIGHT gene page (). By default the RNAi experiments in which reagents targeting the selected gene were screened are displayed, including links to the phenotypic information available for each screen (). This page contains links at the top and bottom that provide users with access to a range of gene-specific data. The gene link displays a GBrowse10
representation of the gene structure and the regions targeted by RNAi reagents and microarray gene expression probes (). The ‘Expression’ link provides access to graphical plots of gene expression data from several different gene expression studies on different microarray platforms (). The protein link gives the sequences of all UniProt11
proteins for a particular gene. The InterPro12
links detail lists of protein domains and gene ontology annotations associated with the gene. The homology link identifies the known homologs in three different homology datasets, Homologene,14
The interactions link reveals a network map of all the known physical and genetic interactions for the gene (). The RNAi reagents link provides a list of all of the reagents with the specified gene as a computed target. From this page one can drill down and view the amplicon sequence, transcript coverage and predicted off-target effects and CAN repeats17,18
for each reagent. Finally, the ‘Alleles’ link displays a table of all the mutant alleles of a gene found in FlyBase9
and their associated phenotypes.
FLIGHT has been designed to allow users to analyze the results of high-throughput experiments in the context of other large-scale datasets. Thus, searches can be carried out using lists of genes and gene lists generated within the database can be saved and combined. Batch searches are available for gene annotations, RNAi screen hits, microarray gene expression scores, gene homologs and interactions. A gene list resulting from one search can be used as the basis for any batch search, using the ‘Link’ function. For example, a user interested in Rho GTPases could start by searching the database with a relevant InterPro motif (e.g., IPR003578) to call up a list of Drosophila Rho GTPases. Using the ‘Link’ function the user can then view which of the GTPases have been identified as hits in published RNAi screens. The results of all batch searches can be saved to a tab-delimited text file by clicking the ‘Download’ button at the foot of the table or on the left hand menu (for multi-page tables). Registered users can save the list of genes from any batch search to their account. Saved lists can be edited, used to create sub-lists, combined (union or intersection) or subtracted in the ‘Account’ section. They can also be used to search the database using the ‘Link’ function.