Posted by: arrogantscientist | July 15, 2010

A quick and dirty guide to FlyBase – Part 1 – Basic gene information

FlyBase[1] is the database used daily by anyone that works on Drosophila. It contains all the information there is to know about the Drosophila melanogaster genome (and others), including gene annotations, expression data, phenotypic data and any stocks publicly available.

The wealth of information available is the main obstacle to be overcome by anyone new to large databases such as FlyBase. There are many in-depth guides on how to use FlyBase, but often only a small snippet of information is what you’re after when you look up a gene.

The best way to understand FlyBase is to use it. The purpose of this guide is to help anyone new to it get into it for the first time and basic information about a gene.

This section will highlight a few of the most immediately useful pieces of information displayed on a typical gene page, using forked as an example.

The phenotype of forked.

The four sections highlighted below provide basic information about the gene forked:

General Information

This section contains the identity of the gene. The Name of the gene is given along with its Symbol (f), which can be used as an abbreviation. The unique CG (Computed Gene) number and FB ID are also given, but are often not stated in publications for named genes. Genes without a name are referred to by their CG number. The Gene Model Status tells you whether the gene is known to or thought to exist (current). Genes found not to exist can still be looked up for reference.

Genomic Location

This section tells you exactly where the gene is in the genome. The important bits are the Chromosome (and arm if the gene is on an autosome), the Sequence Location and the orientation of the gene (shown by a [+] or [–]). The Genomic Maps section gives a visual representation of the area surrounding the gene, showing other nearby genes and their orientations. The buttons Get genome region and Get FastA allow you to download the entire gene sequence, or just the parts you’re interested in (e.g. exons only). The four most useful are: Gene region – the whole sequence as it is in the genome, Transcripts – the mature mRNA sequence(s) produced from the gene, the CDS (coding sequence) – the sections of the mRNA transcript(s) that are actually translated into protein, and the Translations – the protein(s) produced from the gene.

Summary Information

This is the section to look at if you want a quick overview of what a gene does. The molecular function, biological processes and phenotypes annotations tell you what is known, or predicted, about the gene’s function. For a more detailed description of phenotypes, the Phenotypic Descriptions of Classical Alleles button will take you to a page containing information about different alleles, with links to the publications in which they were originally described.

Stocks and Reagents

Every available stock relevant to the gene you’re interested in is listed here, with links to where they can be ordered.

1. S. Tweedie, M. Ashburner, K. Falls, P. Leyland, P. McQuilton, S. Marygold, G. Millburn, D. Osumi-Sutherland,
A. Schroeder, R. Seal, H. Zhang, and The FlyBase Consortium.
FlyBase: enhancing Drosophila Gene Ontology annotations.
Nucleic Acids Research (2009) 37: D555-D559; doi:10.1093/nar/gkn788.

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