FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system - PubMed (original) (raw)

. 2011 Jan;39(Database issue):D111-7.

doi: 10.1093/nar/gkq858. Epub 2010 Nov 19.

Ryan G Christensen, Majid Kazemian, Christopher J Hull, Metewo Selase Enuameh, Matthew D Basciotta, Jessie A Brasefield, Cong Zhu, Yuna Asriyan, David S Lapointe, Saurabh Sinha, Scot A Wolfe, Michael H Brodsky

Affiliations

FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system

Lihua Julie Zhu et al. Nucleic Acids Res. 2011 Jan.

Abstract

FlyFactorSurvey (http://pgfe.umassmed.edu/TFDBS/) is a database of DNA binding specificities for Drosophila transcription factors (TFs) primarily determined using the bacterial one-hybrid system. The database provides community access to over 400 recognition motifs and position weight matrices for over 200 TFs, including many unpublished motifs. Search tools and flat file downloads are provided to retrieve binding site information (as sequences, matrices and sequence logos) for individual TFs, groups of TFs or for all TFs with characterized binding specificities. Linked analysis tools allow users to identify motifs within our database that share similarity to a query matrix or to view the distribution of occurrences of an individual motif throughout the Drosophila genome. Together, this database and its associated tools provide computational and experimental biologists with resources to predict interactions between Drosophila TFs and target cis-regulatory sequences.

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Figures

Figure 1.

Figure 1.

Schematic of data flow into the FlyFactorSurvey (FFS) database. The majority of motifs present in the database originate from B1H binding site selections. Information on the factor constructs and selection conditions is captured within the database for each motif generated. Clones from each selection are sequenced either individually via Sanger sequencing or as a pooled population via SOLEXA sequencing, and binding site motifs are identified from these sequences using MEME (39). The FFS database provides users with access to published and unpublished motif information on our characterized Drosophila TFs as well as links to tools to mine our database of motifs and utilize these motifs for searches within the Drosophila genome.

Figure 2.

Figure 2.

Screen shot of bicoid summary page within FlyFactorSurvey. (top) Header information for each factor contains identification information, the type(s) of DNA binding domains found within the gene and links to factor information in Flybase (36), Unipro (40) and FlyMine (33). (bottom) Recognition motifs determined for the factor through different methods, under different conditions or assayed via different sequencing methods are displayed in independent panels. Each panel displays the recognition motif as a Sequence logo (35) and download buttons to obtain count, position-specific probability (PSPM) or position-specific scoring (PSSM) matrices. The other information panel summarizes the methods used to select and sequence the factor binding sites. For motifs determined using the B1H system, the expression vector and the selection conditions are indicated where different stringencies can result in motifs with different complexity. In this example, only two of the four bicoid motif panels within the database are shown; these panels illustrate that the increased inhibitor concentration used in the selection to generate the lower panel resulted in a more stringent motif. For each individual motif, a direct link is provided to view the relative frequency of the motif in the Drosophila genome using Genome Surveyor (see Figure 3).

Figure 3.

Figure 3.

Screen shot of Genome Surveyor interface directly linked from the Bcd_SOLEXA motif within the FFS database. The relative enrichment (profile) of this motif in 500 bp windows surrounding the eve locus is represented as a Z score relative to the genome-wide average. Three different motif profiles are shown: Single species (D. melanogaster), Multi species (D. melanogaster and D. pseudoobscura) and BMPhylo (11 Drosophila species). BMPhylo motif tracks have been previously described (11). Individual high scoring sequence motif matches are also shown at bottom. This tool provides a rapid assessment of the overrepresentation of any motif in the database within the Drosophila genome and additional functions such as combined motif searches (24).

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