Downloads and Resources

Background

Candidate Drosophila transcription factors

Lists of candidate Drosophila transcription factors with sequence-specific DNA binding activity were derived from several sources. Drosophila genes encoding proteins with potential sequence-specific DNA binding activity were identified by searching the SMART database for Drosophila proteins with potential DNA binding domains and by using Flymine to identify Drosophila genes annotated to contain Interpro domains associated with DNA binding. These lists are compared to a base set of transcription factors described by Adryan and Teichmann in the FlyTF database.

Regions of evolutionary conservation corresponding to likely functional boundaries of each DNA-binding domain are identified by sequence alignment of orthologous genes between multiple fly species using BLAST or Clustal.

Motif construction from selected binding sites

Binding sites selected with the B1H system are analyzed for overrepresented sequence motifs using MEME or Consensus. These motifs are converted into Sequence logos using Weblogo.

Downloads

Datasets

Motifs depicted as frequency matrixes (columns) can be downloaded in the vertical format used by Windowfit, Stubb and Genome Surveyor (see here). In each header, an ID is assigned for each matrix, which contains the gene symbol. The header also provides the flybase gene ID for the transcription factor (or factors for heterodimers).

Dataset A (public)

Motifs depicted as frequency matrixes (rows) can be downloaded in the horizontal format used by Gary Stormo's group (see here) and the JASPAR database (see here). In each header, an ID is assigned for each matrix, which contains the gene symbol. The header also provides the flybase gene ID for the transcription factor (or factors for heterodimers).

Dataset B (public)

Motifs depicted as position weight matrixes (rows) can be downloaded in the vertical format used by Gary Stormo's group (see here) and the JASPAR database (see here). In each header, an ID is assigned for each matrix, which contains the gene symbol. The header also provides the flybase gene ID for the transcription factor (or factors for heterodimers).

Dataset C (public)

Selected sequences obtained using the bacterial one-hybrid method can be downloaded as a tab delimited file. The header for each file contains the name of the resulting matrix ID and the flybase gene ID for the transcription factor (or factors for heterodimers).

Dataset D (public)

Publications

Drosophila homeodomain bacterial one-hybrid data and analysis.

Noyes, M.B. Christensen, R.G., Wakabayashi, A., Stormo, G.D., Brodsky, M.H. and Wolfe, S.A. Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites. Cell. 2008, 133(7) 1277-89. (Link to pdf)

Drosophila segmentation TF bacterial one-hybrid data.

Noyes, M.B., Meng, X., Wakabayashi, A., Sinha, S., Brodsky, M.H., Wolfe, S.W. Systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system. Nucleic Acids Res. 2008, 36(8) 2547-60. (link to pdf).

Additional DNA binding specificity data from an earlier version of the bacterial one-hybrid data.

Meng, X., Brodsky, M.H., Wolfe, S.A. A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors. Nat Biotechnol., 2005, 8 988-94. (link to pdf).

Resources

Information about Drosophila transcription factors and their targets.

General information about all Drosophila genes

Flybase

Flymine

Drosophila transcription factors and previously identified binding sites and CRMs

FlyTF A curated list of candidate Drosophila TFs

Redfly, Flyreg and Bergman website are experimentally determined CRMs and TF binding sites (DNase I footprinting or SELEX) curated from the literature.

ModENCODE Gene expression and TF chromatin immunoprecipitation data for the Drosophila and C. elegans genomes.

BDTNP Multidisciplinary analysis of the DNA binding, expression and targets of TFs regulating early Drosophila embryogenesis.

Cistrack Chromatin immunoprecipitation and other data for Drosophila TFs.

Tools for the analysis of TF binding sites within the Drosophila genome

Genome Surveyor and Stubb and Windowfit Tools created by Saurabh Sinha to identify matches to TF DNA binding motifs obtained by bacterial one-hybrid or other methods.

Target Explorer and ecis-analyst Other tools to identify TF binding sites in genomic sequences.

Additional databases and tools describing and using TF DNA binding specificities

Transfac and Jaspar databases contain DNA binding site information for TFs from a variety of species, including Drosophila.

Uniprobe DNA binding specificity data for TFs from a variety of species determined using the protein binding microarray technology developed by the Bulyk group.

Sormo website and homeodomain predictions Tools from the Stormo group to analyze TF binding site motifs and to predict the binding specificity of homeodomain proteins.

MEME Tools for motif identification, comparison and searching.

BioProspector Alternate tool to identify gapped motifs.

Weblogo Tool to create images (Sequence logos) representing the observed sequence biases in a motif.

STAMP Tool from the Benos group for TF binding site motif comparisons.

Weng website Tools and databases from the Weng group and links to many other groups.


 


Questions and comments can be sent to: Michael Brodsky   or    Scot Wolfe Database and website designed by Julie Zhu