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

    • Position Count Matrices (pcms) for binding site motifs of characterized Cys2-His2 zinc finger finger-subsets (Supplementary figure 11, Enuameh et al. Genome Research 2013).

    • 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 Cys2His2 zinc finger protein bacterial one-hybrid data and analysis.

  • Enuameh, M.S., Asriyan, Y., Richards, A., Christensen, R.G., Hall, V.L., Kazemian, M., Zhu, C., Pham, H., Cheng, Q., Blatti, C., Brasefield, J.A., Basciotta, M.D., Ou, J., McNulty, J.C., Zhu, L.J., Celniker, S.E., Sinha, S., Stormo, G.D., Brodsky, M.H., Wolfe, S.A., Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants. Genome Research. 2013, in press. (Link to pdf)

  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)
  
  
  • Christensen, R.G., Enuameh, M.S., Noyes, M.B., Brodsky, M.H., Wolfe, S.A., Stormo, G.D., Recognition models to predict DNA-binding specificities of homeodomain proteins. Bioinformatics. 2012, 28(12), i84-i89. (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).

  Regualtory network analysis using bacterial one-hybrid data.

  • Cheng, Q., Kazemian, M., Pham, H., Blatti, C., Celniker, S.E., Wolfe, S.A., Brodsky, M.H., Sinha, S., Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy. PLoS Genetics 2013 in press.
  
  
  • Kazemian, M., Blatti, C., Richards, A., McCutchan, M., Wakabayashi-Ito, N., Hammonds, A.S., Celniker, S.E., Kumar, S., Wolfe, S.A., Brodsky, M.H., Sinha, S., Quantitative analysis of the Drosophila segmentation regulatory network using pattern generating potentials. PLoS Biol. 2010 8(8) e1000456 (link to pdf).
  
  
  • Kazemian, M., Brodsky, M.H., Sinha, S., Genome Surveyor 2.0: cis-regulatory analysis in Drosophila. Nucleic Acids Res. 2011, 39, W79-85. (link to pdf).

  Bacterial one-hybrid database information.

  • Zhu, L.J., Christensen, R.G., Kazemian, M., Hull, C.J., Enuameh, M.S., Basciotta, M.D., Brasefield, J.A., Zhu, C., Asriyan, Y., Lapointe, D.S., Sinha, S., Wolfe, S.A., Brodsky, M.H., FlyFactorSurvey: a database of Drosophila transcription factor binding s pecificities determined using the bacterial one-hybrid system. Nucleic Acids Res. 2011, 39, D111-7. (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 are designed by Julie Zhu  and  Jianhong Ou. They are currently maintained by Kai Hu and Julie Zhu.