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General Information
Symbol
Dmel\TFBS_HSA_026941
Species
D. melanogaster
Feature type
FlyBase ID
FBsf0000373347
Collection
Associated gene
Genomic Location
Chromosome (arm)
3R
Sequence location

3R:19,995,327..19,996,753

Sequence Data
Length
Comments
Associated Information
Gene(s) (targeted or local)
    Allele(s)
      Transcripts(s)
        Polypeptide(s)
          Construct
            Experimental Data
            Binding data
            Comments on moiety
            complexity score = 7.16
            Mapped to restriction fragment
            Evidence or Assay
            Collection Information
            Collection: mE1_TFBS_HSA
            Symbol
            Title
            Transcription factor hot spots (high occupancy sites) identified by ChIP of 41 factors in embryos.
            Source and Progenitors
            Species of derivation
            D. melanogaster
            Strain of derivation
            Stage
            Tissue/Position (including subcellular localization)
            Reference
            Vector of progenitor construct
            Description

            Genomic sequences identified as unique regions of transcription factor (TF) binding using HOT spot analysis (HSA); one or many TFs may bind in a given region. A synthesis of ChIP data sets for 41 different transcription factors.

            Additional data
            Sample preparation

            Embryos were collected aged appropriately, then dechorionated and formaldehyde fixed. Fixed embryos were then homogenized, nuclei were pelleted, and chromatin was sheared by sonication.

            Collection preparation

            Chromatin was immunoprecipitated using the appropriate antibody and the recovered material was amplified by PCR.

            Mode of assay

            The recovered material was characterized by Affymetrix whole-genome tiling array.

            Data analysis

            To investigate the co-localization of transcription factors, modENCODE ChIP-chip data sets for 25 factors were integrated with ChIP-chip data sets for an 16 additional factors produced by the Berkeley Drosophila Transcription Network Project (BDTNP, FBrf0192397, FBrf0205197, FBrf0205197). Data sets generated for the same factor were merged and the union was used for further analysis. Highly occupied target (HOT) regions were identified using a Gaussian kernel density estimation across the genome with a bandwidth of 300 bp, using the centers of each of the TF binding peaks as points. The density was then scanned for peaks, and each peak was denoted a HOT region. To determine the complexity of the HOT region, the sum of the Gaussian kernalized distance from the peak to each transcription factor that contributed at least 0.1 to peak's strength was calculated. The reported window around each HOT peak was derived by finding the maximum distance (in bp) from the HOT peak to a contributing TF, and then adding 150 bp (one half of the bandwidth). Each window is centered on the HOT peak. A TF complexity score was assigned to each of 38,562 distinct TF binding sites, corresponding to the number of distinct TFs bound (from 1 to ~21). Of these distinct TF binding sites, a subset of 1,962 hot regions (hotspots) had a TF complexity of eight or greater.

            Cell lines
            Observed in
            Not observed in
            Comments
            Stocks (0)
            External Crossreferences and Linkouts ( 0 )
            Synonyms and Secondary IDs (1)
            Reported As
            Symbol Synonym
            TFBS_HSA_026941
            Secondary FlyBase IDs
              References (2)