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  2. Transcription factor binding site databases - Wikipedia

    en.wikipedia.org/wiki/Transcription_factor...

    transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. database: website [4] CIS-BP collection of transcription factor binding sites models inferred by binding domains. database: website [5] CistromeMap a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human. database: website [6 ...

  3. SMiLE-Seq - Wikipedia

    en.wikipedia.org/wiki/SMiLE-Seq

    SMiLE-seq workflow. SMiLE-seq uses a microfluidic device into which transcription factors, which have been transcribed and translated in vitro, are loaded.Transcription factor samples (~0.3 ng) are modified by the addition of an enhanced green fluorescent protein (eGFP) tag and combined with both target double-stranded DNA molecules (~8 pmol) tagged with Cyanine Dye5 (Cy5) and a double ...

  4. TRANSFAC - Wikipedia

    en.wikipedia.org/wiki/TRANSFAC

    TRANSFAC (TRANScription FACtor database) is a manually curated database of eukaryotic transcription factors, their genomic binding sites and DNA binding profiles. The contents of the database can be used to predict potential transcription factor binding sites .

  5. ChIP sequencing - Wikipedia

    en.wikipedia.org/wiki/ChIP_sequencing

    ChIP-sequencing, also known as ChIP-seq, is a method used to analyze protein interactions with DNA.ChIP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins.

  6. DNA binding site - Wikipedia

    en.wikipedia.org/wiki/DNA_binding_site

    DNA binding sites can be categorized according to their biological function. Thus, we can distinguish between transcription factor-binding sites, restriction sites and recombination sites. Some authors have proposed that binding sites could also be classified according to their most convenient mode of representation. [3]

  7. Chromatin immunoprecipitation - Wikipedia

    en.wikipedia.org/wiki/Chromatin_immunoprecipitation

    Chromatin Immunoprecipitation sequencing, also known as ChIP-seq, is an experimental technique used to identify transcription factor binding events throughout an entire genome. Knowing how the proteins in the human body interact with DNA to regulate gene expression is a key component of our knowledge of human diseases and biological processes.

  8. DNA footprinting - Wikipedia

    en.wikipedia.org/wiki/DNA_footprinting

    The DNA template labeled at the 3' or 5' end, depending on the location of the binding site(s). Labels that can be used are: radioactivity and fluorescence.Radioactivity has been traditionally used to label DNA fragments for footprinting analysis, as the method was originally developed from the Maxam-Gilbert chemical sequencing technique.

  9. Transcription factor - Wikipedia

    en.wikipedia.org/wiki/Transcription_factor

    The DNA binding sites of 519 transcription factors were evaluated. [50] Of these, 169 transcription factors (33%) did not have CpG dinucleotides in their binding sites, and 33 transcription factors (6%) could bind to a CpG-containing motif but did not display a preference for a binding site with either a methylated or unmethylated CpG.

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