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compbio-2017 / Discussion

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[mock] Gene regulation #15

Open shouldsee opened 6 years ago

shouldsee commented 6 years ago

LoL

  1. On which protein is the first ChIP-Seq is performed?

  2. In ChIP-Seq, what factors contribute to a spurious peak? What experimental/computational procedures can you take to reduce such noises?

  3. How is a TF-binding motif represented computationally? How can you use this representation to interrogate observed sequence reads?

  4. What are the necessary and essential conditions for a gene to be transcribed?

  5. List experiment techniques to interrogate

    • RNAPII activity
    • Ribosome activity
    • DNA methylation
    • Chromatin Accessibility
    • Histone modification
    • TF binding-site
    • ncRNA effect site
shouldsee commented 6 years ago

Answers

  1. STAT1, a transcription factor stimulating immune cells.

    • Experimental: Use a control. Probing chromatin accessibility
    • Computational: Peak-calling using dynamic Poisson modelling (MACS). Account for degeneracy of a ~20mer over the genome and adjust read concentration. Cross-validate with other genomic tracks.