Suggestions for ENCODE reports

Try to use ENCODE to explain cytodifferentiation
    Perhaps specifically in liver cells, heart cells, or any cell type you choose. Or in general

    How gene sequences and maps help explain co-expression of specific sets of non-linked genes.
    (Or what patterns, like having the same base sequences used as binding site, upstream or downstream of each gene that is expressed (= its protein synthesized) just in liver cells

    Possible molecular mechanisms of mutual-exclusiveness of expression (transcription? protein synthesis?) of being a liver cell versus being a heart cell, or being a macrophage.

    Do base sequences and locations of genes (or any other aspect) help to explain the branching pathways of progressive divergence and narrowing of cell fate?
    (for example, ectoderm -> neural crest -> nerve ->autonomic...)

If ENCODE obstructed your efforts to solve some particular problem or set of problems, then your group can describe
    * what you wanted/expected to find
    * How you used ENCODE searching to find what you wanted
    * What ENCODE gave you instead
    * What you think might be the explanation
    * How ENCODE could be better and more useful.
Analyse and explain the "junk DNA" debate and hype. Explain different meanings of "junk-ness" of DNA.

Choose some particular gene, or genetic disease that happens to interest you and use ENCODE to find out about it. Explain success or failure of your efforts, and weaknesses or advantages of ENCODE.

What are some key techniques that were used to generate the data?
What are strengths or weaknesses of some?
What is history of some or all of these techniques?
What are strengths and blind spots of some or each?




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