NOTE! This is a read-only copy of the ENCODE2 wiki.
Please go to the ENCODE3 wiki for current information.
Integration paper old
This page is based around the original Biological themes document and aims to bring together the biological questions, analysis strategy and results to summarise current status. In general I have taken images from powerpoints or pdfs presented on AWG calls or subgroup calls, or from workshops to represent the latest analysis. Please add results or links to results into the relevant places. Also useful would be relevant references by PMID.
- Analysis 1: Pink tags are analysis numbers as in the Biological Themes doc (not clickable).
- Paper Introduction
- Focusing the ENCODE analysis: Six Big Questions.
- 0. Definition and validation of elements
- 1. What is the transcript complexity of a mammalian cell?
- 2. What biochemical events/marks are associated with distinct features on chromosomes (and vice versa)?
- 3. What is the higher order organization of chromosomes?
- 4. What patterns of evolutionary constraint and genetic variation are associated with each of the above classes?
- 5. Is there a transcriptional regulatory code in the cell and how is it organized into a larger network?
- 6. What are the similarities and differences in two cell types with relation to all of the issues above?
- 7. How does ENCODE data impact our understanding of other human biology phenomena?