NOTE! This is a read-only copy of the ENCODE2 wiki.
Please go to the ENCODE3 wiki for current information.

Result Vignettes old

From Encode2 Wiki
Jump to: navigation, search

Old Do Not Edit!!

Reminder: ENCODE datasets can be found at


Feel free to add to this dataset, but keep Ian informed of any large dataset addition so we can keep track of things.

Section 0. Definition and validation of elements

PI Leads: Ian Dunham

Section 1. What is the transcript complexity of a mammalian cell?

PI Leads: Tom Gingeras, Barbara Wold, Roderic Guigo

  1. Other Analyses that need to be assigned to Vignetts
    1. Evidence of si RNAs (based on overlapping Tx and short RNAs)
    2. Genome-wide identification of potential regions of si-RNA production based on overlapping sense-antisense transcription and production of short RNAs
    3. Correlation of SNP and structural variations (indels) obtained from DNA PET analysis of K562 and GM as well as 1000 genomes with expression profiles;Integration_Vignette_V04
      1. look for loci with homozygous SNP and/or structural variation and evaluate if these have effect on RNA expression
      2. analyze loci with variations of RNA interaction genes (polymerases, post-transcriptional processing, transport, translation.
    4. Sex-specific splicing and expression (not only RNA but starts and stops)

Section 2. What biochemical events/marks are associated with distinct features on chromosomes (and vice versa)?

PI Leads: Brad Bernstein, Jason Lieb, Peggy Farnham, Jim Kent, Ross Hardison

Still requiring a section:

Analysis 5h: This analysis was left out of the document, but is still relevant: Can we identify:

  • TFs that correlate with open chromatin BECAUSE they trigger nucleosome remodeling.
  • TFs that correlate with open chromatin BECAUSE they can only bind accessible DNA.
  • Punctate histone marks (e.g., H3K4me1) that don't match up with DNase/FAIRE sites.

Section 3. What is the higher order organization of chromosomes?

PI Leads: John Stam, Job Dekker

Section 4. What patterns of evolutionary constraint and genetic variation are associated with each of the above classes?

PI leads: Ewan Birney, Elliott Margulies.

Section 5. Is there a transcriptional regulatory code in the cell and how is it organized into a larger network?

PI Leads: Mike Snyder, Rick Myers

Section 6. What are the similarities and differences in cell types with relation to all of the issues above?

PI Leads: Greg Crawford, Jim Kent

Section 7. How does ENCODE data impact our understanding of other human biology phenomena?

PI Leads: Ross Hardison