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Please go to the ENCODE3 wiki for current information.

Result Vignettes

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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.


Structure Summary

Outline Paper Structure.
Detailed Paper Structure.

Section 1. Description of datasets, quality and basics characteristics

Previously called Description of Data: "Just the facts", Individual Characterisation ==

PI Leads: Ian Dunham

Section 1.1. Methodology, Standards, QC

Section 1.2. RNA

PI Leads: Tom Gingeras, Barbara Wold, Roderic Guigo

  1. Other Analyses that need to be assigned to Vignettes
    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 1.3. TFs

Section 1.4. Open Chromatin

Section 1.5. Chromatin Modifications

Section 1.6. Methylation

Section 1.7. Other

Section 1.8. Constraint: What patterns of evolutionary constraint are associated with ENCODE elements?

PI leads: Elliott Margulies.

Section1.9. Human Variation: What patterns of genetic variation are associated with ENCODE elements?

PI leads: Ewan Birney.

Section 2. Chromosomal features of Protein coding genes: Features of Promoters, enhancers, genes, 3’ ends, &c.

Section 2.1. Supervised approaches.

Section 2.2. Segmentation.

Section 2.3. Predicting new regions.

Section 2.4. Validation (enhancer validation).

Section 3. Chromosomal features of Noncoding genes.

Section 3.1. Supervised approaches.

Section 3.2. Segmentation.

Section 3.3. Predicting new regions.

Section 3.4. Validation (enhancer validation).

Section 3.5. Similarities and differences with protein coding.

Section 4. Relationship of chromatin to gene expression of coding & non-coding genes.

PI Leads: Zhiping Weng

Section 5. Relationship of TFs to chromatin and gene expression.

Section 6. Co-association of TFs to one another and chromatin and gene expression (i.e. regulatory code).

Section 7 Networks of elements

Section 8. Long-range and large-scale chromosomal interactions.

Section 9. Relationship of chromosomal features to variation and disease.

Section 9.1. ENCODE and Disease.

PI Leads: Ross Hardison

Section 10. What are the similarities and differences in cell types with relation to all of the issues above? (doesn't have anywhere specific to go under Mike's scheme)

PI Leads: Greg Crawford, Jim Kent, Ian Dunham