2012-01-31
These are the three papers to be used as the datasets:
- Blow, M. J. et al. ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet 42, 806-810 (2010).
- He, A., Kong, S. W., Ma, Q. & Pu, W. T. Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart. Proceedings of the National Academy of Sciences 108, 5632 -5637 (2011).
- May, D. et al. Large-scale discovery of enhancers from human heart tissue. Nat Genet 44, 89-93 (2012).
The idea is to go with one dataset from these, download the ChiP-Seq data, turn the coordinates into human coordinates, convert these coordinates into sequences, and then run tfSearch using these sequences as the training set.
2012-01-25
First objective: reproduce results from previous studies
- Gather heart enhancer data:
- 1 study in mouse plus 1 follow up study by the same group
- 2 cell line studies
- 77 enhancers (from Narlikar 2010 Genome Research paper)
- Get TFs contributing to each dataset, compare and contrast results (from multiple methods?)
Other tasks:
- Document process of getting oriented with group resources on the wiki
- Start group CiteULike and move papers from np.dcode.org to CiteULike