Agenda:

1. Final data standard for Hi-C. Submitted to steering committee and waiting for reply
2. Discussion of ChIA-PET experimental and data standards (Yi-jun Ruan and group).

Detailed protocols will be published in Nature Protocols (Li et al.), mapping and visualization procedures will be published in Genome Research (Szataj et al.)

First level of ChIA-PET data consists of binding peaks similar to ChIP, then PET clusters are constructed from those binding peaks.

Non-specific ligation data should be distinguished from actual interactions. A two-linker system has been used to add different linkers within different aliquots so that non-specific binding will always generate homo-dimer PETs and a background model (vs genomic distance between the interacting components) can be established. Inter-chromosomal PETs appear to be mostly hetero-dimers.

Interactions may have different features for different factors. Use a number of connection loops to detect actual contact domains.