Mammals Meeting

1. Mammals Meeting 31-March-2009 Or Zuk

2. Motifs: Compare ‘Monkey-like’ Instances to Pouya’s instances Run Genome-wide discovery (using Xie’s ctcf paper method) Motif intersection with curated sets

3. Motifs: We see a good agreement for a single motif (nrsf). Not yet systematically evaluated on a list of motifs 2. Run Genome-wide discovery: Code is ready. Plan is to run on many clades and for each clades get the number of ‘significant’ motifs. Then plot this number vs. branch length to get a ‘saturation curve’ 3. Curated sets – doesn’t look promising so far (we don’t get good enrichments for sets of genes differentially expressed)

4. Chr19 Observation: Siphy overcalls chr19 (compared to phastcons) Qu: What is the cause? Some flaws/biases in the method? Real biology?

5. Chr19 Problem: Neutral models from PAML (per-chromosome)For chr19 – neutral model has a long branch-length.Causes many elements (both AR and genomic) to have highpi-lods scores and appear constraint. Method: Compute pi-lods scores for each element in the genome where background model is per-chromosome Determine a single cutoff (based on FDR) on scores for all the genome

8. Chr19 Since both AR and genomic have highpi-lods scores on chr19, using chr19-cutoff still don’t overcall them Solution: New Method: Compute pi-lods scores for each element in the genome where background model is per-chromosome Determine a different cutoff (based on FDR) for each chromosome on scores