1. How Dead Are the Dead Zones? (16/Sep/2010) Bob Harris Penn State Center for Comparative Genomics and Bioinformatics rsharris@bx.psu.edu

2. How Dead are the Dead Zones? • Looking at ChromHMM and Segway (short-range) segmentations, vs. certain annotated “features” • Nothing fancy; just a simple base counting process

3. Most or much of genome is assigned to dead zone classes. ChromHMM assigns 76% of the genome to dead zones. Segway assigns 42% Dead Zone Classes Promoter Classes Enhancer Classes Other Classes Portion of Genome (full class names given on slide 11)

4. Mappable Bases • Mappability derived from signal tracks • 152 signal tracks are the inputs to the segmentation • What is considered mappable for a given signal track is dependent on the tag extension length for that track • I’m using the union of mappable intervals over all the tracks • A base is counted as mappable if it appears in an interval in any track • Not to be confused with the “mapability track” (wgEncodeMapability)

5. Not dead simply as an artifact of not mapping. Dead Zone Promoter Enhancer Other Mappable Bases

6. Repeats for ChromHMM dead zones Are comparable to other classes. Ditto for Segway’s DF and DFC. Dead Zone Promoter Enhancer Other In Repeats

7. Dead zones contain interesting things like genes. Dead Zone Promoter Enhancer Other In Genes

8. Exon content is low for dead zones. Dead Zone Promoter Enhancer Other In Exons

9. Dead zones are on the Low end for GC content. CpG Ratio is low, but comparable to other non-promoter classes. Dead Zone Promoter Enhancer Other GC Content, CpG Ratio

10. Related Work • Also looked/looking at • SNPs • Sequence composition • More plots and spreadsheet at http://www.bx.psu.edu/~rsharris/encode/index.html#dead_zones • Integration Vignette B02, in progress http://encodewiki.ucsc.edu/EncodeDCC/index.php/Integration_Vignette_B02

11. Data Sources • ChromHMM K562 kitchensink • http://www.broadinstitute.org/~jernst/K562_max_25state_49mark.bed.gz • Lifted over to hg19 • Segway short-range K562 kitchensink • http://noble.gs.washington.edu/~stasis/public/2010/segtools/round5b/kitchensink/k562/round5b.kitchensink.k562.1224-0218a.stws1.bed.gz • Lifted over to hg19 • Signal tracks • http://noble.gs.washington.edu/~stasis/public/2010/encode/round6/rawSignal/ • 152 *.bedGraph.gz files

12. Class Names ChromHmm Segway