1. 1 Q1-Q3 results Roderic Guigó' s lab April 11 th 2007 conference call

2. Pool-unspecific RACEfrags in Q3

3. 3 Pool unspecific unique RF (USPP-filtered) Most pool unspecific unique RF are: Q1: internal exonic (72%) Q2: internal exonic (87%) Q3: external (91%) (of which 63% are exonic) 20 unique RF are in more than 4 pools

4. 4 Q3 Q1 Q2 Q1-Q3: Number of pools a unique RF appears in (unfiltered/filtered)

5. 5 Pool-unspecific RFs in Q3 Possibly due to... 1 - cross-hybridization? is there a correlation between number of pools a RF is found in and the number of non-unique probes it overlaps? no by the way 135,380 / 2,191,331 (6%) of probes from chr21/22 chip have multiple perfect matches in genome

6. 6 Pool-unspecific RFs in Q3 Possibly due to... 2 - high GC content? -> Answer: NO!

7. 7 Pool-unspecific RFs in Q3 Possibly due to... 3 - mis-priming on unknown transcripts of chr21 or chr22 (missed by the simulator)? 4 - genuine chimeric transcripts? 5 - Pooling errors the same gene is present in >1 pool because it has 2 different identifiers (UCSC known genes / RefSeq nomenclature discrepancy we found a few cases like this, not sure yet how widespread it is (systematic survey to come)

8. 8 RF position when compared to genes and exons

9. 9 Q1-Q2-Q3: Projected filtered RF distribution (internal=overlap target gene ; projection done by pool) 39% internal 47% exonic 53% intronic 61% external 71% genic 79% exonic 22% overlap most 5' ex. of tr. 21% intronic 29% intergenic 86% internal 88% exonic 12% intronic 14% external 78% genic 88% exonic 47% overlap most 5' ex. of tr. 12% intronic 22% intergenic 21% internal 47% exonic 53% intronic 79% external 78% genic 69% exonic 23% overlap most 5' ex. of tr. 31% intronic 22% intergenic Q1Q3Q2  chimeric transcripts?

10. 10 Why are Q3 RF mostly external (79%) ? Existence of a systematic swap between certain pairs of pools? For each RF we have computed the overlap with all genes of Q3 and then compared: RF pool with RF overlapping gene pool

11. 11 RF overlapping gene pool

12. 12 Q3 RF compared to Q3 genes  Q3 RF are more overlapping genes of their pool than genes of other pools (no clear pool swap)

13. 13 RF lengths

14. 14 Filtered RF length distribution

15. 15 Q1 filtered RF length distribution

16. 16 Q2 filtered RF length distribution

17. 17 Q3 filtered RF length distribution