1. 1 Transcript isoform entropy: proof of extensive disruption in cancerous tissues William Ritchie July 20 2007

2. 2 Disruption of Alternative splicing in trans or cis elements CIS TRANS Creation of a new isoform Disruption of expression levels

3. 3 Disruption of Alternative splicing leads to 2 types of deregulation (p53, Rac1) 14 28 3 14 28 3 1 2 3 4 8 14 28 32 (Bcl-xs/xl) __

4. 4 14 28 3 14 28 3 1 2 3 4 8 14 28 32 __ 16 17 16 Expression pattern loss Disruption of Alternative splicing may lead to a third type of deregulation

5. 5 Entropy: Definition Measure of disorder in a given system Information theory: uncertainety of an outcome Shannon’s entropy: Given a variable X with probabilities P(xi) for a discrete set of events x1,…,xk

6. 6 Using shannon’s entropy to detect isoform deregulation 14 28 3 16 17 16 1.5 bits 3 bits = 2 1 2 3

7. 7 Using shannon’s entropy to detect isoform deregulation Alternative splicing, polyadenylation (EBI, ATD), initiation (fantom3) Consider events with 10 transcripts, 3 libraries Consider events found in disease and normal tissue

8. 8 Entropy of alternative isoforms

9. 9 Correlation Entropy & proliferation ? Link between cellular proliferation and entropy ? Determining proliferation levels is tricky

10. 10 Determining a proliferation index Determining a proliferation signature w/ microarrays Stuart et al., 2003 Clusters of functionally related genes

11. 11 Correlation Entropy & proliferation !

12. 12 Functions affected by Entropy G.O. TermP-value Enriched terms cellular physiological process1.55E-10 RNA metabolism2.87E-10 RNA processing3.48E-08 mRNA metabolism4.74E-08 RNA splicing, via transesterification reactions8.89E-08 RNA splicing with bulged adenosine as nucleophile8.89E-08 nuclear mRNA splicing, via spliceosome8.89E-08 primary metabolism1.35E-07 RNA splicing1.69E-07 414 genes Splicing machinery itself is subject to high Entropy

13. 13 Splice factors subject to higher AS rates (72% - 5.4 Vs 62% - 3.4) Enrichment in GO “Splicing” terms No significant enrichment in GO terms The enrichment in “splicing” terms is due to high levels of entropy

14. 14 Conclusion Shannon’s entropy detects a loss of information in alternative splicing in cancerous tissues (not spurious isoforms) High entropy gains correlate with high levels of proliferation Splicing machinery itself might be the starting point of this deregulation

15. 15 A theory of generalized deregulation

16. 16 Thanks Daniel Gautheret Sam Granjeaud Denis Puthier Fafa Lopez Mr. Hide