probabilistic ranking

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Integration of Full-Coverage Probabilistic Functional Networks with Relevance to Specific Biological Processes James, K., Wipat, A. & Hallinan, J. School of Computing Science, Newcastle University Data Integration in the Life Sciences 2009

Integrated functional networks ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Dataset bias ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Bias in HTP datasets From Myers and Troyanskaya, Bioinformatics 2007.

Bias & Relevance ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Relevance scoring ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Data sets ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Choice of D value ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Classifier output classification threshold positives negatives TP TN FP FN Increasing specificity Increasing sensitivity

Ranking 3 3 2 8 4.2253 8 1 1 1 7 4.4641 7 7 8 5 6 4.5212 6 5 5 7 5 4.9335 5 4 4 3 4 5.0842 4 2 2 6 3 5.7040 3 8 7 8 2 5.7054 2 6 6 4 1 6.6937 1 A&T Rank Telomere Rank Ageing Rank Conf. Rank Conf. Score Dataset

Evaluation - Clustering ,[object Object],[object Object]

Results 38.35 33.33 29.83 24.67 523 R 37.98 33.80 29.55 24.26 573 C C 8.59 8.90 7.73 6.50 508 R 6.53 7.02 6.14 5.06 573 C T 36.92 31.75 27.73 22.37 523 R 35.19 28.86 26.14 21.29 573 C A >4 nodes >3 nodes >2 nodes % COI Clusters Bias Net

Conclusions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Future work ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Acknowledgements ,[object Object],[object Object],[object Object],[object Object],[object Object]

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probabilistic ranking

1. Integration of Full-Coverage Probabilistic Functional Networks with Relevance to Specific Biological Processes James, K., Wipat, A. & Hallinan, J. School of Computing Science, Newcastle University Data Integration in the Life Sciences 2009

4. Bias in HTP datasets From Myers and Troyanskaya, Bioinformatics 2007.

7. Network integration

8. Network integration

9. Effect of D value

10.

11. Relevance scoring

12.

13.

14. Classifier output classification threshold positives negatives TP TN FP FN Increasing specificity Increasing sensitivity

15. ROC Curves

16. D value

17. D value

18. Ranking 3 3 2 8 4.2253 8 1 1 1 7 4.4641 7 7 8 5 6 4.5212 6 5 5 7 5 4.9335 5 4 4 3 4 5.0842 4 2 2 6 3 5.7040 3 8 7 8 2 5.7054 2 6 6 4 1 6.6937 1 A&T Rank Telomere Rank Ageing Rank Conf. Rank Conf. Score Dataset

19. Results

20.

21. Results 38.35 33.33 29.83 24.67 523 R 37.98 33.80 29.55 24.26 573 C C 8.59 8.90 7.73 6.50 508 R 6.53 7.02 6.14 5.06 573 C T 36.92 31.75 27.73 22.37 523 R 35.19 28.86 26.14 21.29 573 C A >4 nodes >3 nodes >2 nodes % COI Clusters Bias Net

22. Cluster annotation

23.

24.

25.