GMT files and Network are Related

1. GMT files and Network are Related Content of GMT files can be converted to networks based on co-occurrence

2. A synthetic example Neil R. Clark, Ruth Dannenfelser, Christopher M. Tan, Michael E. Komosinski, and AviMa'ayan. Sets2Networks: network inference from repeated observations of sets. BMC Systems Biology. In press Neil Clark

3. Inference live!

4. Analytic Approximation • When applying this approach to real data typically there are many nodes • Sample space of networks can be very large -> computationally demanding • We developed a simple analytical approximation which mimics the action of the algorithm. nij,kis the size of the lines to which both vertices vi and vj belong

5. Validation of PPI Predictions Network inferred from 3290 IP/MS experiments next to known PPI network made from 20 online PPI databases

6. ROC Curves to Evaluate PPI Predictions

7. Validation of Predictions with CORUM Database of Protein Complexes http://mips.helmholtz-muenchen.de/genre/proj/corum

8. Inference of Statistical Relationships in the AERS Database • Adverse Event Reporting System (AERS) database contains records of .... Patient ID 1 Drug 1, Drug 2, ... Side-effect 1, Side-effect 2, ... Patient ID 2 Dug 3, Drug 4, ... Side-effect 3, Side effect 4, ... ……

9. AERS Large-scale Adjacency Matrix

10. AERS subnetwork Drugs Adverse Events

11. Mount Sinai Collaboration Network