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Correlate P hosphorylation Sites to K inases by Conditional Random Fields --- CS 104 Project

Correlate P hosphorylation Sites to K inases by Conditional Random Fields --- CS 104 Project. Lu He, Tuobin W ang . Background and Problem. Problem:

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Correlate P hosphorylation Sites to K inases by Conditional Random Fields --- CS 104 Project

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  1. Correlate Phosphorylation Sites toKinasesby Conditional Random Fields --- CS 104 Project Lu He, TuobinWang

  2. Background and Problem Problem: Given groups of kinases and groups of phosphorylatedproteins, our problem focuses on correlating phosphorylated proteins with corresponding kinases.

  3. Challenges and Methods Challenges: Dependency of amino acids around Phosphorylation site {Y, S, T} !! Method:Conditional Random Fields vs.SVM, HMM

  4. Data Set and Evaluation Phospho.ELM website: In vivo protein-phosphorylationsites that are linked to at least one kinase Evaluation: • 5-fold cross validation • TP, TN, FP, FN

  5. Timeline • Feb 8: Project proposal; • Feb 9 - Feb 14: Collect data, learning relevant knowledge. • Feb 15 - Feb 22: Coding and solving encountered problems. • Feb 23 - Mar 2: Finish coding and experiments; • Mar 3 - Mar 7: Analyzing and discussing the results of experiments. Finishing the final write-up and poster.

  6. Thanks !

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