Correlate Phosphorylation Sites to Kinases by Conditional Random Fields --- CS 104 Project Lu He, Tuobin Wang.

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Presentation transcript:

Correlate Phosphorylation Sites to Kinases by Conditional Random Fields --- CS 104 Project Lu He, Tuobin Wang

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

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

Data Set and Evaluation Phospho.ELM website: In vivo protein-phosphorylation sites that are linked to at least one kinase Evaluation: 1.5-fold cross validation 2. TP, TN, FP, FN

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.

Thanks !