Show & Tell Limsoon Wong KRDL Datamining: Turning Biological Data into Gold

Show & Tell Jonathan’s rules: Blue or Circle Jessica’s rules: All the rest What is Datamining? Whose block is this? Jonathan’s blocks Jessica’s blocks

Show & Tell What is Datamining? Question: Can you explain how?

Show & Tell What are the Benefits?  To the patient:  Better drug, better treatment  To the pharma:  Save time, save cost, make more $  To the scientist:  Better science

Show & Tell The Datamining Process

Show & Tell Epitope Prediction TRAP-559AA MNHLGNVKYLVIVFLIFFDLFLVNGRDVQNNIVDEIKYSE EVCNDQVDLYLLMDCSGSIRRHNWVNHAVPLAMKLIQQLN LNDNAIHLYVNVFSNNAKEIIRLHSDASKNKEKALIIIRS LLSTNLPYGRTNLTDALLQVRKHLNDRINRENANQLVVIL TDGIPDSIQDSLKESRKLSDRGVKIAVFGIGQGINVAFNR FLVGCHPSDGKCNLYADSAWENVKNVIGPFMKAVCVEVEK TASCGVWDEWSPCSVTCGKGTRSRKREILHEGCTSEIQEQ CEEERCPPKWEPLDVPDEPEDDQPRPRGDNSSVQKPEENI IDNNPQEPSPNPEEGKDENPNGFDLDENPENPPNPDIPEQ KPNIPEDSEKEVPSDVPKNPEDDREENFDIPKKPENKHDN QNNLPNDKSDRNIPYSPLPPKVLDNERKQSDPQSQDNNGN RHVPNSEDRETRPHGRNNENRSYNRKYNDTPKHPEREEHE KPDNNKKKGESDNKYKIAGGIAGGLALLACAGLAYKFVVP GAATPYAGEPAPFDETLGEEDKDLDEPEQFRLPEENEWN

Show & Tell Epitope Prediction Results  Prediction by our ANN model for HLA-A11  29 predictions  22 epitopes  76% specificity Rank by BIMAS Number of experimental binders 19 (52.8%) 5 (13.9%) 12 (33.3%)  Prediction by BIMAS matrix for HLA-A*1101

Show & Tell Gene Expression Analysis  Clustering gene expression profiles  Classifying gene expression profiles  find stable differentially expressed genes

Show & Tell Gene Expression Analysis Results The Discovery System Correlation test Voter selection Class prediction

Show & Tell Protein Interaction Extraction “What are the protein-protein interaction pathways from the latest reported discoveries?”

Show & Tell Protein Interaction Extraction Results  Rule-based system for processing free texts in scientific abstracts  Specialized in  extracting protein names  extracting protein-protein interactions

Show & Tell Transcription Start Prediction

Show & Tell Transcription Start Prediction Results

Show & Tell Medical Record Analysis  Looking for patterns that are  valid  novel  useful  understandable

Show & Tell Medical Record Analysis Results  DeEPs, a novel “emerging pattern’’ method  Beats C4.5, CBA, LB, NB, TAN in 21 out of 32 UCI benchmarks  Works for gene expressions

Show & Tell Under the Hood  Artificial neural network  Neighbourhood analysis  Non-linear analysis  Template matching  Emerging pattern  Hidden markov models  Bayesian inference  Decision tree induction ...

Show & Tell Behind the Scene  Epitope Prediction  Vladimir Brusic  Judice Koh  Seah Seng Hong  Zhang Guanglan  Yu Kun  Transcription Start Prediction  Vladimir Bajic  Seah Seng Hong  Gene Expression Analysis  Zhang Louxin  Zhang Zhuo  Zhu Song  Medical Records  Li Jinyan  Protein Interaction Extraction  Ng See Kiong  Zhang Zhuo