Limsoon Wong KRDL
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Datamining: Turning Biological Data into Gold. Limsoon Wong KRDL. Jonathan’s blocks. Jessica’s blocks. Whose block is this?. What is Datamining?. Jonathan’s rules: Blue or Circle Jessica’s rules: All the rest. What is Datamining?. Question: Can you explain how?. - PowerPoint PPT Presentation
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Show & Tell
Limsoon WongKRDL
Datamining: Turning Biological Data
into Gold
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Jonathan’s rules : Blue or CircleJessica’s rules : All the rest
What is Datamining?
Whose block is this?
Jonathan’s blocks
Jessica’s blocks
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What is Datamining?
Question: Can you explain how?
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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
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The Datamining Process
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Epitope Prediction
TRAP-559AAMNHLGNVKYLVIVFLIFFDLFLVNGRDVQNNIVDEIKYSEEVCNDQVDLYLLMDCSGSIRRHNWVNHAVPLAMKLIQQLNLNDNAIHLYVNVFSNNAKEIIRLHSDASKNKEKALIIIRSLLSTNLPYGRTNLTDALLQVRKHLNDRINRENANQLVVILTDGIPDSIQDSLKESRKLSDRGVKIAVFGIGQGINVAFNRFLVGCHPSDGKCNLYADSAWENVKNVIGPFMKAVCVEVEKTASCGVWDEWSPCSVTCGKGTRSRKREILHEGCTSEIQEQCEEERCPPKWEPLDVPDEPEDDQPRPRGDNSSVQKPEENIIDNNPQEPSPNPEEGKDENPNGFDLDENPENPPNPDIPEQKPNIPEDSEKEVPSDVPKNPEDDREENFDIPKKPENKHDNQNNLPNDKSDRNIPYSPLPPKVLDNERKQSDPQSQDNNGNRHVPNSEDRETRPHGRNNENRSYNRKYNDTPKHPEREEHEKPDNNKKKGESDNKYKIAGGIAGGLALLACAGLAYKFVVPGAATPYAGEPAPFDETLGEEDKDLDEPEQFRLPEENEWN
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Epitope Prediction Results
Prediction by our ANN model for HLA-A11 29 predictions 22 epitopes 76% specificity
1 66 100Rank by BIMAS
Number of experimental binders 19 (52.8%) 5 (13.9%) 12 (33.3%)
Prediction by BIMAS matrix for HLA-A*1101
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Gene Expression Analysis
Clustering gene expression profiles Classifying gene expression profiles
find stable differentially expressed genes
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Gene Expression Analysis Results
The Discovery System• Correlation test• Voter selection• Class prediction
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Protein Interaction Extraction“What are the protein-protein interaction pathways
from the latest reported discoveries?”
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Protein Interaction Extraction Results
Rule-based system for processing free texts in scientific abstracts
Specialized in extracting
protein names extracting
protein-protein interactions
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Transcription Start Prediction
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Transcription Start Prediction Results
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Medical Record Analysis
Looking for patterns that are valid novel useful understandable
age sex chol ecg heart sick49 M 266 Hyp 171 N64 M 211 Norm 144 N58 F 283 Hyp 162 N58 M 284 Hyp 160 Y58 M 224 Abn 173 Y
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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
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Under the Hood
Artificial neural network Neighbourhood analysis Non-linear analysis Template matching Emerging pattern Hidden markov models Bayesian inference Decision tree induction ...
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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
