Datamining:
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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?.

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Limsoon Wong KRDL

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Limsoon wong krdl

Datamining:

Turning Biological Data

into Gold

Limsoon Wong

KRDL


What is datamining

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 datamining1

What is Datamining?

Question: Can you explain how?


What are the benefits

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


The datamining process

The Datamining Process


Epitope prediction

Epitope Prediction

TRAP-559AA

MNHLGNVKYLVIVFLIFFDLFLVNGRDVQNNIVDEIKYSE

EVCNDQVDLYLLMDCSGSIRRHNWVNHAVPLAMKLIQQLN

LNDNAIHLYVNVFSNNAKEIIRLHSDASKNKEKALIIIRS

LLSTNLPYGRTNLTDALLQVRKHLNDRINRENANQLVVIL

TDGIPDSIQDSLKESRKLSDRGVKIAVFGIGQGINVAFNR

FLVGCHPSDGKCNLYADSAWENVKNVIGPFMKAVCVEVEK

TASCGVWDEWSPCSVTCGKGTRSRKREILHEGCTSEIQEQ

CEEERCPPKWEPLDVPDEPEDDQPRPRGDNSSVQKPEENI

IDNNPQEPSPNPEEGKDENPNGFDLDENPENPPNPDIPEQ

KPNIPEDSEKEVPSDVPKNPEDDREENFDIPKKPENKHDN

QNNLPNDKSDRNIPYSPLPPKVLDNERKQSDPQSQDNNGN

RHVPNSEDRETRPHGRNNENRSYNRKYNDTPKHPEREEHE

KPDNNKKKGESDNKYKIAGGIAGGLALLACAGLAYKFVVP

GAATPYAGEPAPFDETLGEEDKDLDEPEQFRLPEENEWN


Epitope prediction results

1 66 100

Epitope Prediction Results

  • Prediction by our ANN model for HLA-A11

    • 29 predictions

    • 22 epitopes

    • 76% specificity

  • Prediction by BIMAS matrix for HLA-A*1101

Number of experimental binders

19 (52.8%) 5 (13.9%) 12 (33.3%)

Rank by BIMAS


Gene expression analysis

Gene Expression Analysis

  • Clustering gene expression profiles

  • Classifying gene expression profiles

    • find stable differentially expressed genes


Gene expression analysis results

Gene Expression Analysis Results

  • The Discovery System

    • Correlation test

    • Voter selection

    • Class prediction


Protein interaction extraction

WEB

Protein Interaction Extraction

“What are the protein-protein interaction pathways

from the latest reported discoveries?”


Protein interaction extraction results

Protein Interaction Extraction Results

  • Rule-based system for processing free texts in scientific abstracts

  • Specialized in

    • extracting protein names

    • extracting protein-protein interactions

Jak1


Transcription start prediction

Transcription Start Prediction


Transcription start prediction results

Transcription Start Prediction Results


Medical record analysis

Medical Record Analysis

  • Looking for patterns that are

    • valid

    • novel

    • useful

    • understandable


Medical record analysis results

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


Under the hood

Under the Hood

  • Artificial neural network

  • Neighbourhood analysis

  • Non-linear analysis

  • Template matching

  • Emerging pattern

  • Hidden markov models

  • Bayesian inference

  • Decision tree induction

  • ...


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

Behind the Scene


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