Analysis of the Gene Expression Data with 4ft-Miner

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Analysis of the Gene Expression Data with
4ft-Miner

• Emilia Ylirinne
• Tampere University of Technology
• Finland

07.10.2005
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Outline

• GUHA method in brief
• 4ft-quantifiers and 4ft-Miner
• Data Mining process
• Results
• Conclusions

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GUHA Method

• General Unary Hypotheses Automaton
• Introduced in 1960s by Hájek
• Exploratory data analysis based on association
  rules

? ? ?
Boolean attributes ? and ? are associated in the
sense of 4ft-quantifier ?.
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GUHA Method

• Also conditional association rules

? ? ?/?
? ? ?

• Four fold table corresponding to

M ? ? ?
? a b
? ? c d
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Examples of 4ft-quantifiers

• Founded implication (FUI) gtp, Base, where
• 0ltp1 and Basegt0 satisfies condition
• a/(ab)p and aBase

M ? ? ?
? a b
? ? c d
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Examples of 4ft-quantifiers

• Double founded implication (DFUI) ltgtp, Base,
• where 0ltp1 and Basegt0 satisfies condition
• a/(abc)p and aBase

M ? ? ?
? a b
? ? c d
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4ft-Miner

• A part of academic system LISp-Miner
• http//lispminer.vse.cz/
• Mines for both association and conditional
  association rules

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Data Mining

• The small dataset 74 x 822 gene expression
  matrix was used
• We tried to find potential synexpression groups
  from data set
• Preprocessing based on work of Becquet et al
  (2002)
• With mid-range based approach we got matrix with
  boolean values 0 and 1

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Data Mining Tasks
Task 1 Task 2
4ft-quantifier DFUI DFUI
Input value for p 0.8 1.0
Type of rule ordinary conditional
Input value for Base 10 10
Length of antecedent 1 15
Length of succedent 1 1
Number of output rules 2 73
Time of solution 3 secs 19 secs
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Results

• Example of Task 1
• - AAGACAGTGG ltgt85,11 AAGGAGATGG

Suc ? Suc
Ant 11 0
? Ant 2 61
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Results

• Example of task 2
• GGCAAGAAGA ?TCACAAGCAA ?TGTGCTAAAT ?TGTGTTGAGA
• ltgt100,10 GCTTTTAAGG / TACAAGAGGA

Suc ? Suc
Ant 10 0
Ant 0 3
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Conclusions

• This study was very preliminary, but there are
  advantages, which 4ft-Miner can offer
• LISp-Miner contains 15 quantifiers
• We found numerous results
• Even pure equivalencies can be found with
  conditional association rules
• A biologist should be consulted of significance
  of these results