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Transcript 
Analysis of
the Gene Expression Data
with 4ft-Miner
07.10.2005
Emilia Ylirinne
Tampere University of Technology
Finland
Outline
•
•
•
•
•
GUHA method in brief
4ft-quantifiers and 4ft-Miner
Data Mining process
Results
Conclusions
GUHA Method
• General Unary Hypotheses Automaton
• Introduced in 1960´s by Hájek
• Exploratory data analysis based on
association rules:

Boolean attributes  and  are associated in the
sense of 4ft-quantifier .
GUHA Method
• Also conditional association rules
  /
• Four fold table corresponding to   
M



a
b

c
d
Examples of 4ft-quantifiers
Founded implication (FUI) =>p, Base, where
0<p≤1 and Base>0 satisfies condition:
a/(a+b)≥p and a≥Base
M



a
b

c
d
Examples of 4ft-quantifiers
Double founded implication (DFUI) <=>p, Base,
where 0<p≤1 and Base>0 satisfies condition:
a/(a+b+c)≥p and a≥Base
M



a
b

c
d
4ft-Miner
• A part of academic system LISp-Miner
• http://lispminer.vse.cz/
• Mines for both association and conditional
association rules
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
Data Mining Tasks
4ft-quantifier
Input value for p
Type of rule
Input value for Base
Length of antecedent
Length of succedent
Number of output rules
Time of solution
Task 1
DFUI
0.8
ordinary
10
1
1
2
3 secs
Task 2
DFUI
1.0
conditional
10
1…5
1
73
19 secs
Results
• Example of Task 1
- AAGACAGTGG <=>85%,11 AAGGAGATGG
Suc
 Suc
Ant
11
0
 Ant
2
61
Results
• Example of task 2
GGCAAGAAGA TCACAAGCAA
TGTGCTAAAT TGTGTTGAGA
<=>100%,10 GCTTTTAAGG / TACAAGAGGA
Suc
 Suc
Ant
10
0
Ant
0
3
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
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