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Analysis of the Gene Expression Data with 4ft-Miner

Analysis of the Gene Expression Data with 4ft-Miner. Emilia Ylirinne Tampere University of Technology Finland. 07.10.2005. Outline. GUHA method in brief 4ft-quantifiers and 4ft-Miner Data Mining process Results Conclusions. GUHA Method. General Unary Hypotheses Automaton

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Analysis of the Gene Expression Data with 4ft-Miner

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  1. Analysis of the Gene Expression Data with 4ft-Miner Emilia Ylirinne Tampere University of Technology Finland 07.10.2005

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

  3. 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 .

  4. GUHA Method • Also conditional association rules   /    • Four fold table corresponding to

  5. 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

  6. 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

  7. 4ft-Miner • A part of academic system LISp-Miner • http://lispminer.vse.cz/ • Mines for both association and conditional association rules

  8. 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

  9. Data Mining Tasks

  10. Results • Example of Task 1 - AAGACAGTGG <=>85%,11 AAGGAGATGG

  11. Results • Example of task 2 GGCAAGAAGA TCACAAGCAA TGTGCTAAAT TGTGTTGAGA <=>100%,10 GCTTTTAAGG / TACAAGAGGA

  12. 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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