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APT: An Automated Probe Tracker From Gene Expression Data.

Gautam Kumar, Rajnish Kumar, Manoj Kumar Pal

    IEEE/ACM Transactions on Computational Biology and Bioinformatics
    |December 12, 2019
    PubMed
    Summary
    This summary is machine-generated.

    This study introduces APT, an automatic probe-set selection tool that outperforms ArrayMining and GEO2R in identifying diagnostic probes for diseases. APT achieves higher success rates and improved sensitivity and specificity in probe detection.

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    Area of Science:

    • Bioinformatics
    • Computational Biology
    • Genomics

    Background:

    • Semi-automatic tools like ArrayMining and GEO2R are popular for detecting diagnostic probes but have limitations.
    • Existing tools rank probes by statistical significance, requiring user input or offering limited gene outputs.
    • This necessitates a more automated and accurate method for diagnostic probe selection.

    Purpose of the Study:

    • To develop a fully automatic probe-set selection method.
    • To improve the accuracy and efficiency of identifying diagnostic probes for pathophysiological conditions.
    • To compare the performance of the new method against existing popular tools.

    Main Methods:

    • Developed an automatic probe-set selection tool named APT.
    • Utilized a voting system combining outputs from t-Test, Mann-Whitney Test, and Empirical Bayes Moderated t-test.
    • Demonstrated that statistical method parameters can be mathematically linked to group fisher's discriminant ratio.

    Main Results:

    • APT achieved an 88.97% success rate in identifying reported probes, surpassing ArrayMining (80.40%) and GEO2R (87.60%).
    • The new method showed superior performance in sensitivity and specificity across 10-fold cross-validation and 5 new test cases.
    • APT offers a fully automatic approach, eliminating the need for manual probe number input.

    Conclusions:

    • APT represents a significant advancement in automatic diagnostic probe selection.
    • The method provides higher accuracy, sensitivity, and specificity compared to current popular tools.
    • APT offers a more efficient and reliable approach for identifying disease-related diagnostic probes.