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Functional Interpretation of Gene Sets: Semantic-Based Clustering of Gene Ontology Terms on the BioTest Platform

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Man-Machine Interactions 5 (ICMMI 2017)

Part of the book series: Advances in Intelligent Systems and Computing ((AISC,volume 659))

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Abstract

Modern high-throughput technologies based on genome, transcriptome or proteome profiling provide abundance of data that needs to be processed, analyzed and, finally, interpreted. Effective and efficient analysis of data coming from molecular profiling is crucial for a detailed diagnosis, prognosis, and prediction of therapy outcome. Meaningful conclusions can be drawn only by the use of sophisticated methods for biomedical and molecular data analysis and interpretation. In this study we present the approach for functional interpretation of gene or protein sets with clusters of Gene Ontology terms. We analyze transcription profiles of human cell line K562 and we show that clustering allows grouping functionally related GO terms and therefore obtaining more concise and comprehensive description. By applying cluster-specific data aggregation tool we are able to calculate statistics for the individual clusters of GO terms and compare the number of differentially expressed genes between two sample pairs. The presented tool is implemented as a part of annotation module available on the BioTest remote platform for hypothesis testing and analysis of biomedical data.

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Acknowledgements

This work was partially supported by The National Centre for Research and Development grant No PBS3/B3/32/2015 and was carried out in part within the statutory research project of the Institute of Informatics (RAU2). Presented system was developed and installed on the infrastructure of the Ziemowit computer cluster (www.ziemowit.hpc.polsl.pl) in the Laboratory of Bioinformatics and Computational Biology, The Biotechnology, Bioengineering and Bioinformatics Centre Silesian BIO-FARMA, created in the POIG.02.01.00-00-166/08 and expanded in the POIG.02.03.01-00-040/13 projects.

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Authors and Affiliations

  1. Institute of Informatics, Silesian University of Technology, ul. Akademicka 16, 44-100, Gliwice, Poland

    Aleksandra Gruca

  2. Institute of Automatic Control, Silesian University of Technology, ul. Akademicka 16, 44-100, Gliwice, Poland

    Roman Jaksik & Krzysztof Psiuk-Maksymowicz

Authors
  1. Aleksandra Gruca
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  2. Roman Jaksik
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  3. Krzysztof Psiuk-Maksymowicz
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Corresponding author

Correspondence to Aleksandra Gruca .

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Editors and Affiliations

  1. Institute of Informatics, Silesian University of Technology, Gliwice, Poland

    Aleksandra Gruca

  2. Institute of Informatics, Silesian University of Technology, Gliwice, Poland

    Tadeusz Czachórski

  3. Institute of Informatics, Silesian University of Technology, Gliwice, Poland

    Katarzyna Harezlak

  4. Institute of Informatics, Silesian University of Technology, Gliwice, Poland

    Stanisław Kozielski

  5. Institute of Informatics, Silesian University of Technology, Gliwice, Poland

    Agnieszka Piotrowska

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Gruca, A., Jaksik, R., Psiuk-Maksymowicz, K. (2018). Functional Interpretation of Gene Sets: Semantic-Based Clustering of Gene Ontology Terms on the BioTest Platform. In: Gruca, A., Czachórski, T., Harezlak, K., Kozielski, S., Piotrowska, A. (eds) Man-Machine Interactions 5. ICMMI 2017. Advances in Intelligent Systems and Computing, vol 659. Springer, Cham. https://doi.org/10.1007/978-3-319-67792-7_13

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  • DOI: https://doi.org/10.1007/978-3-319-67792-7_13

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