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

  • Aleksandra Gruca
  • Roman Jaksik
  • Krzysztof Psiuk-Maksymowicz
Conference paper
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 659)

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.

Keywords

Gene Ontology Clustering Semantic similarity BioTest platform DNA microarrays Molecular profiling Functional interpretation 

Notes

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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Copyright information

© Springer International Publishing AG 2018

Authors and Affiliations

  • Aleksandra Gruca
    • 1
  • Roman Jaksik
    • 2
  • Krzysztof Psiuk-Maksymowicz
    • 2
  1. 1.Institute of InformaticsSilesian University of TechnologyGliwicePoland
  2. 2.Institute of Automatic ControlSilesian University of TechnologyGliwicePoland

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