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A multi-objective based PSO approach for inferring pathway activity utilizing protein interactions

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Abstract

The pathway information of a given microarray gene expression data can be collected from the available public databases. Inferring the activity of a pathway is a crucial task in functional genomics. In general, the set of genes that are associated with a given pathway are equally considered for measuring goodness. But the contribution of each gene should be quantified differently. In the current study, we have quantified the degrees of relevance of different genes participating in a pathway by optimizing different goodness measures of pathway activity. Two popular goodness measures, namely t-score and z-score are modified to measure the goodness of the weighted gene vectors. Moreover, another goodness measure based on the protein-protein interaction scores of pairs of genes participated in a pathway is utilized as another objective function. All these measures are designed to handle the weighted importance of individual genes. The search capability of a multiobjective based particle swarm optimization (PSO) is utilized for searching the appropriate relevance vectors for different genes. The proposed approach is applied to five real-life gene expression datasets, and the performance is compared with eight existing feature selection methods. The comparative results demonstrate the superiority of the proposed particle swarm optimization based technique. The efficacy of the performance of the proposed method is validated by using a statistical significance test, and further, a biological significant test is done to justify the biological relevance of the extracted pathway-based gene markers.

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Acknowledgments

Pratik Dutta acknowledges Visvesvaraya PhD Scheme for Electronics and IT, an initiative of Ministry of Electronics and Information Technology (MeitY), Government of India for fellowship support. Dr. Sriparna Saha gratefully acknowledges the Young Faculty Research Fellowship (YFRF) Award, supported by Visvesvaraya PhD scheme for Electronics and IT, Ministry of Electronics and Information Technology (MeitY), Government of India, being implemented by Digital India Corporation (formerly Media Lab Asia) for carrying out this research.

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Authors and Affiliations

  1. Department of Computer Science and Engineering, Indian Institute of Technology Patna, Bihta, India

    Pratik Dutta & Sriparna Saha

  2. Department of Information Technology, Indian Institute of Engineering Science and Technology Shibpur, Howrah, India

    Sukanya Naskar

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  1. Pratik Dutta
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  2. Sriparna Saha
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  3. Sukanya Naskar
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Correspondence to Sriparna Saha.

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Dutta, P., Saha, S. & Naskar, S. A multi-objective based PSO approach for inferring pathway activity utilizing protein interactions. Multimed Tools Appl 80, 30283–30303 (2021). https://doi.org/10.1007/s11042-020-09269-8

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