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Construction of a Comprehensive Protein–Protein Interaction Map for Vitiligo Disease to Identify Key Regulatory Elements: A Systemic Approach

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Abstract

Vitiligo is an idiopathic disorder characterized by depigmented patches on the skin due to progressive loss of melanocytes. Several genetic, immunological, and pathophysiological investigations have established vitiligo as a polygenetic disorder with multifactorial etiology. However, no definite model explaining the interplay between these causative factors has been established hitherto. Therefore, we studied the disorder at the system level to identify the key proteins involved by exploring their molecular connectivity in terms of topological parameters. The existing research data helped us in collating 215 proteins involved in vitiligo onset or progression. Interaction study of these proteins leads to a comprehensive vitiligo map with 4845 protein nodes linked with 107,416 edges. Based on centrality measures, a backbone network with 500 nodes has been derived. This has presented a clear overview of the proteins and processes involved and the crosstalk between them. Clustering backbone proteins revealed densely connected regions inferring major molecular interaction modules essential for vitiligo. Finally, a list of top order proteins that play a key role in the disease pathomechanism has been formulated. This includes SUMO2, ESR1, COPS5, MYC, SMAD3, and Cullin proteins. While this list is in fair agreement with the available literature, it also introduces new candidate proteins that can be further explored. A subnetwork of 64 vitiligo core proteins was built by analyzing the backbone and seed protein networks. Our finding suggests that the topology, along with functional clustering, provides a deep insight into the behavior of proteins. This in turn aids in the illustration of disease condition and discovery of significant proteins involved in vitiligo.

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Abbreviations

BC:

Betweenness Centrality

PPI:

Protein–Protein Interaction

PPIN:

Protein–Protein Interaction network

PDB:

Protein Data Bank

CC:

Closeness Centrality

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Acknowledgements

The authors thankfully acknowledge the help, support, and guidance provided by Dr. Ajay Pandey, Department of Mechanical Engineering, MANIT, Bhopal.

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  1. Department of Biological Science and Engineering, Maulana Azad National Institute of Technology (MANIT), Bhopal, 462003, India

    Anvita Gupta Malhotra, Mohit Jha, Sudha Singh & Khushhali M. Pandey

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  1. Anvita Gupta Malhotra
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Malhotra, A.G., Jha, M., Singh, S. et al. Construction of a Comprehensive Protein–Protein Interaction Map for Vitiligo Disease to Identify Key Regulatory Elements: A Systemic Approach. Interdiscip Sci Comput Life Sci 10, 500–514 (2018). https://doi.org/10.1007/s12539-017-0213-z

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