miRPin

microRNA Protein Interactome

Extracellular miRNA-protein interaction dataset curated using publicly available resources

Publication DOI:10.1101/2024.12.23.630210
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Published in Biophysical Chemistry

miRPin: A comprehensive resource of predicted microRNA-protein interactions in the extracellular space

Biophysical Chemistry, 2025

MicroRNAs (miRNAs) have been detected in the extracellular milieu, where they interact with proteins and modulate cellular signaling pathways. Despite their significance, the current understanding of extracellular miRNA-protein interactions is limited. This study addresses this gap by integrating multiple publicly available resources to predict and analyze these interactions. We identified 6,244 extracellular proteins and 1,177 miRNAs, resulting in 122,440 miRNA-protein interaction pairs and 11,020 unique interactions.

Our analysis revealed key motifs in both miRNAs and proteins that facilitate these interactions. The data is accessible through miRPin, a user-friendly web server (https://englishop.co.in/miRPin) designed for exploring miRNA-protein interactions. miRPin’s curated datasets and intuitive interface provide researchers with valuable tools to investigate miRNA-protein dynamics, contributing to advancements in molecular biology and therapeutic development.

Publications

Published Article

DOI: 10.1016/j.bpc.2025.107421

Preprint Article

DOI: 10.1101/2024.12.23.630210

Authors

Vishal Kumar Sahu1, Subhayan Sur1, Sanjana Agarwal1, Harish Madhyastha2, Amit Ranjan1**, Soumya Basu1*

1Cancer and Translational Research Centre, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Tathawade, Pune - 411033, India
2Department of Cardiovascular Physiology, Faculty of Medicine, University of Miyazaki, Miyazaki 8891692, Japan

Acknowledgements

  • Authors acknowledge Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Pune, India for research infrastructure and the Department of Science & Technology (DST), Government of India for providing DST-FIST grant (SR/FST/LS-I/2017/70) to support research infrastructure and instruments.
  • VKS acknowledges the Council of Scientific and Industrial Research (CSIR), New Delhi, India for CSIR-SRF fellowship (File No.: 09/1340(11487)/2021-EMR-I).
  • SS acknowledges Department of Biotechnology, Government of India for Ramalingaswami Re-entry Fellowship grant (File No.: BT/RLF/Re-entry/47/2021).
  • SB acknowledges intramural grant Intramural of Dr. D. Y. Patil Vidyapeeth (DPU), Pune, India (DPU/644-43/2021).

Citation

If you use miRPin in your research, please cite the following paper

Sahu, V. K., Sur, S., Agarwal, S., Madhyastha, H., Ranjan, A., & Basu, S. (2025). miRPin: A comprehensive resource of predicted microRNA-protein interactions in the extracellular space. In Biophysical Chemistry (p. 107421). Elsevier BV. https://doi.org/10.1016/j.bpc.2025.107421

Database Features

Comprehensive Data

Curated extracellular miRNA-protein interactions from multiple sources

GSEA Analysis

Gene set enrichment analysis for proteins and miRNAs

Motif Discovery

MEME-based motif identification in interaction sequences

Docking Results

Molecular docking analysis for interaction validation