Generation of a Compendium of Transcription Factor Cascades and Identification of Potential Therapeutic Targets using Graph Machine Learning

Sonish Sivarajkumar; Pratyush Tandale; Ankit Bhardwaj; Kipp W. Johnson; Anoop Titus; Benjamin S. Glicksberg; Shameer Khader; Kamlesh K. Yadav; Lakshminarayanan Subramanian

arXiv · 2311.17969

Generation of a Compendium of Transcription Factor Cascades and Identification of Potential Therapeutic Targets using Graph Machine Learning

Sonish Sivarajkumar·Pratyush Tandale·Ankit Bhardwaj·Kipp W. Johnson·Anoop Titus·Benjamin S. Glicksberg·Shameer Khader·Kamlesh K. Yadav·Lakshminarayanan Subramanian

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Abstract

Transcription factors (TFs) play a vital role in the regulation of gene expression thereby making them critical to many cellular processes. In this study, we used graph machine learning methods to create a compendium of TF cascades using data extracted from the STRING database. A TF cascade is a sequence of TFs that regulate each other, forming a directed path in the TF network. We constructed a knowledge graph of 81,488 unique TF cascades, with the longest cascade consisting of 62 TFs. Our results highlight the complex and intricate nature of TF interactions, where multiple TFs work together to regulate gene expression. We also identified 10 TFs with the highest regulatory influence based on centrality measurements, providing valuable information for researchers interested in studying specific TFs. Furthermore, our pathway enrichment analysis revealed significant enrichment of various pathways and functional categories, including those involved in cancer and other diseases, as well as those involved in development, differentiation, and cell signaling. The enriched pathways identified in this study may have potential as targets for therapeutic intervention in diseases associated with dysregulation of transcription factors. We have released the dataset, knowledge graph, and graphML methods for the TF cascades, and created a website to display the results, which can be accessed by researchers interested in using this dataset. Our study provides a valuable resource for understanding the complex network of interactions between TFs and their regulatory roles in cellular processes.

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Sonish Sivarajkumar, Pratyush Tandale, Ankit Bhardwaj, Kipp W. Johnson, Anoop Titus, Benjamin S. Glicksberg, Shameer Khader, Kamlesh K. Yadav, Lakshminarayanan Subramanian. 2023-11-29. Generation of a Compendium of Transcription Factor Cascades and Identification of Potential Therapeutic Targets using Graph Machine Learning. https://arxiv.org/abs/2311.17969

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