Drug Target Set Enrichment Analysis (DTSEA): A Network-Based Approach for Drug Repurposing to COVID-19

Su, Yinchun; Wu, Jiashuo; Li, Xiangmei; Ji, Li; Zhao, Xilong; Pan, Bingyue; Zhao, Yurong; Kong, Qingfei; Han, Junwei

doi:10.2139/ssrn.4301052

Cited by 2 publications

(2 citation statements)

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“…The simplest method involves application of neighbourhood models from collaborative filtering to this class of problems [69]. A slightly more sophisticated approach is to use network diffusion based approaches [70,71]. Such methods are unfortunately not as accurate as matrix completion based techniques; furthermore current network based techniques are formulated as matrix completion and not network diffusion for the same reason.…”

Section: Graph Regularised Binary Matrix Completion (Grbmc)mentioning

confidence: 99%

WITHDRAWN: Antibiotic Bacteria Interaction: Dataset and Benchmarking

Chatterjee,

Majumdar,

Chouzenoux

2024

Preprint

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This study introduces a dataset for drug-bacteria associations (DBA) that affects humans. Our contribution extends beyond merely curating the association matrix; we also conduct genomic similarity computations for all known bacteria impacting humans and assess structural similarities for all antibiotic drugs. This is a first of a kind dataset serving the fundamental goal of streamlining antibiotic repurposing for bacterial infections. We conducted thorough benchmarking on this dataset using state-of-the-art drug repurposing models. Furthermore, we applied this dataset to three case studies involving drug-resistant bacterial infections. Our results indicate that the dataset coupled with the algorithms are indeed effective for repurposing drugs with the potential for treating drug resistant bacterial infections.

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Section: Graph Regularised Binary Matrix Completion (Grbmc)mentioning

confidence: 99%

WITHDRAWN: Antibiotic Bacteria Interaction: Dataset and Benchmarking

Chatterjee,

Majumdar,

Chouzenoux

2024

Preprint

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“…We used over‐representation analysis (Boyle et al , 2004) to identify biological processes from GO and Disease enriched terms from DisGeNET (Piñero et al , 2019) associated with these nodes. Next, for both networks we performed a Drug Target Set Enrichment Analysis (DTSEA), using the respective R package (Su et al , 2023), to identify the available drugs and diseases according to each network. We performed semantic similarity analysis among the nodes of each network and compared their distribution by Wilcoxon test.…”

Section: Methodsmentioning

confidence: 99%

Integrated systems biology approach identifies gene targets for endothelial dysfunction

Pinheiro‐de‐Sousa,

Fonseca‐Alaniz,

Giudice

et al. 2023

Molecular Systems Biology

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Endothelial dysfunction (ED) is critical in the development and progression of cardiovascular (CV) disorders, yet effective therapeutic targets for ED remain elusive due to limited understanding of its underlying molecular mechanisms. To address this gap, we employed a systems biology approach to identify potential targets for ED. Our study combined multi omics data integration, with siRNA screening, high content imaging and network analysis to prioritise key ED genes and identify a pro‐ and anti‐ED network. We found 26 genes that, upon silencing, exacerbated the ED phenotypes tested, and network propagation identified a pro‐ED network enriched in functions associated with inflammatory responses. Conversely, 31 genes ameliorated ED phenotypes, pointing to potential ED targets, and the respective anti‐ED network was enriched in hypoxia, angiogenesis and cancer‐related processes. An independent screen with 17 drugs found general agreement with the trends from our siRNA screen and further highlighted DUSP1, IL6 and CCL2 as potential candidates for targeting ED. Overall, our results demonstrate the potential of integrated system biology approaches in discovering disease‐specific candidate drug targets for endothelial dysfunction.

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Drug Target Set Enrichment Analysis (DTSEA): A Network-Based Approach for Drug Repurposing to COVID-19

Cited by 2 publications

References 0 publications

WITHDRAWN: Antibiotic Bacteria Interaction: Dataset and Benchmarking

WITHDRAWN: Antibiotic Bacteria Interaction: Dataset and Benchmarking

Integrated systems biology approach identifies gene targets for endothelial dysfunction

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