CORN 2.0 - Condition Orientated Regulatory Networks 2.0
Gene regulation is a fundamental process that allows organisms to adapt to their environment and increase complexity through the action of nucleic acid-binding proteins (NBPs), such as transcription factors (TFs), which regulate specific sets of genes under distinct conditions. These regulatory inte...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-01-01
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| Series: | Computational and Structural Biotechnology Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037025001242 |
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| author | Ricky Wai Tak Leung Xinying Zhang Zhuobin Chen Yuyun Liang Simei Huang Zixin Yang Xueqing Zong Xiaosen Jiang Runming Lin Wenbin Deng Yaohua Hu Jing Qin |
| author_facet | Ricky Wai Tak Leung Xinying Zhang Zhuobin Chen Yuyun Liang Simei Huang Zixin Yang Xueqing Zong Xiaosen Jiang Runming Lin Wenbin Deng Yaohua Hu Jing Qin |
| author_sort | Ricky Wai Tak Leung |
| collection | DOAJ |
| description | Gene regulation is a fundamental process that allows organisms to adapt to their environment and increase complexity through the action of nucleic acid-binding proteins (NBPs), such as transcription factors (TFs), which regulate specific sets of genes under distinct conditions. These regulatory interactions form transcriptional regulatory networks (TRNs), which can be further broken down into transcriptional regulatory sub-networks (TRSNs) centered around individual TFs. TRSNs are more stable and practical for analysis, making them ideal for studying gene regulation under specific conditions. Condition-Oriented Regulatory Networks (CORN, https://qinlab.sysu.edu.cn/corn/home) is a comprehensive library of condition-based TRSNs, including those induced by natural compounds, small molecules, drug treatments, and gene perturbations. CORN 2.0 represents a significant update, associating 7540 specific conditions with 71934 TRSNs across 52 human cell lines, involving 542 transcription factors (TFs). Notably, CORN 2.0 includes 1550 natural compound-triggered TRSNs, providing a valuable resource for studying the pharmacological effects of natural products. This study demonstrates the utility of CORN in three key areas: personalized medicine, induced pluripotency transitions, and natural compound-associated pharmacology. By linking specific conditions to their corresponding TRSNs, CORN enables researchers to explore how gene regulatory networks are altered under various conditions, offering insights into disease mechanisms and potential therapeutic interventions. |
| format | Article |
| id | doaj-art-88ccb30e251a46dc81efc8312384a2f7 |
| institution | OA Journals |
| issn | 2001-0370 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj-art-88ccb30e251a46dc81efc8312384a2f72025-08-20T02:12:08ZengElsevierComputational and Structural Biotechnology Journal2001-03702025-01-01271518152810.1016/j.csbj.2025.04.003CORN 2.0 - Condition Orientated Regulatory Networks 2.0Ricky Wai Tak Leung0Xinying Zhang1Zhuobin Chen2Yuyun Liang3Simei Huang4Zixin Yang5Xueqing Zong6Xiaosen Jiang7Runming Lin8Wenbin Deng9Yaohua Hu10Jing Qin11School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China; Division of Science, Engineering and Health Studies, College of Professional and Continuing Education, The Hong Kong Polytechnic University, Hong Kong SAR, ChinaSchool of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, ChinaSchool of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, ChinaSchool of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, ChinaSchool of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, ChinaSchool of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, ChinaSchool of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, ChinaCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, ChinaBGI-Shenzhen, Shenzhen, Guangdong 518103, ChinaSchool of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China; Corresponding authors.School of Mathematical Sciences, Shenzhen University, Shenzhen, Guangdong 518060, China; Corresponding authors.School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China; Corresponding authors.Gene regulation is a fundamental process that allows organisms to adapt to their environment and increase complexity through the action of nucleic acid-binding proteins (NBPs), such as transcription factors (TFs), which regulate specific sets of genes under distinct conditions. These regulatory interactions form transcriptional regulatory networks (TRNs), which can be further broken down into transcriptional regulatory sub-networks (TRSNs) centered around individual TFs. TRSNs are more stable and practical for analysis, making them ideal for studying gene regulation under specific conditions. Condition-Oriented Regulatory Networks (CORN, https://qinlab.sysu.edu.cn/corn/home) is a comprehensive library of condition-based TRSNs, including those induced by natural compounds, small molecules, drug treatments, and gene perturbations. CORN 2.0 represents a significant update, associating 7540 specific conditions with 71934 TRSNs across 52 human cell lines, involving 542 transcription factors (TFs). Notably, CORN 2.0 includes 1550 natural compound-triggered TRSNs, providing a valuable resource for studying the pharmacological effects of natural products. This study demonstrates the utility of CORN in three key areas: personalized medicine, induced pluripotency transitions, and natural compound-associated pharmacology. By linking specific conditions to their corresponding TRSNs, CORN enables researchers to explore how gene regulatory networks are altered under various conditions, offering insights into disease mechanisms and potential therapeutic interventions.http://www.sciencedirect.com/science/article/pii/S2001037025001242Personalized medicineInduced pluripotencyCell fateGene regulatory networkNatural productsNatural compounds |
| spellingShingle | Ricky Wai Tak Leung Xinying Zhang Zhuobin Chen Yuyun Liang Simei Huang Zixin Yang Xueqing Zong Xiaosen Jiang Runming Lin Wenbin Deng Yaohua Hu Jing Qin CORN 2.0 - Condition Orientated Regulatory Networks 2.0 Computational and Structural Biotechnology Journal Personalized medicine Induced pluripotency Cell fate Gene regulatory network Natural products Natural compounds |
| title | CORN 2.0 - Condition Orientated Regulatory Networks 2.0 |
| title_full | CORN 2.0 - Condition Orientated Regulatory Networks 2.0 |
| title_fullStr | CORN 2.0 - Condition Orientated Regulatory Networks 2.0 |
| title_full_unstemmed | CORN 2.0 - Condition Orientated Regulatory Networks 2.0 |
| title_short | CORN 2.0 - Condition Orientated Regulatory Networks 2.0 |
| title_sort | corn 2 0 condition orientated regulatory networks 2 0 |
| topic | Personalized medicine Induced pluripotency Cell fate Gene regulatory network Natural products Natural compounds |
| url | http://www.sciencedirect.com/science/article/pii/S2001037025001242 |
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