Independent component analysis of Corynebacterium glutamicum transcriptomes reveals its transcriptional regulatory network

Zhao, Jianxiao; Sun, Xi; Mao, Zhitao; Zheng, Yangyang; Geng, Zhouxiao; Zhang, Yuhan; Ma, Hongwu; Wang, Zhiwen

doi:10.1016/j.micres.2023.127485

Cited by 2 publications

(2 citation statements)

References 66 publications

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“…Though IMs derived in this study provided regulatory information for the reconstruction of the TRN of L. plantarum, the performance of ICA decomposition was limited by the size of the expression matrix, compared to other ICA-based studies of bacterial transcriptomes (e.g., ICA of Corynebacterium glutamicum collected 263 samples from 29 independent projects [38] ). Compared to well-studied organisms such as Escherichia coli, the amount of existing transcriptomic data of Lactobacillus plantarum on NCBI Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/) [39] is much smaller.…”

Section: Discussionmentioning

confidence: 97%

Systematic elucidation of independently modulated genes inLactobacillus plantarumreveals a trade-off between secondary and primary metabolism

Qiu,

Huang,

Liang

et al. 2023

Preprint

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Lactobacillus plantarumis a probiotic bacteria widely used in food and health industries, but its gene regulatory information is limited in existing databases, which impedes the research of its physiology and its applications. To obtain a better understanding of the transcriptional regulatory network ofL. plantarum, independent component analysis (ICA) of its transcriptomes was used to derive 45 sets of independently modulated genes (iModulons). Those iModulons were annotated for associated transcription factors (TFs) and functional pathways, and active iModulons in response to different growth conditions were identified and characterized in detail. Eventually, the analysis of iModulon activities reveals a trade-off between regulatory activities of secondary and primary metabolism inL. plantarum.

show abstract

Section: Discussionmentioning

confidence: 97%

Systematic elucidation of independently modulated genes inLactobacillus plantarumreveals a trade-off between secondary and primary metabolism

Qiu,

Huang,

Liang

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…Though IMs derived in this study provided regulatory information for the reconstruction of the TRN of L. plantarum, the performance of ICA decomposition was limited by the size of the expression matrix, compared to other ICA-based studies of bacterial transcriptomes (e.g., ICA of Corynebacterium glutamicum collected 263 samples from 29 independent projects (Zhao et al, 2023)). Compared to well-studied organisms such as E. coli, the amount of existing transcriptomic data of L. plantarum on NCBI Gene Expression Omnibus (https:// www.…”

Section: Discussionmentioning

confidence: 97%

Systematic elucidation of independently modulated genes in Lactiplantibacillus plantarum reveals a trade‐off between secondary and primary metabolism

Qiu,

Huang,

Liang

et al. 2024

Microbial Biotechnology

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Lactiplantibacillus plantarum is a probiotic bacterium widely used in food and health industries, but its gene regulatory information is limited in existing databases, which impedes the research of its physiology and its applications. To obtain a better understanding of the transcriptional regulatory network of L. plantarum, independent component analysis of its transcriptomes was used to derive 45 sets of independently modulated genes (iModulons). Those iModulons were annotated for associated transcription factors and functional pathways, and active iModulons in response to different growth conditions were identified and characterized in detail. Eventually, the analysis of iModulon activities reveals a trade‐off between regulatory activities of secondary and primary metabolism in L. plantarum.

show abstract

Independent component analysis of Corynebacterium glutamicum transcriptomes reveals its transcriptional regulatory network

Cited by 2 publications

References 66 publications

Systematic elucidation of independently modulated genes inLactobacillus plantarumreveals a trade-off between secondary and primary metabolism

Systematic elucidation of independently modulated genes inLactobacillus plantarumreveals a trade-off between secondary and primary metabolism

Systematic elucidation of independently modulated genes in Lactiplantibacillus plantarum reveals a trade‐off between secondary and primary metabolism

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