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The transcription f...
The transcription factor network of E. coli steers global responses to shifts in RNAP concentration
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- L. B. Almeida, Bilena (author)
- Tampere Univ, Fac Med & Hlth Technol, Lab Biosyst Dynam, Tampere, Finland
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- M. Bahrudeen, Mohamed N. (author)
- Tampere Univ, Fac Med & Hlth Technol, Lab Biosyst Dynam, Tampere, Finland
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- Chauhan, Vatsala (author)
- Tampere Univ, Fac Med & Hlth Technol, Lab Biosyst Dynam, Tampere, Finland
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- Dash, Suchintak (author)
- Tampere Univ, Fac Med & Hlth Technol, Lab Biosyst Dynam, Tampere, Finland
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- Kandavalli, Vinodh (author)
- Uppsala universitet,Institutionen för cell- och molekylärbiologi
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- Hakkinen, Antti (author)
- Univ Helsinki, Res Program Syst Oncol, Res Programs Unit, Fac Med, FI-00014 Helsinki, Finland
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- Lloyd-Price, Jason (author)
- Google LLC, 111 8th Ave, New York, NY 10010 USA
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- S. D. Cristina, Palma (author)
- Tampere Univ, Fac Med & Hlth Technol, Lab Biosyst Dynam, Tampere, Finland
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- Baptista, Ines S. C. (author)
- Tampere Univ, Fac Med & Hlth Technol, Lab Biosyst Dynam, Tampere, Finland
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- Gupta, Abhishekh (author)
- Univ Connecticut, Ctr Quantitat Med, Sch Med, 263 Farmington Av, Farmington, CT 06030 USA.;Univ Connecticut, Dept Cell Biol, Sch Med, 263 Farmington Av, Farmington, CT 06030 USA
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- Kesseli, Juha (author)
- Tampere Univ, Fac Med & Hlth Technol, Prostate Canc Res Ctr, Tampere, Finland.;Tampere Univ Hosp, Tays Canc Ctr, Tampere, Finland
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- Dufour, Eric (author)
- Tampere Univ, Fac Med & Hlth Technol, Mitochondrial Bioenerget & Metab, BioMediTech, Tampere, Finland
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- Smolander, Olli-Pekka (author)
- Tallinn Univ Technol, Dept Chem & Biotechnol, Tallinn, Estonia
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- Nykter, Matti (author)
- Tampere Univ, Fac Med & Hlth Technol, Prostate Canc Res Ctr, Tampere, Finland.;Tampere Univ Hosp, Tays Canc Ctr, Tampere, Finland
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- Auvinen, Petri (author)
- Univ Helsinki, Inst Biotechnol, Viikinkaari 5D, Helsinki 00790, Finland
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- Jacobs, Howard T. (author)
- Tampere Univ, Fac Med & Hlth Technol, FI-33014 Tampere, Finland.;La Trobe Univ, Dept Environm & Genet, Melbourne, Vic 3086, Australia
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- M. D. Oliveira, Samuel (author)
- Boston Univ, Dept Elect & Comp Engn, Boston, MA USA
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- S. Ribeiro, Andre (author)
- Tampere Univ, Fac Med & Hlth Technol, Lab Biosyst Dynam, Tampere, Finland.;NOVA Univ Lisbon, Ctr Technol & Syst CTS Uninova, P-2829516 Monte De Caparica, Portugal
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(creator_code:org_t)
- 2022-06-24
- 2022
- English.
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In: Nucleic Acids Research. - : Oxford University Press. - 0305-1048 .- 1362-4962. ; 50:12, s. 6801-6819
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Abstract
Subject headings
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- The robustness and sensitivity of gene networks to environmental changes is critical for cell survival. How gene networks produce specific, chronologically ordered responses to genome-wide perturbations, while robustly maintaining homeostasis, remains an open question. We analysed if short- and mid-term genome-wide responses to shifts in RNA polymerase (RNAP) concentration are influenced by the known topology and logic of the transcription factor network (TFN) of Escherichia coli. We found that, at the gene cohort level, the magnitude of the single-gene, mid-term transcriptional responses to changes in RNAP concentration can be explained by the absolute difference between the gene's numbers of activating and repressing input transcription factors (TFs). Interestingly, this difference is strongly positively correlated with the number of input TFs of the gene. Meanwhile, short-term responses showed only weak influence from the TFN. Our results suggest that the global topological traits of the TFN of E. coli shape which gene cohorts respond to genome-wide stresses.
Subject headings
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Biokemi och molekylärbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biochemistry and Molecular Biology (hsv//eng)
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- ref (subject category)
- art (subject category)
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L. B. Almeida, B ...
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M. Bahrudeen, Mo ...
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Chauhan, Vatsala
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Dash, Suchintak
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Kandavalli, Vino ...
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Hakkinen, Antti
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Lloyd-Price, Jas ...
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S. D. Cristina, ...
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Baptista, Ines S ...
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Gupta, Abhishekh
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Kesseli, Juha
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Dufour, Eric
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Smolander, Olli- ...
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Nykter, Matti
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Auvinen, Petri
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Jacobs, Howard T ...
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M. D. Oliveira, ...
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S. Ribeiro, Andr ...
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Bioinformatics a ...
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Biochemistry and ...
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Nucleic Acids Re ...
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Uppsala University