ATLANTIS - Attractor Landscape Analysis Toolbox for Cell Fate Discovery and Reprogramming

Abstract Boolean modelling of biological networks is a well-established technique for abstracting dynamical biomolecular regulation in cells. Specifically, decoding linkages between salient regulatory network states and corresponding cell fate outcomes can help uncover pathological foundations of di...

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Autores principales:	Osama Shiraz Shah, Muhammad Faizyab Ali Chaudhary, Hira Anees Awan, Fizza Fatima, Zainab Arshad, Bibi Amina, Maria Ahmed, Hadia Hameed, Muhammad Furqan, Shareef Khalid, Amir Faisal, Safee Ullah Chaudhary
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/2f7851b8e389489cae1ee358c76f0e63
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spelling	oai:doaj.org-article:2f7851b8e389489cae1ee358c76f0e632021-12-02T11:41:25ZATLANTIS - Attractor Landscape Analysis Toolbox for Cell Fate Discovery and Reprogramming10.1038/s41598-018-22031-32045-2322https://doaj.org/article/2f7851b8e389489cae1ee358c76f0e632018-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-22031-3https://doaj.org/toc/2045-2322Abstract Boolean modelling of biological networks is a well-established technique for abstracting dynamical biomolecular regulation in cells. Specifically, decoding linkages between salient regulatory network states and corresponding cell fate outcomes can help uncover pathological foundations of diseases such as cancer. Attractor landscape analysis is one such methodology which converts complex network behavior into a landscape of network states wherein each state is represented by propensity of its occurrence. Towards undertaking attractor landscape analysis of Boolean networks, we propose an Attractor Landscape Analysis Toolbox (ATLANTIS) for cell fate discovery, from biomolecular networks, and reprogramming upon network perturbation. ATLANTIS can be employed to perform both deterministic and probabilistic analyses. It has been validated by successfully reconstructing attractor landscapes from several published case studies followed by reprogramming of cell fates upon therapeutic treatment of network. Additionally, the biomolecular network of HCT-116 colorectal cancer cell line has been screened for therapeutic evaluation of drug-targets. Our results show agreement between therapeutic efficacies reported by ATLANTIS and the published literature. These case studies sufficiently highlight the in silico cell fate prediction and therapeutic screening potential of the toolbox. Lastly, ATLANTIS can also help guide single or combinatorial therapy responses towards reprogramming biomolecular networks to recover cell fates.Osama Shiraz ShahMuhammad Faizyab Ali ChaudharyHira Anees AwanFizza FatimaZainab ArshadBibi AminaMaria AhmedHadia HameedMuhammad FurqanShareef KhalidAmir FaisalSafee Ullah ChaudharyNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-11 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Osama Shiraz Shah Muhammad Faizyab Ali Chaudhary Hira Anees Awan Fizza Fatima Zainab Arshad Bibi Amina Maria Ahmed Hadia Hameed Muhammad Furqan Shareef Khalid Amir Faisal Safee Ullah Chaudhary ATLANTIS - Attractor Landscape Analysis Toolbox for Cell Fate Discovery and Reprogramming
description	Abstract Boolean modelling of biological networks is a well-established technique for abstracting dynamical biomolecular regulation in cells. Specifically, decoding linkages between salient regulatory network states and corresponding cell fate outcomes can help uncover pathological foundations of diseases such as cancer. Attractor landscape analysis is one such methodology which converts complex network behavior into a landscape of network states wherein each state is represented by propensity of its occurrence. Towards undertaking attractor landscape analysis of Boolean networks, we propose an Attractor Landscape Analysis Toolbox (ATLANTIS) for cell fate discovery, from biomolecular networks, and reprogramming upon network perturbation. ATLANTIS can be employed to perform both deterministic and probabilistic analyses. It has been validated by successfully reconstructing attractor landscapes from several published case studies followed by reprogramming of cell fates upon therapeutic treatment of network. Additionally, the biomolecular network of HCT-116 colorectal cancer cell line has been screened for therapeutic evaluation of drug-targets. Our results show agreement between therapeutic efficacies reported by ATLANTIS and the published literature. These case studies sufficiently highlight the in silico cell fate prediction and therapeutic screening potential of the toolbox. Lastly, ATLANTIS can also help guide single or combinatorial therapy responses towards reprogramming biomolecular networks to recover cell fates.
format	article
author	Osama Shiraz Shah Muhammad Faizyab Ali Chaudhary Hira Anees Awan Fizza Fatima Zainab Arshad Bibi Amina Maria Ahmed Hadia Hameed Muhammad Furqan Shareef Khalid Amir Faisal Safee Ullah Chaudhary
author_facet	Osama Shiraz Shah Muhammad Faizyab Ali Chaudhary Hira Anees Awan Fizza Fatima Zainab Arshad Bibi Amina Maria Ahmed Hadia Hameed Muhammad Furqan Shareef Khalid Amir Faisal Safee Ullah Chaudhary
author_sort	Osama Shiraz Shah
title	ATLANTIS - Attractor Landscape Analysis Toolbox for Cell Fate Discovery and Reprogramming
title_short	ATLANTIS - Attractor Landscape Analysis Toolbox for Cell Fate Discovery and Reprogramming
title_full	ATLANTIS - Attractor Landscape Analysis Toolbox for Cell Fate Discovery and Reprogramming
title_fullStr	ATLANTIS - Attractor Landscape Analysis Toolbox for Cell Fate Discovery and Reprogramming
title_full_unstemmed	ATLANTIS - Attractor Landscape Analysis Toolbox for Cell Fate Discovery and Reprogramming
title_sort	atlantis - attractor landscape analysis toolbox for cell fate discovery and reprogramming
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/2f7851b8e389489cae1ee358c76f0e63
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ATLANTIS - Attractor Landscape Analysis Toolbox for Cell Fate Discovery and Reprogramming

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