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

Scientific Reports
Osama Shiraz ShahSafee Ullah Chaudhary

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...Continue Reading

References

Apr 1, 1973·Journal of Theoretical Biology·L Glass, S A Kauffman
Sep 1, 1997·Molecular and Cellular Biology·A SewingH Land
Apr 30, 1999·Science·S Artavanis-TsakonasR J Lake
Dec 11, 1999·Nature·L H HartwellA W Murray
Jan 27, 2000·Cell·D Hanahan, R A Weinberg
Nov 22, 2001·The Journal of Biological Chemistry·Jennifer K RicherKathryn B Horwitz
Mar 20, 2002·Nature Reviews. Cancer·R FoddeH Clevers
Jun 8, 2002·Annual Review of Neuroscience·Nicholas Gaiano, Gord Fishell
Nov 15, 2002·Nature·Hiroaki Kitano
Nov 16, 2002·Proceedings of the National Academy of Sciences of the United States of America·George Adrian CalinCarlo M Croce
Mar 24, 2004·Proceedings of the National Academy of Sciences of the United States of America·Fangting LiChao Tang
Jun 10, 2004·British Journal of Cancer·S BamfordR Wooster
May 21, 2005·Physical Review Letters·Sui HuangDonald E Ingber
Apr 19, 2006·Cancer Research·Astrid LièvrePierre Laurent-Puig
Dec 15, 2006·Cancer Letters·Alessandra Montecucco, Giuseppe Biamonti
Apr 6, 2007·BMC Systems Biology·Steffen KlamtErnst D Gilles
Feb 20, 2008·Advances in Genetics·Esteban Ballestar, Manel Esteller
Sep 18, 2008·Nature Reviews. Molecular Cell Biology·Guy Karlebach, Ron Shamir
Oct 25, 2008·Nature·Jeremy K Nicholson, John C Lindon
Mar 19, 2009·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·David S P TanJorge S Reis-Filho
Jul 15, 2009·Seminars in Cell & Developmental Biology·Sui HuangStuart Kauffman
Jan 19, 2010·Proceedings of the National Academy of Sciences of the United States of America·Anja RagvinThomas S Becker
Feb 9, 2010·Nature Methods·Andrew R CohenMichel Cayouette
Apr 10, 2010·Bioinformatics·Christoph MüsselHans A Kestler
Feb 24, 2011·IEEE Transactions on Neural Networks·Daizhan ChengZhiqiang Li
Mar 8, 2011·Cell·Douglas Hanahan, Robert A Weinberg
May 10, 2012·Cold Spring Harbor Perspectives in Biology·M Albert Basson
Aug 9, 2012·BMC Systems Biology·Tomáš HelikarJim A Rogers
Aug 31, 2012·Frontiers in Physiology·Debashis Sahoo
Mar 22, 2014·Cancer Cell·Patricia A J Muller, Karen H Vousden
Jul 2, 2014·PloS One·Panuwat TrairatphisanThomas Sauter
Sep 18, 2014·Proceedings of the National Academy of Sciences of the United States of America·Chunhe Li, Jin Wang
Dec 19, 2014·BMC Bioinformatics·Jose A GomezPaul I Barton
Sep 1, 2015·PLoS Computational Biology·Åsmund FlobakAstrid Lægreid
Feb 6, 2016·BMC Bioinformatics·Andrea ParoniMarco Antoniotti
Jun 22, 2016·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Kwang-Hyun ChoSang-Min Park
Oct 30, 2016·Bio Systems·Célia BianeHanna Klaudel

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Citations

Sep 25, 2018·Frontiers in Physiology·Nuno D MendesClaudine Chaouiya

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Software Mentioned

GINsim
BooleSim
MATLAB Biograph object
Graphviz
CellNetAnalyzer
Cell Collective
BoolNet
DA
MATLAB
ATLANTIS

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