NDLI: Inferring catalysis in biological systems

Content Provider	IET Digital Library
Author	Kondofersky, Ivan Theis, Fabian J. Fuchs, Christiane
Abstract	In systems biology, one is often interested in the communication patterns between several species, such as genes, enzymes or proteins. These patterns become more recognisable when temporal experiments are performed. This temporal communication can be structured by reaction networks such as gene regulatory networks or signalling pathways. Mathematical modelling of data arising from such networks can reveal important details, thus helping to understand the studied system. In many cases, however, corresponding models still deviate from the observed data. This may be due to unknown but present catalytic reactions. From a modelling perspective, the question of whether a certain reaction is catalysed leads to a large increase of model candidates. For large networks the calibration of all possible models becomes computationally infeasible. We propose a method which determines a substantially reduced set of appropriate model candidates and identifies the catalyst of each reaction at the same time. This is incorporated in a multiple-step procedure which first extends the network by additional latent variables and subsequently identifies catalyst candidates using similarity analysis methods. Results from synthetic data examples suggest a good performance even for non-informative data with few observations. Applied on CD95 apoptotic pathway our method provides new insights into apoptosis regulation.
Starting Page	210
Ending Page	218
Page Count	9
ISSN	17518849
Volume Number	10
e-ISSN	17518857
Issue Number	Issue 6, Dec (2016)
Alternate Webpage(s)	https://digital-library.theiet.org/content/journals/iet-syb/10/6
Alternate Webpage(s)	https://digital-library.theiet.org/content/journals/10.1049/iet-syb.2015.0087
Journal	IET Systems Biology
Publisher Date	2016-12-01
Access Restriction	Open
Rights Holder	© The Institution of Engineering and Technology
Subject Keyword	Biochemical Network Biochemistry Biological System Biology And Medical Computing Biology Computing Biomolecular Interactions Calibration Catalysis Catalyst Catalysts Catalytic Reactions Charge Transfer Complexes Cluster Communication Pattern Differentiation Apoptotic Pathway Enzymes Gene Regulatory Network Genes Genetics Heterogeneous Catalysis at SurFace And Other Surface Reactions Inferring Catalysis Interactions of Clusters (collisions And Reactions) Latent Variables Mathematical Data Modelling Measurement Standard And Calibration Molecular Clusters Multiple-step Procedure Noninformative Data Physical Chemistry of Biomolecular Solutions And Condensed State Proteins Reaction Network Signalling Pathways Similarity Analysis Method System Biology Time-resolved Communication Time-resolved Experiments
Content Type	Text
Resource Type	Article
Subject	Cell Biology Genetics Molecular Biology Modeling and Simulation Biotechnology

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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