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Combining network m...
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Pedicini, MarcoIstituto per le Applicazioni del Calcolo “Mauro Picone”, Consiglio Nazionale delle Ricerche (CNR), Rome, Italy
(författare)
Combining network modeling and gene expression microarray analysis to explore the dynamics of Th1 and Th2 cell regulation.
- Artikel/kapitelEngelska2010
Förlag, utgivningsår, omfång ...
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2010-12-16
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Public Library of Science (PLoS),2010
Nummerbeteckningar
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LIBRIS-ID:oai:gup.ub.gu.se/143108
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https://gup.ub.gu.se/publication/143108URI
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https://doi.org/10.1371/journal.pcbi.1001032DOI
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https://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-98579URI
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Ämneskategori:ref swepub-contenttype
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Ämneskategori:art swepub-publicationtype
Anmärkningar
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Two T helper (Th) cell subsets, namely Th1 and Th2 cells, play an important role in inflammatory diseases. The two subsets are thought to counter-regulate each other, and alterations in their balance result in different diseases. This paradigm has been challenged by recent clinical and experimental data. Because of the large number of genes involved in regulating Th1 and Th2 cells, assessment of this paradigm by modeling or experiments is difficult. Novel algorithms based on formal methods now permit the analysis of large gene regulatory networks. By combining these algorithms with in silico knockouts and gene expression microarray data from human T cells, we examined if the results were compatible with a counter-regulatory role of Th1 and Th2 cells. We constructed a directed network model of genes regulating Th1 and Th2 cells through text mining and manual curation. We identified four attractors in the network, three of which included genes that corresponded to Th0, Th1 and Th2 cells. The fourth attractor contained a mixture of Th1 and Th2 genes. We found that neither in silico knockouts of the Th1 and Th2 attractor genes nor gene expression microarray data from patients with immunological disorders and healthy subjects supported a counter-regulatory role of Th1 and Th2 cells. By combining network modeling with transcriptomic data analysis and in silico knockouts, we have devised a practical way to help unravel complex regulatory network topology and to increase our understanding of how network actions may differ in health and disease.
Ämnesord och genrebeteckningar
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Algorithms
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Computational Biology
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methods
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Computer Simulation
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Databases
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Genetic
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Gene Expression Profiling
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Gene Knockout Techniques
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Gene Regulatory Networks
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Humans
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Oligonucleotide Array Sequence Analysis
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Phenotype
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Th1 Cells
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metabolism
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physiology
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Th2 Cells
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metabolism
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physiology
Biuppslag (personer, institutioner, konferenser, titlar ...)
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Barrenäs, Fredrik,1981Gothenburg University,Göteborgs universitet,Institutionen för kliniska vetenskaper, Avdelningen för pediatrik,Institute of Clinical Sciences, Department of Pediatrics,The Unit for Clinical Systems Biology, University of Gothenburg, Gothenburg, Sweden(Swepub:gu)xbarfr
(författare)
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Clancy, TrevorDepartment of Tumor Biology, Institute of Cancer Research, the Norwegian Radium Hospital, Oslo, Norway
(författare)
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Castiglione, FilippoIstituto per le Applicazioni del Calcolo “Mauro Picone”, Consiglio Nazionale delle Ricerche (CNR), Rome, Italy
(författare)
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Hovig, EivindDepartment of Tumor Biology, Institute of Cancer Research, the Norwegian Radium Hospital, Oslo, Norway / The Institute for Medical Informatics, Rikshospitalet, Oslo University Hospital, Oslo, Norway / Department of Informatics, University of Oslo, Oslo, Norway
(författare)
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Kanduri, Kartiek,1986Gothenburg University,Göteborgs universitet,Institutionen för kliniska vetenskaper, Avdelningen för pediatrik,Institute of Clinical Sciences, Department of Pediatrics,The Unit for Clinical Systems Biology, University of Gothenburg, Gothenburg, Sweden(Swepub:gu)xkanka
(författare)
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Santoni, DanieleIstituto per le Applicazioni del Calcolo “Mauro Picone”, Consiglio Nazionale delle Ricerche (CNR), Rome, Italy / Barcelona Institute for Research in Biomedicine (IRB), Barcelona Science Park, Barcelona, Spain
(författare)
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Benson, Mikael,1954Gothenburg University,Göteborgs universitet,Institutionen för kliniska vetenskaper, Avdelningen för pediatrik,Institute of Clinical Sciences, Department of Pediatrics,The Unit for Clinical Systems Biology, University of Gothenburg, Gothenburg, Sweden / Unit for Pediatric Allergology, Queen Silvia Children's Hospital, Gothenburg, Sweden(Swepub:liu)mikbe05
(författare)
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Istituto per le Applicazioni del Calcolo “Mauro Picone”, Consiglio Nazionale delle Ricerche (CNR), Rome, ItalyInstitutionen för kliniska vetenskaper, Avdelningen för pediatrik
(creator_code:org_t)
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Ingår i:PLoS computational biology: Public Library of Science (PLoS)6:121553-73581553-734X
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