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Generation of Reali...
Generation of Realistic Gene Regulatory Networks by Enriching for Feed-Forward Loops
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- Zhivkoplias, Erik K. (författare)
- Stockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab)
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Vavulov, Oleg (författare)
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- Hillerton, Thomas (författare)
- Stockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab)
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- Sonnhammer, Erik L. L. (författare)
- Stockholms universitet,Institutionen för biokemi och biofysik,Science for Life Laboratory (SciLifeLab)
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(creator_code:org_t)
- 2022-02-10
- 2022
- Engelska.
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Ingår i: Frontiers in Genetics. - : Frontiers Media SA. - 1664-8021. ; 13
- Relaterad länk:
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https://doi.org/10.3...
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https://www.frontier...
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https://urn.kb.se/re...
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https://doi.org/10.3...
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Abstract
Ämnesord
Stäng
- The regulatory relationships between genes and proteins in a cell form a gene regulatory network (GRN) that controls the cellular response to changes in the environment. A number of inference methods to reverse engineer the original GRN from large-scale expression data have recently been developed. However, the absence of ground-truth GRNs when evaluating the performance makes realistic simulations of GRNs necessary. One aspect of this is that local network motif analysis of real GRNs indicates that the feed-forward loop (FFL) is significantly enriched. To simulate this properly, we developed a novel motif-based preferential attachment algorithm, FFLatt, which outperformed the popular GeneNetWeaver network generation tool in reproducing the FFL motif occurrence observed in literature-based biological GRNs. It also preserves important topological properties such as scale-free topology, sparsity, and average in/out-degree per node. We conclude that FFLatt is well-suited as a network generation module for a benchmarking framework with the aim to provide fair and robust performance evaluation of GRN inference methods.
Ämnesord
- NATURVETENSKAP -- Biologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences (hsv//eng)
Nyckelord
- network biology
- gene regulatory networks
- gene-gene interaction
- network motif structure
- network generation
- network simulation
- benchmarking
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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