NDLI: A comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiae

Content Provider	PubMed Central
Author	Ludwig, Geistlinger Csaba, Gergely Simon, Dirmeier Küffner, Robert Zimmer, Ralf
Copyright Year	2013
Abstract	Existing machine-readable resources for large-scale gene regulatory networks usually do not provide context information characterizing the activating conditions for a regulation and how targeted genes are affected. Although this information is essentially required for data interpretation, available networks are often restricted to not condition-dependent, non-quantitative, plain binary interactions as derived from high-throughput screens. In this article, we present a comprehensive Petri net based regulatory network that controls the diauxic shift in Saccharomyces cerevisiae. For 100 specific enzymatic genes, we collected regulations from public databases as well as identified and manually curated >400 relevant scientific articles. The resulting network consists of >300 multi-input regulatory interactions providing (i) activating conditions for the regulators; (ii) semi-quantitative effects on their targets; and (iii) classification of the experimental evidence. The diauxic shift network compiles widespread distributed regulatory information and is available in an easy-to-use machine-readable form. Additionally, we developed a browsable system organizing the network into pathway maps, which allows to inspect and trace the evidence for each annotated regulation in the model.
Related Links	http://dx.doi.org/10.1093/nar/gkt631
Ending Page	8463
Page Count	12
Starting Page	8452
File Format	PDF
ISSN	03051048
e-ISSN	13624962
Journal	Nucleic Acids Research
Issue Number	18
Volume Number	41
Language	English
Publisher	Oxford University Press
Publisher Date	2013-10-01
Access Restriction	Open
Rights Holder	Oxford University Press
Subject Keyword	Genetics Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Genetics

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