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Karlebach G, Robinson PN. Computing Minimal Boolean Models of Gene Regulatory Networks. J Comput Biol 2024; 31:117-127. [PMID: 37889991 DOI: 10.1089/cmb.2023.0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2023] Open
Abstract
Models of gene regulatory networks (GRNs) capture the dynamics of the regulatory processes that occur within the cell as a means to understanding the variability observed in gene expression between different conditions. Arguably the simplest mathematical construct used for modeling is the Boolean network, which dictates a set of logical rules for transition between states described as Boolean vectors. Due to the complexity of gene regulation and the limitations of experimental technologies, in most cases knowledge about regulatory interactions and Boolean states is partial. In addition, the logical rules themselves are not known a priori. Our goal in this work is to create an algorithm that finds the network that fits the data optimally, and identify the network states that correspond to the noise-free data. We present a novel methodology for integrating experimental data and performing a search for the optimal consistent structure via optimization of a linear objective function under a set of linear constraints. In addition, we extend our methodology into a heuristic that alleviates the computational complexity of the problem for datasets that are generated by single-cell RNA-Sequencing (scRNA-Seq). We demonstrate the effectiveness of these tools using simulated data, and in addition a publicly available scRNA-Seq dataset and the GRN that is associated with it. Our methodology will enable researchers to obtain a better understanding of the dynamics of GRNs and their biological role.
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Affiliation(s)
- Guy Karlebach
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
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Garcia-Albornoz M, Holman SW, Antonisse T, Daran-Lapujade P, Teusink B, Beynon RJ, Hubbard SJ. A proteome-integrated, carbon source dependent genetic regulatory network in Saccharomyces cerevisiae. Mol Omics 2021; 16:59-72. [PMID: 31868867 DOI: 10.1039/c9mo00136k] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Integrated regulatory networks can be powerful tools to examine and test properties of cellular systems, such as modelling environmental effects on the molecular bioeconomy, where protein levels are altered in response to changes in growth conditions. Although extensive regulatory pathways and protein interaction data sets exist which represent such networks, few have formally considered quantitative proteomics data to validate and extend them. We generate and consider such data here using a label-free proteomics strategy to quantify alterations in protein abundance for S. cerevisiae when grown on minimal media using glucose, galactose, maltose and trehalose as sole carbon sources. Using a high quality-controlled subset of proteins observed to be differentially abundant, we constructed a proteome-informed network, comprising 1850 transcription factor interactions and 37 chaperone interactions, which defines the major changes in the cellular proteome when growing under different carbon sources. Analysis of the differentially abundant proteins involved in the regulatory network pointed to their significant roles in specific metabolic pathways and function, including glucose homeostasis, amino acid biosynthesis, and carbohydrate metabolic process. We noted strong statistical enrichment in the differentially abundant proteome of targets of known transcription factors associated with stress responses and altered carbon metabolism. This shows how such integrated analysis can lend further experimental support to annotated regulatory interactions, since the proteomic changes capture both magnitude and direction of gene expression change at the level of the affected proteins. Overall this study highlights the power of quantitative proteomics to help define regulatory systems pertinent to environmental conditions.
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Affiliation(s)
- M Garcia-Albornoz
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester M13 9PT, UK.
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Geistlinger L, Csaba G, Santarelli M, Ramos M, Schiffer L, Turaga N, Law C, Davis S, Carey V, Morgan M, Zimmer R, Waldron L. Toward a gold standard for benchmarking gene set enrichment analysis. Brief Bioinform 2020; 22:545-556. [PMID: 32026945 PMCID: PMC7820859 DOI: 10.1093/bib/bbz158] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/11/2019] [Accepted: 11/09/2019] [Indexed: 12/22/2022] Open
Abstract
MOTIVATION Although gene set enrichment analysis has become an integral part of high-throughput gene expression data analysis, the assessment of enrichment methods remains rudimentary and ad hoc. In the absence of suitable gold standards, evaluations are commonly restricted to selected datasets and biological reasoning on the relevance of resulting enriched gene sets. RESULTS We develop an extensible framework for reproducible benchmarking of enrichment methods based on defined criteria for applicability, gene set prioritization and detection of relevant processes. This framework incorporates a curated compendium of 75 expression datasets investigating 42 human diseases. The compendium features microarray and RNA-seq measurements, and each dataset is associated with a precompiled GO/KEGG relevance ranking for the corresponding disease under investigation. We perform a comprehensive assessment of 10 major enrichment methods, identifying significant differences in runtime and applicability to RNA-seq data, fraction of enriched gene sets depending on the null hypothesis tested and recovery of the predefined relevance rankings. We make practical recommendations on how methods originally developed for microarray data can efficiently be applied to RNA-seq data, how to interpret results depending on the type of gene set test conducted and which methods are best suited to effectively prioritize gene sets with high phenotype relevance. AVAILABILITY http://bioconductor.org/packages/GSEABenchmarkeR. CONTACT ludwig.geistlinger@sph.cuny.edu.
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Affiliation(s)
- Ludwig Geistlinger
- Graduate School of Public Health and Health Policy, City University of New York, New York, NY 10027, USA
| | - Gergely Csaba
- Institute for Implementation Science and Population Health, City University of New York, New York, NY 10027, USA
| | - Mara Santarelli
- Institute for Bioinformatics, Ludwig-Maximilians-Universität München, 80333 Munich, Germany
| | - Marcel Ramos
- Roswell Park Cancer Institute, Buffalo, NY 14203, USA
| | - Lucas Schiffer
- Graduate School of Arts and Sciences, Boston University, Boston, MA 02215, USA
| | - Nitesh Turaga
- Epigenetics and Development Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Charity Law
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Sean Davis
- Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | | | | | | | - Levi Waldron
- Graduate School of Public Health and Health Policy, City University of New York, New York, NY 10027, USA
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Closed-loop cycles of experiment design, execution, and learning accelerate systems biology model development in yeast. Proc Natl Acad Sci U S A 2019; 116:18142-18147. [PMID: 31420515 PMCID: PMC6731661 DOI: 10.1073/pnas.1900548116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Systems biology involves the development of large computational models of biological systems. The radical improvement of systems biology models will necessarily involve the automation of model improvement cycles. We present here a general approach to automating systems biology model improvement. Humans are eukaryotic organisms, and the yeast Saccharomyces cerevisiae is widely used in biology as a “model” for eukaryotic cells. The yeast diauxic shift is the most studied cellular transformation. We combined multiple software tools with integrated laboratory robotics to execute three semiautomated cycles of diauxic shift model improvement. All the experiments were formalized and communicated to a cloud laboratory automation system (Eve) for execution. The resulting improved model is relevant to understanding cancer, the immune system, and aging. One of the most challenging tasks in modern science is the development of systems biology models: Existing models are often very complex but generally have low predictive performance. The construction of high-fidelity models will require hundreds/thousands of cycles of model improvement, yet few current systems biology research studies complete even a single cycle. We combined multiple software tools with integrated laboratory robotics to execute three cycles of model improvement of the prototypical eukaryotic cellular transformation, the yeast (Saccharomyces cerevisiae) diauxic shift. In the first cycle, a model outperforming the best previous diauxic shift model was developed using bioinformatic and systems biology tools. In the second cycle, the model was further improved using automatically planned experiments. In the third cycle, hypothesis-led experiments improved the model to a greater extent than achieved using high-throughput experiments. All of the experiments were formalized and communicated to a cloud laboratory automation system (Eve) for automatic execution, and the results stored on the semantic web for reuse. The final model adds a substantial amount of knowledge about the yeast diauxic shift: 92 genes (+45%), and 1,048 interactions (+147%). This knowledge is also relevant to understanding cancer, the immune system, and aging. We conclude that systems biology software tools can be combined and integrated with laboratory robots in closed-loop cycles.
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Berchtold E, Csaba G, Zimmer R. RelExplain-integrating data and networks to explain biological processes. Bioinformatics 2018; 33:1837-1844. [PMID: 28165113 DOI: 10.1093/bioinformatics/btx060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 01/31/2017] [Indexed: 11/14/2022] Open
Abstract
Motivation The goal of many genome-wide experiments is to explain the changes between the analyzed conditions. Typically, the analysis is started with a set of differential genes DG and the first step is to identify the set of relevant biological processes BP . Current enrichment methods identify the involved biological process via statistically significant overrepresentation of differential genes in predefined sets, but do not further explain how the differential genes interact with each other or which other genes might be important for the enriched process. Other network-based methods determine subnetworks of interacting genes containing many differential genes, but do not employ process knowledge for a more focused analysis. Results RelExplain is a method to analyze a given biological process bp (e.g. identified by enrichment) in more detail by computing an explanation using the measured DG and a given network. An explanation is a subnetwork that contains the differential genes in the process bp and connects them in the best way given the experimental data using also genes that are not differential or not in bp . RelExplain takes into account the functional annotations of nodes and the edge consistency of the measurements. Explanations are compact networks of the relevant part of the bp and additional nodes that might be important for the bp . Our evaluation showed that RelExplain is better suited to retrieve manually curated subnetworks from unspecific networks than other algorithms. The interactive RelExplain tool allows to compute and inspect sub-optimal and alternative optimal explanations. Availability and Implementation A webserver is available at https://services.bio.ifi.lmu.de/relexplain . Contact berchtold@bio.ifi.lmu.de. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Evi Berchtold
- Department of Informatics, Institute of Bioinformatics, Ludwig-Maximilians-Universität München, Amalienstraße 17, München, Germany
| | - Gergely Csaba
- Department of Informatics, Institute of Bioinformatics, Ludwig-Maximilians-Universität München, Amalienstraße 17, München, Germany
| | - Ralf Zimmer
- Department of Informatics, Institute of Bioinformatics, Ludwig-Maximilians-Universität München, Amalienstraße 17, München, Germany
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Hu Y, Qin Y, Liu G. Collection and Curation of Transcriptional Regulatory Interactions in Aspergillus nidulans and Neurospora crassa Reveal Structural and Evolutionary Features of the Regulatory Networks. Front Microbiol 2018; 9:27. [PMID: 29403467 PMCID: PMC5780447 DOI: 10.3389/fmicb.2018.00027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 01/08/2018] [Indexed: 12/21/2022] Open
Abstract
Transcriptional regulation has important roles in various biological processes (e.g., development and metabolism) in filamentous fungi. However, regulatory interactions between transcription factors (TFs) and their target genes in these species have only been described in different forms by primary scientific literature, which limits the integrated analysis of these data. Here, we extensively curated the reported transcriptional regulatory interactions in Aspergillus nidulans and Neurospora crassa. For each interaction, the identifiers of involved proteins or genes were unified, and the types of supporting experiments were recorded. Then, transcriptional regulatory networks were reconstructed from the interactions supported by classical low-throughput experiments. Analysis of the networks revealed the presence of hub targets regulated by multiple TFs and network motifs of other structures (e.g., regulatory loops). Comparison of the regulatory interactions between the two species identified 33 conserved interactions supported by classical experiments in both species, most of which are involved in the regulation of metabolic genes. We anticipate the curated data would serve as a catalog for the studies of transcriptional regulation in filamentous fungi.
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Affiliation(s)
- Yibo Hu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, China.,Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | - Yuqi Qin
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, China.,National Glycoengineering Research Center, Shandong University, Jinan, China
| | - Guodong Liu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, China
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Wang Z, Danziger SA, Heavner BD, Ma S, Smith JJ, Li S, Herricks T, Simeonidis E, Baliga NS, Aitchison JD, Price ND. Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast. PLoS Comput Biol 2017; 13:e1005489. [PMID: 28520713 PMCID: PMC5453602 DOI: 10.1371/journal.pcbi.1005489] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 06/01/2017] [Accepted: 03/30/2017] [Indexed: 01/24/2023] Open
Abstract
Gene regulatory and metabolic network models have been used successfully in many organisms, but inherent differences between them make networks difficult to integrate. Probabilistic Regulation Of Metabolism (PROM) provides a partial solution, but it does not incorporate network inference and underperforms in eukaryotes. We present an Integrated Deduced And Metabolism (IDREAM) method that combines statistically inferred Environment and Gene Regulatory Influence Network (EGRIN) models with the PROM framework to create enhanced metabolic-regulatory network models. We used IDREAM to predict phenotypes and genetic interactions between transcription factors and genes encoding metabolic activities in the eukaryote, Saccharomyces cerevisiae. IDREAM models contain many fewer interactions than PROM and yet produce significantly more accurate growth predictions. IDREAM consistently outperformed PROM using any of three popular yeast metabolic models and across three experimental growth conditions. Importantly, IDREAM's enhanced accuracy makes it possible to identify subtle synthetic growth defects. With experimental validation, these novel genetic interactions involving the pyruvate dehydrogenase complex suggested a new role for fatty acid-responsive factor Oaf1 in regulating acetyl-CoA production in glucose grown cells.
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Affiliation(s)
- Zhuo Wang
- Key laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Samuel A. Danziger
- Institute for Systems Biology, Seattle, Washington, United States of America
- Center for Infectious Disease Research, Seattle, Washington, United States of America
| | - Benjamin D. Heavner
- Institute for Systems Biology, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Shuyi Ma
- Institute for Systems Biology, Seattle, Washington, United States of America
- Center for Infectious Disease Research, Seattle, Washington, United States of America
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana-Champaign, Illinois, United States of America
| | - Jennifer J. Smith
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Song Li
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Thurston Herricks
- Institute for Systems Biology, Seattle, Washington, United States of America
| | | | - Nitin S. Baliga
- Institute for Systems Biology, Seattle, Washington, United States of America
- Departments of Biology and Microbiology & Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
- Lawrence Berkeley National Lab, Berkeley, California, United States of America
| | - John D. Aitchison
- Institute for Systems Biology, Seattle, Washington, United States of America
- Center for Infectious Disease Research, Seattle, Washington, United States of America
| | - Nathan D. Price
- Institute for Systems Biology, Seattle, Washington, United States of America
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Junier I, Rivoire O. Conserved Units of Co-Expression in Bacterial Genomes: An Evolutionary Insight into Transcriptional Regulation. PLoS One 2016; 11:e0155740. [PMID: 27195891 PMCID: PMC4873041 DOI: 10.1371/journal.pone.0155740] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 05/03/2016] [Indexed: 12/18/2022] Open
Abstract
Genome-wide measurements of transcriptional activity in bacteria indicate that the transcription of successive genes is strongly correlated beyond the scale of operons. Here, we analyze hundreds of bacterial genomes to identify supra-operonic segments of genes that are proximal in a large number of genomes. We show that these synteny segments correspond to genomic units of strong transcriptional co-expression. Structurally, the segments contain operons with specific relative orientations (co-directional or divergent) and nucleoid-associated proteins are found to bind at their boundaries. Functionally, operons inside a same segment are highly co-expressed even in the apparent absence of regulatory factors at their promoter regions. Remote operons along DNA can also be co-expressed if their corresponding segments share a transcriptional or sigma factor, without requiring these factors to bind directly to the promoters of the operons. As evidence that these results apply across the bacterial kingdom, we demonstrate them both in the Gram-negative bacterium Escherichia coli and in the Gram-positive bacterium Bacillus subtilis. The underlying process that we propose involves only RNA-polymerases and DNA: it implies that the transcription of an operon mechanically enhances the transcription of adjacent operons. In support of a primary role of this regulation by facilitated co-transcription, we show that the transcription en bloc of successive operons as a result of transcriptional read-through is strongly and specifically enhanced in synteny segments. Finally, our analysis indicates that facilitated co-transcription may be evolutionary primitive and may apply beyond bacteria.
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Affiliation(s)
- Ivan Junier
- CNRS, TIMC-IMAG, F-38000 Grenoble, France.,Univ. Grenoble Alpes, TIMC-IMAG, F-38000 Grenoble, France
| | - Olivier Rivoire
- CNRS, LIPhy, F-38000 Grenoble, France.,Univ. Grenoble Alpes, LIPhy, F-38000 Grenoble, France
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Geistlinger L, Csaba G, Zimmer R. Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis. BMC Bioinformatics 2016; 17:45. [PMID: 26791995 PMCID: PMC4721010 DOI: 10.1186/s12859-016-0884-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 01/08/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Enrichment analysis of gene expression data is essential to find functional groups of genes whose interplay can explain experimental observations. Numerous methods have been published that either ignore (set-based) or incorporate (network-based) known interactions between genes. However, the often subtle benefits and disadvantages of the individual methods are confusing for most biological end users and there is currently no convenient way to combine methods for an enhanced result interpretation. RESULTS We present the EnrichmentBrowser package as an easily applicable software that enables (1) the application of the most frequently used set-based and network-based enrichment methods, (2) their straightforward combination, and (3) a detailed and interactive visualization and exploration of the results. The package is available from the Bioconductor repository and implements additional support for standardized expression data preprocessing, differential expression analysis, and definition of suitable input gene sets and networks. CONCLUSION The EnrichmentBrowser package implements essential functionality for the enrichment analysis of gene expression data. It combines the advantages of set-based and network-based enrichment analysis in order to derive high-confidence gene sets and biological pathways that are differentially regulated in the expression data under investigation. Besides, the package facilitates the visualization and exploration of such sets and pathways.
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Affiliation(s)
- Ludwig Geistlinger
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, Amalienstrasse 1780333, Munich, Germany.
| | - Gergely Csaba
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, Amalienstrasse 1780333, Munich, Germany.
| | - Ralf Zimmer
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, Amalienstrasse 1780333, Munich, Germany.
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Kuang YT, Bhat R, Davies R. Mechanisms of Repair of Low Water Activity and pH-Injured Z
ygosaccharomyces rouxii
YSa40 in Glycerol and Sucrose/CPB Liquid Holding System. J FOOD PROCESS PRES 2015. [DOI: 10.1111/jfpp.12328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Yeoh Tow Kuang
- School of Hospitality, Tourism and Culinary Arts; Taylor's University; Lakeside Campus Subang Jaya 47500 Selangor Malaysia
| | - Rajeev Bhat
- Food Technology Division; School of Industrial Technology; Universiti Sains Malaysia; Penang 11800 Malaysia
| | - Roland Davies
- Department of Food and Nutritional Sciences; University of Reading; Reading United Kingdom
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Costanzo MC, Engel SR, Wong ED, Lloyd P, Karra K, Chan ET, Weng S, Paskov KM, Roe GR, Binkley G, Hitz BC, Cherry JM. Saccharomyces genome database provides new regulation data. Nucleic Acids Res 2013; 42:D717-25. [PMID: 24265222 PMCID: PMC3965049 DOI: 10.1093/nar/gkt1158] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is the community resource for genomic, gene and protein information about the budding yeast Saccharomyces cerevisiae, containing a variety of functional information about each yeast gene and gene product. We have recently added regulatory information to SGD and present it on a new tabbed section of the Locus Summary entitled 'Regulation'. We are compiling transcriptional regulator-target gene relationships, which are curated from the literature at SGD or imported, with permission, from the YEASTRACT database. For nearly every S. cerevisiae gene, the Regulation page displays a table of annotations showing the regulators of that gene, and a graphical visualization of its regulatory network. For genes whose products act as transcription factors, the Regulation page also shows a table of their target genes, accompanied by a Gene Ontology enrichment analysis of the biological processes in which those genes participate. We additionally synthesize information from the literature for each transcription factor in a free-text Regulation Summary, and provide other information relevant to its regulatory function, such as DNA binding site motifs and protein domains. All of the regulation data are available for querying, analysis and download via YeastMine, the InterMine-based data warehouse system in use at SGD.
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Affiliation(s)
- Maria C Costanzo
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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