AraCyc: A Biochemical Pathway Database for Arabidopsis1

By Lukas A. Mueller, Peifen Zhang, Seung Yon Rhee. Plant Physiology, 2003

454 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/61cf068f740ab8c195cb80c27fe75d46e76b1a7e

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In Molecular Biology

Citations in the corpus

Inaugural Article: The protein expression landscape of the Arabidopsis root (2012, unknown): “To place our results in a functional context, we examined the overlap of our root cellular proteome and the Arabidopsis Plant Metabolic Network (30, 31).”
Approaches for extracting practical information from gene co-expression networks in plant biology. (2007, methodology): “In this report, the authors retrieved 1,330 genes associated with metabolism from the AraCyc database (Mueller et al. 2003; http://arabidopsis.org/tools/aracyc/).”
The Botany Array Resource: e-Northerns, Expression Angling, and promoter analyses. (2005, methodology): “…a number of portals for analysing microarray data have been developed, including TAIR (Garcia-Hernandez et al. , 2002; Rhee et al. , 2003), AraCyc (Mueller et al. , 2003), MAPMAN (Thimm et al. , 2004), and GENEVESTIGATOR (Zimmermann et al. , 2004), and for other plant species, e.g. BarleyBase…”
Expression profiling of Arabidopsis stigma tissue identifies stigma-specific genes (2005, unknown): “1,100 enzymatic reactions to 185 metabolic pathways (Mueller et al. 2003).”
Maize Metabolic Network Construction and Transcriptome Analysis (2013, background): “Th ese include the Plant Metabolic Network (PlantCyc) (Zhang et al., 2010) and species-specifi c metabolic networks for both dicots (Mueller et al., 2003, 2005; Zhang et al., 2005; Urbanczyk-Wochniak and Sumner, 2007) and monocots (Jaiswal et al., 2006; http://pathway.gramene.org/…”
An “Electronic Fluorescent Pictograph” Browser for Exploring and Analyzing Large-Scale Biological Data Sets (2007, methodology): “Among the various portals for analyzing microarray data that have been developed are TAIR [5,6], AraCyc [7], MAPMAN [8], GENEVESTIGATOR [9], and several tools of the Bio-Array Resource [10].”
Potential of metabolomics as a functional genomics tool. (2004, methodology): “A tool to visualize biochemical pathways of Arabidopsis [ 53 ].”
Computational prediction of human metabolic pathways from the complete human genome (2004, background): “Table 6 indicates whether or not each HumanCyc pathway is present in the EcoCyc E. coli PGDB and in the AraCyc PGDB for A. thaliana [13].”
MetaCyc: a multiorganism database of metabolic pathways and enzymes (2005, methodology): “Arabidopsis pathways are 5 exported to AraCyc, the Arabidopsis metabolism database (5) that was computationally predicted using MetaCyc as the reference database.”
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology (2010, background): “thaliana [66, 67].”
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases (2009, methodology): “More than 100 groups have used Pathway Tools and MetaCyc to create PGDBs for their organisms of interest, including important model organisms such as Saccharomyces cerevisiae (5), Arabidopsis thaliana (6), Oryza sativa (7), Mus musculus (8), Bos taurus (9), Medicago truncatula (10), Populus trichoca”
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases (2013, methodology): “More than 250 groups have used Pathway Tools and MetaCyc to create PGDBs for their organisms of interest, including important model organisms such as Saccharomyces cerevisiae (5), Arabidopsis thaliana (6), Oryza sativa (7), Mus musculus (8), Bos taurus (9), Medicago truncatula (10), Populus trichoca”
The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases (2007, methodology): “More than 80 groups have used Pathway Tools and MetaCyc to create PGDBs for their organisms of interest, including important model organisms such as Saccharomyces cerevisiae (4), Arabidopsis thaliana ( 5 ), Oryza sativa (6), Mus musculus (7), Bos taurus (8), Medicago truncatula (9), Dictyostelium di”
VANTED: A system for advanced data analysis and visualization in the context of biological networks (2006, methodology): “AraCyc [15].”
PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments (2006, methodology): “Given the initial limitation of only a few arrays per exper-iment, tools were first developed to visualize data on a one-experiment-at-a-time basis ([6-8]).”