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AraCyc specifications


Unique identifier OMICS_02670
Name AraCyc
Restrictions to use None
Version 5.0
Maintained Yes


  • Plants and Fungi
    • Arabidopsis thaliana

Publications for AraCyc

AraCyc citations


SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases

PMCID: 5946812
PMID: 29762652
DOI: 10.1093/database/bay035

[…] luding bacteria [Escherichia coli in EcoCyc ()], fungi (Saccharomyces cerevisiae in YeastCyc, mammals [Bos taurus in CattleCyc ()] and plants such as Arabidopsis thaliana in AraCyc (, ), Medicago truncatula in MedicCyc (), Fragaria vesca in FragariaCyc (), Oryza sativa in RiceCyc () and Zea mays in MaizeCyc (). While most PGDBs are created at the species level, this is no […]


When Transcriptomics and Metabolomics Work Hand in Hand: A Case Study Characterizing Plant CDF Transcription Factors

PMCID: 5876533
PMID: 29495643
DOI: 10.3390/ht7010007

[…] vealed a clear enrichment of terms related to abiotic stress responses, no conclusive evidence for the specific induction or repression of entire pathways could be unveiled by tools like MAPMAN [] or AraCyc []. Hence, it was concluded that phenotypic analyses and the transcriptomics datasets are not sufficient to fully disclose the molecular intricacies that confer enhanced drought resistance to t […]


The odd one out: Arabidopsis reticulon 20 does not bend ER membranes but has a role in lipid regulation

Sci Rep
PMCID: 5797236
PMID: 29396477
DOI: 10.1038/s41598-018-20840-0

[…] are predicted to be involved in sterol biosynthesis. RTN20 and RTN19 feature a predicted 3BETAHSD/D domain with a putative decarboxylating sterol-4-alpha-carboxylate 3-dehydrogenase activity (BLASTP, AraCyc) indicating a role in sterol regulation. For RTN17, 18, and 21 no conserved domain is predicted at the N-terminus (BLASTP). Reticulons in yeast have been shown to interact with other proteins, […]


A review of computational tools for design and reconstruction of metabolic pathways

PMCID: 5851934
PMID: 29552648
DOI: 10.1016/j.synbio.2017.11.002

[…] Chemical Translation Service and UniChem provide a simple web application that can interconvert metabolite IDs across different databases. Organism-specific GSMs or knowledge-bases (e.g., EcoCyc , AraCyc , and HumanCyc ) are often constructed or extracted from the larger databases, to ensure the design or identification of alternative pathways within an organism's native network. While certain […]


Relationships between drought, heat and air humidity responses revealed by transcriptome metabolome co analysis

BMC Plant Biol
PMCID: 5504741
PMID: 28693422
DOI: 10.1186/s12870-017-1062-y

[…] nd replicate measurement order using the nlme package in R []. Mapping of masses to metabolites was performed with MassTRIX [] and with ChemSpider [] using the metabolism data sources ChEMBL, BioCyc, AraCyc, MassBank, KEGG and Golm Metabolome Database and a maximum deviation of 2 ppm; matching results were ranked according to increasing monoisotopic mass distance. […]


Utility and Limitations of Using Gene Expression Data to Identify Functional Associations

PLoS Comput Biol
PMCID: 5147789
PMID: 27935950
DOI: 10.1371/journal.pcbi.1005244

[…] A. thaliana metabolic pathways (AraCyc pathways), the genes belonging to these pathways and supporting evidence were obtained from the Plant Metabolic Network (version 8, []). To examine a broader set of gene function in addition to […]


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AraCyc institution(s)
The Arabidopsis Information Resource, Department of Plant Biology, Carnegie Institution of Washington, Stanford, CA, USA

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