Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants
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Cites background or methods from "Genome-Wide Prediction of Metabolic..."
...Name to ID conversion Open [41] BiofOmics • Transcriptomics • Proteomics • Metabolomics Biofilm - Experiment library - Data depository Open [113] BioCyc/MetaCyc • Genomics • Proteomics • Metabolomics Unspecified - Online encyclopedia of metabolism - Predicted metabolic pathways in sequenced genomes - Enzyme data set - Metabolite database Open [111] Cell Illustrator 5.0 • Genomic • Transcriptomics • Proteomics Unspecified - Draw biological pathway models and simulations - Run biological cellular simulations and graphical display results Licensed [74] CellML (Open source XML language) • Transcriptomics • Proteomics • Metabolomics Unspecified - Open source language for biological cellular models Open [73] COBRA • Transcriptomics • Proteomics • Metabolomics • Fluxomics Unspecified - Genome scale integrated modeling of cell metabolism and macro-molecular expression Open [12,79] Metabolites 2019, 9, 76 12 of 31 Table 2....
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...Plant Metabolic Network (PMN) • Genomics • Proteomics • Metabolomics Plants - Plant-specific database containing pathways, enzymes, reactions, and compounds Open [100]...
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...Software Tool Omics Integrated Domain Functionality Type of license Reference MADMAX (Management and analysis database for multiple omics experiments) • Metagenomics • Transcriptomics • Metabolomics Plants, Medical and Clinical - Integrates omics data - Statistical analysis and pathway mapping Open [123] MapMan • Metagenomics • Transcriptomics • Metabolomics Plants (developed for use with Arabidopsis....
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...- Rapidly design new pathway maps based on user data and genome-scale models - Visualize data related to genes or proteins on the associated reactions and pathways - Identify trends in common genomic data types Open (MIT license) [116] Gaggle Variety of omics platformbioinformatics solutions Unspecified - Inoperability of the following tools: - Bioinformatics resource manager - Cytoscape - DataMatrixViewer - KEGG - Genome Browser - MeV - PIPE - BioTapestry - N-Browse Open [117] Metabolites 2019, 9, 76 13 of 31 Table 2....
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...Software Tool Omics Integrated Domain Functionality Type of license Reference GIM3E (Gene Inactivation Moderated by Metabolism, Metabolomics and Expression) • Transcriptomics • Metabolomics Unspecified - Establishes metabolite use requirements with metabolomics data - Model-paired transcriptomics data to find experimentally supported solutions - Calculates the turnover (production/consumption) flux of metabolites Open; Phython based and requires COBRApy 0.2.x. [118] INMEX (Integrative meta-analysis of expression data) • Transcriptomics • Metabolomics Medical and Clinical - Meta and integrative analysis of data - Pathway analysis Open [119] IMPaLA (Integrated Molecular Pathway Level Analysis) • Transcriptomics • Proteomics • Metabolomics Medical and clinical - Enrichment analysis - Pathway analysis Academic only [120] Ingenuity Pathway Analysis • Metagenomics • Transcriptomics • Proteomics • Metabolomics Medical (human) and clinical....
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292 citations
References
88,255 citations
"Genome-Wide Prediction of Metabolic..." refers methods in this paper
...Then, protein sequences were BLASTed against the Phytozome protein sequences, all splicing variants included, using BLAST+ 2.2.28+ (Camacho et al., 2009)....
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...Trends Plant Sci 19: 447–459 Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+: architecture and applications....
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...Pairwise sequence comparisons are performed using BLAST (Altschul et al., 1990; e value threshold# 1e-2) against RPSD v3....
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...Protein sequences from a genome are first subjected to an all-againstall BLAST followed by clustering using the Markov cluster algorithm (Enright et al., 2002) with the inflation value (cluster granularity parameter) set to 2....
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...Please follow the restrictions of BLAST and PRIAM....
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13,223 citations
"Genome-Wide Prediction of Metabolic..." refers background or methods in this paper
...…database by filtering for those sequences annotated with (1) a four-part EC number (IUBMB, 1992), (2) a MetaCyc reaction identifier in MetaCyc (Caspi et al., 2014) or PlantCyc (Zhang et al., 2010), or (3) a leaf-node Gene Ontology (Blake et al., 2013) term under catalytic activity…...
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...To compile the list of signature enzyme reactions, we extracted MetaCyc (Caspi et al., 2014) reactions producing terpenes from these three building blocks....
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...0, catalytic functions are defined as EF classes, which are based on either four-part EC numbers orMetaCyc reaction identifiers (Caspi et al., 2014)....
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...Specialized metabolism was classified into subdomains based on the metabolites they produce or metabolize (Wink, 2010; Caspi et al., 2014)....
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...1 was compiled from manually curated or experimentally supported data in SwissProt (UniProt Consortium, 2011; November 2014 release), BRENDA (Schomburg et al., 2013; November 2014 release), MetaCyc (Caspi et al., 2014; November 2014 release), and PlantCyc (Zhang et al., 2010; November 2014 release)....
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8,742 citations
3,932 citations
"Genome-Wide Prediction of Metabolic..." refers methods in this paper
...Protein sequences from a genome are first subjected to an all-againstall BLAST followed by clustering using the Markov cluster algorithm (Enright et al., 2002) with the inflation value (cluster granularity parameter) set to 2....
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