R36G8H last accessed: 2022-11-04

BioCyc Knowledge Library
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:01.065070

biocyc
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:01.065070

Other names: BioCyc Database Collection, BioCyc Knowledge Library, biocyc

The BioCyc collection of Pathway/Genome Databases (PGDBs) provides electronic reference sources on the pathways and genomes of hundreds of organisms with completely sequenced genomes. Each database contains the genome, predicted metabolic pathways, predicted genes that encode missing enzymes in metabolic pathways, and predicted operons (bacteria only). Tools available through BioCyc include a genome browser, displays of individual pathways and of the entire metabolic map, 'omics viewers for painting 'omics data onto the metabolic map and genome map, and an extensive collection of tools for comparative genomics and comparative pathway analysis.

Webpage:

http://biocyc.org/

Licence:

Name: other
URL: https://bioinformatics.ai.sri.com/ptools/licensing/all-reg.shtml

Publications:

Publications
More detailed information about this field from each metasource.

The EcoCyc Database
PMID: 11752253
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:01.065070

The MetaCyc Database
PMID: 11752254
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:01.065070

The EcoCyc Database PubMed citations: 135.

135 articles citing: The EcoCyc Database

1H, 13C and 15N assignment of stem-loop SL1 from the 5'-UTR of SARS-CoV-2. PMID:34453696
Genome-Scale Metabolic Models and Machine Learning Reveal Genetic Determinants of Antibiotic Resistance in Escherichia coli and Unravel the Underlying Metabolic Adaptation Mechanisms. PMID:34342537
Review of Machine Learning Methods for the Prediction and Reconstruction of Metabolic Pathways. PMID:34222327
Cell Lysis Directed by SulA in Response to DNA Damage in Escherichia coli. PMID:33926096
A Klebsiella pneumoniae ST307 outbreak clone from Germany demonstrates features of extensive drug resistance, hypermucoviscosity, and enhanced iron acquisition. PMID:33298160
Quantifying the distribution of protein oligomerization degree reflects cellular information capacity. PMID:33077848
The EcoCyc Database. PMID:30406744
Bioinformatics in Latin America and SoIBio impact, a tale of spin-off and expansion around genomes and protein structures. PMID:28981567
MCE domain proteins: conserved inner membrane lipid-binding proteins required for outer membrane homeostasis. PMID:28819315
Unveiling the Hybrid Genome Structure of Escherichia coli RR1 (HB101 RecA+). PMID:28421066
bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria and Escherichia coli. PMID:27694198
ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods. PMID:27242037
Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions. PMID:27099342
Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported. PMID:26873250
Gene selection and cloning approaches for co-expression and production of recombinant protein-protein complexes. PMID:26671275
Revisiting operons: an analysis of the landscape of transcriptional units in E. coli. PMID:26538447
The EcoCyc Database. PMID:26442933
MetaPathways v2.5: quantitative functional, taxonomic and usability improvements. PMID:26076725
Spatial features for Escherichia coli genome organization. PMID:25652224
Differential reconstructed gene interaction networks for deriving toxicity threshold in chemical risk assessment. PMID:24268022
Plant promoters: an approach of structure and function. PMID:24122284
Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling. PMID:23899370
Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution. PMID:23829427
Computational analyses of transcriptomic data reveal the dynamic organization of the Escherichia coli chromosome under different conditions. PMID:23599001
Global genomic arrangement of bacterial genes is closely tied with the total transcriptional efficiency. PMID:23434046
High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris. PMID:23098413
Recombinant E. coli expressing Vitreoscilla haemoglobin prefers aerobic metabolism under microaerobic conditions: a proteome-level study. PMID:22922188
Multiple long-term, experimentally-evolved populations of Escherichia coli acquire dependence upon citrate as an iron chelator for optimal growth on glucose. PMID:22909317
Robust detection of hierarchical communities from Escherichia coli gene expression data. PMID:22383870
Identification of aberrant pathways and network activities from high-throughput data. PMID:22287794
Sequence of the hyperplastic genome of the naturally competent Thermus scotoductus SA-01. PMID:22115438
Trade-offs and constraints in allosteric sensing. PMID:22096453
Genetics of Coxiella burnetii: on the path of specialization. PMID:22082290
Multi-membership gene regulation in pathway based microarray analysis. PMID:21939531
Functional characterization of bacterial sRNAs using a network biology approach. PMID:21876160
High-throughput workflow for monitoring and mining bioprocess data and its application to inferring the physiological response of Escherichia coli to perturbations. PMID:21841033
Modeling Three-Dimensional Chromosome Structures Using Gene Expression Data. PMID:21760653
Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough. PMID:21738675
Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis. PMID:21693016
CycADS: an annotation database system to ease the development and update of BioCyc databases. PMID:21474551
Analysis of membrane proteins in metagenomics: networks of correlated environmental features and protein families. PMID:20430783
Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis. PMID:20426876
A protocol for generating a high-quality genome-scale metabolic reconstruction. PMID:20057383
Stability of metabolic correlations under changing environmental conditions in Escherichia coli--a systems approach. PMID:19829699
A fast and efficient gene-network reconstruction method from multiple over-expression experiments. PMID:19686586
LeishCyc: a biochemical pathways database for Leishmania major. PMID:19497128
Mass spectrometric screening of transcriptional regulators involved in antibiotic biosynthesis in Streptomyces coelicolor A3(2). PMID:19468766
Database resources in metabolomics: an overview. PMID:19418229
Metabolite profiling reveals YihU as a novel hydroxybutyrate dehydrogenase for alternative succinic semialdehyde metabolism in Escherichia coli. PMID:19372223
Steady-state kinetic modeling constrains cellular resting states and dynamic behavior. PMID:19266013
Model-based redesign of global transcription regulation. PMID:19188257
Predicting protein linkages in bacteria: which method is best depends on task. PMID:18816389
MetNet: Software to Build and Model the Biogenetic Lattice of Arabidopsis. PMID:18629120
Functional genomics via metabolic footprinting: monitoring metabolite secretion by Escherichia coli tryptophan metabolism mutants using FT-IR and direct injection electrospray mass spectrometry. PMID:18629082
ISMB 2003 Text Mining SIG Meeting Report. PMID:18629019
The topology of the bacterial co-conserved protein network and its implications for predicting protein function. PMID:18590549
Inferring modules of functionally interacting proteins using the Bond Energy Algorithm. PMID:18559112
The hidden universal distribution of amino acid biosynthetic networks: a genomic perspective on their origins and evolution. PMID:18541022
Functional annotations in bacterial genomes based on small RNA signatures. PMID:18478081
Application of functional genomics to pathway optimization for increased isoprenoid production. PMID:18344344
SIGffRid: a tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statistics. PMID:18237374
Investigation of factors affecting prediction of protein-protein interaction networks by phylogenetic profiling. PMID:17967189
Multidimensional annotation of the Escherichia coli K-12 genome. PMID:17940092
Orthologous transcription factors in bacteria have different functions and regulate different genes. PMID:17845071
Cross-species cluster co-conservation: a new method for generating protein interaction networks. PMID:17803817
PHIDIAS: a pathogen-host interaction data integration and analysis system. PMID:17663773
A network perspective on the evolution of metabolism by gene duplication. PMID:17326820
Cataloging the relationships between proteins: a review of interaction databases. PMID:16943573
Bio-ontologies: current trends and future directions. PMID:16899495
The life-cycle of operons. PMID:16789824
A case study in pathway knowledgebase verification. PMID:16603083
BioWarehouse: a bioinformatics database warehouse toolkit. PMID:16556315
Extraction of phylogenetic network modules from the metabolic network. PMID:16533389
Low degree metabolites explain essential reactions and enhance modularity in biological networks. PMID:16524470
BIOZON: a system for unification, management and analysis of heterogeneous biological data. PMID:16480510
Hubs of knowledge: using the functional link structure in Biozon to mine for biologically significant entities. PMID:16480496
Asymmetrical evolution of cytochrome bd subunits. PMID:16474982
BIOZON: a hub of heterogeneous biological data. PMID:16381854
Mapping of orthologous genes in the context of biological pathways: An application of integer programming. PMID:16373500
Preferential attachment in the evolution of metabolic networks. PMID:16281983
In silico reconstruction of the metabolic pathways of Lactobacillus plantarum: comparing predictions of nutrient requirements with those from growth experiments. PMID:16269766
Insights on the evolution of metabolic networks of unicellular translationally biased organisms from transcriptomic data and sequence analysis. PMID:16187158
Querying and computing with BioCyc databases. PMID:15961440
A universally applicable method of operon map prediction on minimally annotated genomes using conserved genomic context. PMID:15942028
Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication. PMID:15942025
Operon formation is driven by co-regulation and not by horizontal gene transfer. PMID:15930492
Microbial metabolomics: replacing trial-and-error by the unbiased selection and ranking of targets. PMID:15895265
Evidence of selection for low cognate amino acid bias in amino acid biosynthetic enzymes. PMID:15853887
Gene fusions and gene duplications: relevance to genomic annotation and functional analysis. PMID:15757509
A novel method for accurate operon predictions in all sequenced prokaryotes. PMID:15701760
Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases. PMID:15642112
Computational prediction of human metabolic pathways from the complete human genome. PMID:15642094
Complete genome sequencing of Anaplasma marginale reveals that the surface is skewed to two superfamilies of outer membrane proteins. PMID:15618402
EcoCyc: a comprehensive database resource for Escherichia coli. PMID:15608210
EchoBASE: an integrated post-genomic database for Escherichia coli. PMID:15608209
An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs. PMID:15604458
RpoS-regulated genes of Escherichia coli identified by random lacZ fusion mutagenesis. PMID:15576800
OptStrain: a computational framework for redesign of microbial production systems. PMID:15520298
Global transcriptome analysis of the heat shock response of Shewanella oneidensis. PMID:15516594
Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states. PMID:15342562
Genome-wide transcriptional profiling of the Escherichia coli response to a proline-rich antimicrobial peptide. PMID:15328082
IdentiCS--identification of coding sequence and in silico reconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequence. PMID:15312235
Linear fuzzy gene network models obtained from microarray data by exhaustive search. PMID:15304201
A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases. PMID:15189570
Prolinks: a database of protein functional linkages derived from coevolution. PMID:15128449
Network analysis of metabolic enzyme evolution in Escherichia coli. PMID:15113413
Bioinformatic identification of novel regulatory DNA sequence motifs in Streptomyces coelicolor. PMID:15072583
Transcriptional organization of the Clostridium acetobutylicum genome. PMID:15060177
A guide to building image-centric databases. PMID:15043221
Quantifying modularity in the evolution of biomolecular systems. PMID:14993205
The metabolic world of Escherichia coli is not small. PMID:14757824
The aMAZE LightBench: a web interface to a relational database of cellular processes. PMID:14681453
MetaCyc: a multiorganism database of metabolic pathways and enzymes. PMID:14681452
RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. PMID:14681419
GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins. PMID:14681418
coliBASE: an online database for Escherichia coli, Shigella and Salmonella comparative genomics. PMID:14681417
The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli. PMID:14681416
Genome evolution reveals biochemical networks and functional modules. PMID:14673105
PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis. PMID:14604444
Enzyme-specific profiles for genome annotation: PRIAM. PMID:14602924
Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 by using a genome-scale in silico metabolic model. PMID:14563875
In silico atomic tracing by substrate-product relationships in Escherichia coli intermediary metabolism. PMID:14559781
Sigma 32-dependent promoter activity in vivo: sequence determinants of the groE promoter. PMID:13129951
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). PMID:12952533
Honor thy symbionts. PMID:12923294
CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle. PMID:12853624
Phydbac (phylogenomic display of bacterial genes): An interactive resource for the annotation of bacterial genomes. PMID:12824402
AraCyc: a biochemical pathway database for Arabidopsis. PMID:12805578
eVOC: a controlled vocabulary for unifying gene expression data. PMID:12799354
Metabolic networks of microbial systems. PMID:12740044
Thirteen years of building constraint-based in silico models of Escherichia coli. PMID:12700248
A microarray-based antibiotic screen identifies a regulatory role for supercoiling in the osmotic stress response of Escherichia coli. PMID:12566398
A knowledge framework for computational molecular-disease relationships in cancer. PMID:12463795
Network genomics--a novel approach for the analysis of biological systems in the post-genomic era. PMID:12463419
GeneCensus: genome comparisons in terms of metabolic pathway activity and protein family sharing. PMID:12384605
The MetaCyc Database PubMed citations: 106.

106 articles citing: The MetaCyc Database

Co-elicitation of lignocelluloytic enzymatic activities and metabolites production in an Aspergillus-Streptomyces co-culture during lignocellulose fractionation. PMID:35243445
The crewed journey to Mars and its implications for the human microbiome. PMID:35125119
Elevated atmospheric CO2 alters the microbial community composition and metabolic potential to mineralize organic phosphorus in the rhizosphere of wheat. PMID:35074003
Biochar Addition Altered Bacterial Community and Improved Photosynthetic Rate of Seagrass: A Mesocosm Study of Seagrass Thalassia hemprichii. PMID:34925287
Navigating Multi-Scale Cancer Systems Biology Towards Model-Driven Clinical Oncology and Its Applications in Personalized Therapeutics. PMID:34900668
Technical note: overcoming host contamination in bovine vaginal metagenomic samples with nanopore adaptive sequencing. PMID:34791313
Path to improving the life cycle and quality of genome-scale models of metabolism. PMID:34555324
Review of Machine Learning Methods for the Prediction and Reconstruction of Metabolic Pathways. PMID:34222327
Growth faltering regardless of chronic diarrhea is associated with mucosal immune dysfunction and microbial dysbiosis in the gut lumen. PMID:34158595
Prokaryotic communities from a lava tube cave in La Palma Island (Spain) are involved in the biogeochemical cycle of major elements. PMID:34026356
A model of dopamine and serotonin-kynurenine metabolism in cortisolemia: Implications for depression. PMID:33970902
Strategies for Enhancing in vitro Degradation of Linuron by Variovorax sp. Strain SRS 16 Under the Guidance of Metabolic Modeling. PMID:33937210
An Overview of Biological and Computational Methods for Designing Mechanism-Informed Anti-biofilm Agents. PMID:33927701
Stepwise pathogenic evolution of Mycobacterium abscessus. PMID:33926925
Longitudinal Profiling of the Macaque Vaginal Microbiome Reveals Similarities to Diverse Human Vaginal Communities. PMID:33906914
A Novel Gene Cluster Is Involved in the Degradation of Lignin-Derived Monoaromatics in Thermus oshimai JL-2. PMID:33741620
Gene Annotation in High Schools: Successful Student Pipeline and Teacher Professional Development in Bioscience Using GENI-ACT. PMID:33584559
Intraspecific Variability Largely Affects the Leaf Metabolomics Response to Isosmotic Macrocation Variations in Two Divergent Lettuce (Lactuca sativa L.) Varieties. PMID:33466229
Thermodynamic Limits and Optimality of Microbial Growth. PMID:33286054
Dysbiotic Lesional Microbiome With Filaggrin Missense Variants Associate With Atopic Dermatitis in India. PMID:33282748
Metagenomic Information Recovery from Human Stool Samples Is Influenced by Sequencing Depth and Profiling Method. PMID:33233349
Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses. PMID:32706331
Identification of enzymatic genes with the potential to reduce biomass recalcitrance through lignin manipulation in Arabidopsis. PMID:32514309
TranCEP: Predicting the substrate class of transmembrane transport proteins using compositional, evolutionary, and positional information. PMID:31935244
Manually curated genome-scale reconstruction of the metabolic network of Bacillus megaterium DSM319. PMID:31822710
An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs. PMID:31681429
Maturation of the infant rhesus macaque gut microbiome and its role in the development of diarrheal disease. PMID:31451108
The three-legged stool of understanding metabolism: integrating metabolomics with biochemical genetics and computational modeling. PMID:31294216
Trait ontology analysis based on association mapping studies bridges the gap between crop genomics and Phenomics. PMID:31159731
Consistency, Inconsistency, and Ambiguity of Metabolite Names in Biochemical Databases Used for Genome-Scale Metabolic Modelling. PMID:30736318
A Genome-Scale Metabolic Reconstruction of Phytophthora infestans With the Integration of Transcriptional Data Reveals the Key Metabolic Patterns Involved in the Interaction of Its Host. PMID:30042788
New perspectives: systems medicine in cardiovascular disease. PMID:29699591
Multiomics tools for the diagnosis and treatment of rare neurological disease. PMID:29536202
Metabolic Reconstruction and Modeling Microbial Electrosynthesis. PMID:28827682
A Web Tool for Generating High Quality Machine-readable Biological Pathways. PMID:28287524
A network-based pathway-expanding approach for pathway analysis. PMID:28155638
Host-Microbiome Interaction and Cancer: Potential Application in Precision Medicine. PMID:28018236
ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods. PMID:27242037
Different Transcriptional Responses from Slow and Fast Growth Rate Strains of Listeria monocytogenes Adapted to Low Temperature. PMID:26973610
Pathway-based variant enrichment analysis on the example of dilated cardiomyopathy. PMID:26547721
Publisher’s Note:Abstraction for data integration:Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction. PMID:26101093
The Listeria monocytogenes strain 10403S BioCyc database. PMID:25819074
Patterns of metabolite changes identified from large-scale gene perturbations in Arabidopsis using a genome-scale metabolic network. PMID:25670818
Comparison of human cell signaling pathway databases--evolution, drawbacks and challenges. PMID:25632107
Comparative genomics of Lactobacillus crispatus suggests novel mechanisms for the competitive exclusion of Gardnerella vaginalis. PMID:25480015
Pathway-based analysis tools for complex diseases: a review. PMID:25462153
BioModels linked dataset. PMID:25182954
Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum 'Diapherotrites'. PMID:25083931
Systematic permutation testing in GWAS pathway analyses: identification of genetic networks in dilated cardiomyopathy and ulcerative colitis. PMID:25052024
High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource. PMID:24927599
mzGroupAnalyzer--predicting pathways and novel chemical structures from untargeted high-throughput metabolomics data. PMID:24846183
PATHOME: an algorithm for accurately detecting differentially expressed subpathways. PMID:24681952
Reconstruction and visualization of carbohydrate, N-glycosylation pathways in Pichia pastoris CBS7435 using computational and system biology approaches. PMID:24432138
A systematic comparison of the MetaCyc and KEGG pathway databases. PMID:23530693
Network pharmacology strategies toward multi-target anticancer therapies: from computational models to experimental design principles. PMID:23530504
Mining disease fingerprints from within genetic pathways. PMID:23304411
Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target prediction. PMID:23146171
Ten years of pathway analysis: current approaches and outstanding challenges. PMID:22383865
Sequence of the hyperplastic genome of the naturally competent Thermus scotoductus SA-01. PMID:22115438
Reactome pathway analysis to enrich biological discovery in proteomics data sets. PMID:21751369
Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis. PMID:21693016
CycADS: an annotation database system to ease the development and update of BioCyc databases. PMID:21474551
Genomic heterogeneity within conservedmetabolic pathways of Arthrobacter species - a bioinformatic approach. PMID:21423891
Loss of genetic redundancy in reductive genome evolution. PMID:21379323
Plasticity in the purine-thiamine metabolic network of Salmonella. PMID:21135073
High-throughput generation, optimization and analysis of genome-scale metabolic models. PMID:20802497
Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions. PMID:20627862
Comparative genomics of metabolic networks of free-living and parasitic eukaryotes. PMID:20356377
Visualizing post genomics data-sets on customized pathway maps by ProMeTra-aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example. PMID:19698148
LeishCyc: a biochemical pathways database for Leishmania major. PMID:19497128
Database resources in metabolomics: an overview. PMID:19418229
Network integration and graph analysis in mammalian molecular systems biology. PMID:19045817
MetNet: Software to Build and Model the Biogenetic Lattice of Arabidopsis. PMID:18629120
The genome of the versatile nitrogen fixer Azorhizobium caulinodans ORS571. PMID:18522759
Activation of MAP kinase signaling through ERK5 but not ERK1 expression is associated with lymph node metastases in oral squamous cell carcinoma (OSCC). PMID:18472963
Environmental variability and modularity of bacterial metabolic networks. PMID:17888177
Using gene expression data and network topology to detect substantial pathways, clusters and switches during oxygen deprivation of Escherichia coli. PMID:17488495
TBestDB: a taxonomically broad database of expressed sequence tags (ESTs). PMID:17202165
An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits. PMID:17112314
Discovering functional gene expression patterns in the metabolic network of Escherichia coli with wavelets transforms. PMID:16524469
WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data. PMID:16423281
An approach for clustering gene expression data with error information. PMID:16409635
In silico reconstruction of the metabolic pathways of Lactobacillus plantarum: comparing predictions of nutrient requirements with those from growth experiments. PMID:16269766
Automation of gene assignments to metabolic pathways using high-throughput expression data. PMID:16135255
Querying and computing with BioCyc databases. PMID:15961440
Automated metabolic reconstruction for Methanococcus jannaschii. PMID:15810431
A mechanism for the association of amino acids with their codons and the origin of the genetic code. PMID:15764708
Molecular models of protein targets from Mycobacterium tuberculosis. PMID:15759144
Computational prediction of human metabolic pathways from the complete human genome. PMID:15642094
Genome2D: a visualization tool for the rapid analysis of bacterial transcriptome data. PMID:15128451
Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery. PMID:15078855
MiCoViTo: a tool for gene-centric comparison and visualization of yeast transcriptome states. PMID:15053844
A guide to building image-centric databases. PMID:15043221
Pathway length and evolutionary constraint in amino acid biosynthesis. PMID:15042343
MetaCyc: a multiorganism database of metabolic pathways and enzymes. PMID:14681452
Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms. PMID:14681421
Metabolic reconstruction of sulfur assimilation in the extremophile Acidithiobacillus ferrooxidans based on genome analysis. PMID:14675496
PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis. PMID:14604444
Enzyme-specific profiles for genome annotation: PRIAM. PMID:14602924
Protein complexes and functional modules in molecular networks. PMID:14517352
Honor thy symbionts. PMID:12923294
AraCyc: a biochemical pathway database for Arabidopsis. PMID:12805578
eVOC: a controlled vocabulary for unifying gene expression data. PMID:12799354
MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. PMID:12540299
The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. PMID:12519987
Network genomics--a novel approach for the analysis of biological systems in the post-genomic era. PMID:12463419

Tags:

Tags
More detailed information about this field from each metasource.

metabolic and signaling pathways
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metabolic pathways
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

dna
metasource: re3data.org
version: re3data.org: BioCyc Database Collection; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R36G8H last accessed: 2022-11-04

gene expression
metasource: re3data.org
version: re3data.org: BioCyc Database Collection; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R36G8H last accessed: 2022-11-04

metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:01.065070

genomes
metasource: re3data.org
version: re3data.org: BioCyc Database Collection; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R36G8H last accessed: 2022-11-04

life sciences
metasource: re3data.org
version: re3data.org: BioCyc Database Collection; editing status 2021-09-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R36G8H last accessed: 2022-11-04

molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:01.065070

endocrinology and metabolism
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:01.065070

enzymes
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:01.065070

database management
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:01.065070

metabolic and signaling pathways metabolic and signaling pathways dna gene expression genomes life sciences molecular interactions, pathways and networks endocrinology and metabolism enzyme data management

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MetaCyc

BsubCyc

HumanCyc

EcoCyc E. coli Database

BioCarta Pathways

YeastCyc

MetaCrop 2.0

Small Molecule Pathway Database

Pathway Commons

Reactome - a curated knowledgebase of biological pathways

RNApathwaysDB

SYSTOMONAS

LAMP

Pathway Ontology

Pathguide

BioSilico

PMAP

ECMDB

MANET

Integrated Pathway Analysis and Visualization System