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Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary

https://doi.org/10.1093/bioinformatics/bti430
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Ligand-receptor interactions
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Basic Local Alignment Search Tool
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A database for post-genome analysis
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Bile acid biosynthesis
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Gene Ontology: tool for the unification of biology
inferredcites →https://doi.org/10.1038/ng0502-19openalex-snapshot
GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways
inferredcites →https://doi.org/10.1081/bip-200025659openalex-snapshot
A Knowledge-Based Clustering Algorithm Driven by Gene Ontology
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Nutritional Homeostasis in Batch and Steady-State Culture of Yeast
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Identifying periodically expressed transcripts in microarray time series data
inferredcites →https://doi.org/10.1093/bioinformatics/btg420openalex-snapshot
A graph-theoretic modeling on GO space for biological interpretation of gene clusters
inferredcites →https://doi.org/10.1093/bioinformatics/btg455openalex-snapshot
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes
inferredcites →https://doi.org/10.1093/bioinformatics/bth087openalex-snapshot
NetAffx Gene Ontology Mining Tool: a visual approach for microarray data analysis
inferredcites →https://doi.org/10.1093/bioinformatics/bth088openalex-snapshot
GOstat: find statistically overrepresented Gene Ontologies within a group of genes
inferredcites →https://doi.org/10.1093/bioinformatics/bth456openalex-snapshot
GO::TermFinder—open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
inferredcites →https://doi.org/10.1093/bioinformatics/bth495openalex-snapshot
OntologyTraverser: an R package for GO analysis
inferredcites →https://doi.org/10.1093/bioinformatics/btn430openalex-snapshot
Identifying periodically expressed transcripts in microarray time series data
inferredcites →https://doi.org/10.1093/nar/25.17.3389openalex-snapshot
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
inferredcites →https://doi.org/10.1093/nar/27.1.29openalex-snapshot
KEGG: Kyoto Encyclopedia of Genes and Genomes
inferredcites →https://doi.org/10.1093/nar/28.1.27openalex-snapshot
KEGG: Kyoto Encyclopedia of Genes and Genomes
inferredcites →https://doi.org/10.1093/nar/gkg046openalex-snapshot
The InterPro Database, 2003 brings increased coverage and new features
inferredcites →https://doi.org/10.1093/nar/gkg555openalex-snapshot
OntoBlast function: from sequence similarities directly to potential functional annotations by ontology terms
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Automated Gene Ontology annotation for anonymous sequence data
inferredcites →https://doi.org/10.1093/nar/gkg624openalex-snapshot
Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate
inferredcites →https://doi.org/10.1093/nar/gkh108openalex-snapshot
The CyberCell Database (CCDB): a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli
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GFINDer: Genome Function INtegrated Discoverer through dynamic annotation, statistical analysis, and mining
inferredcites →https://doi.org/10.1093/nar/gkh476openalex-snapshot
ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics
inferredcites →https://doi.org/10.1101/gr.226602openalex-snapshot
Pathway Processor: A Tool for Integrating Whole-Genome Expression Results into Metabolic Networks
inferredcites →https://doi.org/10.1101/gr.985203openalex-snapshot
eVOC: A Controlled Vocabulary for Unifying Gene Expression Data
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A Direct Approach to False Discovery Rates
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Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
inferredcites →https://doi.org/10.1126/science.1100330openalex-snapshot
The Complete Genome Sequence of Propionibacterium Acnes , a Commensal of Human Skin
inferredcites →https://doi.org/10.1146/annurev.bi.60.070191.003353openalex-snapshot
RNA POLYMERASE II
inferredcites →https://doi.org/10.1186/1471-2105-4-56openalex-snapshot
PathMAPA: a tool for displaying gene expression and performing statistical tests on metabolic pathways at multiple levels for Arabidopsis
inferredcites →https://doi.org/10.1186/gb-2003-4-4-r28openalex-snapshot
GoMiner: a resource for biological interpretation of genomic and proteomic data

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inferred← citeshttps://doi.org/10.1007/s00299-023-03053-2openalex-snapshot
Dose effects of restorer gene modulate pollen fertility in cotton CMS-D2 restorer lines via auxin signaling and flavonoid biosynthesis
inferred← citeshttps://doi.org/10.1007/s00299-023-03079-6openalex-snapshot
A comprehensive investigation of the regulatory roles of OsERF096, an AP2/ERF transcription factor, in rice cold stress response
inferred← citeshttps://doi.org/10.1007/s00299-024-03155-5openalex-snapshot
Multi-omics revealed molecular mechanism of biphenyl phytoalexin formation in response to yeast extract-induced oxidative stress in Sorbus aucuparia suspension cells
inferred← citeshttps://doi.org/10.1007/s00299-025-03671-yopenalex-snapshot
Transcriptomic insights into gibberellin-3-mediated regulation of bud dormancy and metabolic transition in pitaya (Hylocereus polyrhizus)
inferred← citeshttps://doi.org/10.1007/s00299-026-03914-6openalex-snapshot
Comparative multi-omics uncover conserved and lineage-specific defense strategies to southern corn rust in temperate and tropical maize
inferred← citeshttps://doi.org/10.1007/s00343-017-6023-7openalex-snapshot
Improvement of Nannochloropsis oceanica growth performance through chemical mutation and characterization of fast growth physiology by transcriptome profiling
inferred← citeshttps://doi.org/10.1007/s00343-019-8019-yopenalex-snapshot
Transcriptome analysis of kelp Saccharina japonica unveils its weird transcripts and metabolite shift of main components at different sporophyte developmental stages
inferred← citeshttps://doi.org/10.1007/s00343-019-8202-1openalex-snapshot
Domestication of marine microalga Nannochloropsis oceanica to freshwater medium and the physiological responses
inferred← citeshttps://doi.org/10.1007/s00343-019-9056-2openalex-snapshot
Transcriptomic analysis reveals putative osmoregulation mechanisms in the kidney of euryhaline turbot Scophthalmus maximus responded to hypo-saline seawater
inferred← citeshttps://doi.org/10.1007/s00343-020-9302-7openalex-snapshot
Comparative transcriptome analysis of abalone Haliotis discus hannai with green and gray egg colors
inferred← citeshttps://doi.org/10.1007/s00343-021-0444-zopenalex-snapshot
Transcriptome of hepatopancreas in kuruma shrimp Marsupenaeus japonicus under low-salinity stress
inferred← citeshttps://doi.org/10.1007/s00343-021-1076-zopenalex-snapshot
Transcriptome analysis of Porphyridium purpureum under salinities of 0 and 68
inferred← citeshttps://doi.org/10.1007/s00343-024-3127-8openalex-snapshot
Identification and construction of lncRNA-miRNA-mRNA ceRNA networks associated with temperature changes in Sebastiscus marmoratus
inferred← citeshttps://doi.org/10.1007/s00343-024-4080-2openalex-snapshot
Comparative transcriptome analysis revealed host defense responses in endosymbiotic gill of Bathymodiolus mussels inhabiting cold seeps and hydrothermal vents
inferred← citeshttps://doi.org/10.1007/s00343-025-4256-4openalex-snapshot
Transcriptomic dynamics in the hepatopancreas of Macrobrachium rosenbergii during thermal elimination of infection with Decapod Iridescent Virus 1
inferred← citeshttps://doi.org/10.1007/s00343-025-4331-xopenalex-snapshot
Transcriptomic insights into the adaptive mechanisms of antennal glands in mud crab (Scylla paramamosain) to acute chloride-type low-salinity alkaline water stress
inferred← citeshttps://doi.org/10.1007/s00344-015-9535-4openalex-snapshot
Transcriptome Sequencing Determined Flowering Pathway Genes in Aechmea fasciata Treated with Ethylene
inferred← citeshttps://doi.org/10.1007/s00344-019-09944-7openalex-snapshot
RNA-Seq Analysis Reveals Differential Responses of Potato (Solanum tuberosum L.) Plantlets Cultured in vitro to Red, Blue, Green, and White Light-emitting Diodes (LEDs)
inferred← citeshttps://doi.org/10.1007/s00344-019-10010-5openalex-snapshot
New Insights on ‘GALA’ Apple Fruit Development: Sugar and Acid Accumulation: A Transcriptomic Approach
inferred← citeshttps://doi.org/10.1007/s00344-020-10074-8openalex-snapshot
Physiological and Transcriptome Profiling Analyses Reveal Important Roles of Coronatine in Improving Drought Tolerance of Tobacco
inferred← citeshttps://doi.org/10.1007/s00344-021-10443-xopenalex-snapshot
Genome-Wide Transcriptomic Analysis Reveals the Gene Regulatory Network Controlled by SRL1 in Regulating Rice Leaf Rolling
inferred← citeshttps://doi.org/10.1007/s00344-022-10613-5openalex-snapshot
Gene Expression, Hormone Signaling, and Nutrient Uptake in the Root Regermination of Grafted Watermelon Plants with Different Pumpkin Rootstocks
inferred← citeshttps://doi.org/10.1007/s00344-025-11923-0openalex-snapshot
Mechanism of Specific Inhibition of Thorn Formation by Salicylic Acid in Lycium ruthenicum
inferred← citeshttps://doi.org/10.1007/s00344-026-12468-6openalex-snapshot
Melatonin Alleviates Cadmium Stress in Loquat Seedlings by Modulating the Gene Expression Related to Antioxidant Defense and Transmembrane Transporters as Well as DNA Methylation Pattern
inferred← citeshttps://doi.org/10.1007/s00425-017-2818-1openalex-snapshot
Transcriptomic and proteomic feature of salt stress-regulated network in Jerusalem artichoke (Helianthus tuberosus L.) root based on de novo assembly sequencing analysis
inferred← citeshttps://doi.org/10.1007/s00425-019-03281-5openalex-snapshot
Energy metabolism involved in fertility of the wheat TCMS line YS3038
inferred← citeshttps://doi.org/10.1007/s00425-020-03407-0openalex-snapshot
Comparative transcriptomic analysis of resistant and susceptible tea cultivars in response to Empoasca onukii (Matsuda) damage
inferred← citeshttps://doi.org/10.1007/s00425-020-03544-6openalex-snapshot
Systematic identification and characterization of circular RNAs involved in flag leaf senescence of rice
inferred← citeshttps://doi.org/10.1007/s00425-021-03696-zopenalex-snapshot
Production of purple Ma bamboo (Dendrocalamus latiflorus Munro) with enhanced drought and cold stress tolerance by engineering anthocyanin biosynthesis
inferred← citeshttps://doi.org/10.1007/s00425-021-03801-2openalex-snapshot
Transcriptomic and physiological analysis reveals interplay between salicylic acid and drought stress in citrus tree floral initiation
inferred← citeshttps://doi.org/10.1007/s00425-022-03921-3openalex-snapshot
Loss of anthocyanidin synthase gene is associated with white flowers of Salvia miltiorrhiza Bge. f. alba, a natural variant of S. miltiorrhiza
inferred← citeshttps://doi.org/10.1007/s00425-023-04181-5openalex-snapshot
Effects of stacking breeding on the methylome and transcriptome profile of transgenic rice with glyphosate tolerance
inferred← citeshttps://doi.org/10.1007/s00425-023-04217-wopenalex-snapshot
Metabolic characteristics of self-pollinated wheat seed under red and blue light during early development
inferred← citeshttps://doi.org/10.1007/s00425-024-04347-9openalex-snapshot
Transcriptome analysis in Aegilops tauschii unravels further insights into genetic control of stripe rust resistance
inferred← citeshttps://doi.org/10.1007/s00425-024-04440-zopenalex-snapshot
Identification and functional analysis of floral terpene synthase genes in Curcuma alismatifolia
inferred← citeshttps://doi.org/10.1007/s00425-024-04573-1openalex-snapshot
Investigating the mechanism of auxin-mediated fulvic acid-regulated root growth in Oryza sativa through physiological and transcriptomic analyses
inferred← citeshttps://doi.org/10.1007/s00427-018-0621-zopenalex-snapshot
Transcriptome analysis of scyphozoan jellyfish Rhopilema esculentum from polyp to medusa identifies potential genes regulating strobilation
inferred← citeshttps://doi.org/10.1007/s00427-019-00639-3openalex-snapshot
Transcriptome analysis provides insight into the role of the melanin pathway in two differently pigmented strains of the turtle Pelodiscus sinensis
inferred← citeshttps://doi.org/10.1007/s00438-008-0340-7openalex-snapshot
Exploring the transcriptome of the burrowing nematode Radopholus similis
inferred← citeshttps://doi.org/10.1007/s00438-013-0781-5openalex-snapshot
Identification and characterization of a repertoire of genes differentially expressed in developing top ear shoots between a superior hybrid and its parental inbreds in Zea mays L.
inferred← citeshttps://doi.org/10.1007/s00438-015-1007-9openalex-snapshot
Genome-wide identification, classification and functional analyses of the bHLH transcription factor family in the pig, Sus scrofa
inferred← citeshttps://doi.org/10.1007/s00438-015-1013-yopenalex-snapshot
Pathways associated with lignin biosynthesis in lignomaniac jute fibres
inferred← citeshttps://doi.org/10.1007/s00438-016-1216-xopenalex-snapshot
A comparative transcriptome analysis of two sets of backcross inbred lines differing in lint-yield derived from a Gossypium hirsutum × Gossypium barbadense population
inferred← citeshttps://doi.org/10.1007/s00438-016-1242-8openalex-snapshot
Transcriptome analysis reveals that constant heat stress modifies the metabolism and structure of the porcine longissimus dorsi skeletal muscle
inferred← citeshttps://doi.org/10.1007/s00438-017-1324-2openalex-snapshot
Comparative transcript profiling of fertile and sterile flower buds from multiple-allele-inherited male sterility in Chinese cabbage (Brassica campestris L. ssp. pekinensis)
inferred← citeshttps://doi.org/10.1007/s00438-017-1330-4openalex-snapshot
Transcriptome analysis of drought-responsive genes regulated by hydrogen sulfide in wheat (Triticum aestivum L.) leaves
inferred← citeshttps://doi.org/10.1007/s00438-017-1379-0openalex-snapshot
Comparative genomics and transcriptome analysis of Lactobacillus rhamnosus ATCC 11443 and the mutant strain SCT-10-10-60 with enhanced l-lactic acid production capacity
inferred← citeshttps://doi.org/10.1007/s00438-017-1382-5openalex-snapshot
Comparative transcriptome analysis of Apis mellifera antennae of workers performing different tasks
inferred← citeshttps://doi.org/10.1007/s00438-018-1449-yopenalex-snapshot
Identification of transposons near predicted lncRNA and mRNA pools of Prunus mume using an integrative transposable element database constructed from Rosaceae plant genomes
inferred← citeshttps://doi.org/10.1007/s00438-019-01571-xopenalex-snapshot
Charting oat (Avena sativa) embryo and endosperm transcription factor expression reveals differential expression of potential importance for seed development
inferred← citeshttps://doi.org/10.1007/s00438-019-01621-4openalex-snapshot
A comparative transcriptomic analysis in late embryogenesis of the red claw crayfish Cherax quadricarinatus
inferred← citeshttps://doi.org/10.1007/s00438-019-01624-1openalex-snapshot
Transcriptomic and metabolomic analyses reveal several critical metabolic pathways and candidate genes involved in resin biosynthesis in Pinus massoniana
inferred← citeshttps://doi.org/10.1007/s00438-020-01713-6openalex-snapshot
Investigation of genes associated with petal variations between diploid and autotetraploid in Chinese cabbage (Brassica rapa L. ssp. pekinensis) by RNA-seq and sRNA-seq
inferred← citeshttps://doi.org/10.1007/s00438-021-01803-zopenalex-snapshot
Transcriptome and metabolite analysis related to branch development in two genotypes of Eucalyptus urophylla
inferred← citeshttps://doi.org/10.1007/s00438-025-02301-2openalex-snapshot
Comparative evaluation of MG-RAST, MEGAN6 and Kraken2 for whole metagenome analysis of saffron corms for bacterial community structure and function
inferred← citeshttps://doi.org/10.1007/s00438-026-02452-wopenalex-snapshot
Integrated transcriptomic and metabolomic investigation reveals that graphene oxide reduces nicosulfuron detriment in sweet corn
inferred← citeshttps://doi.org/10.1007/s00468-016-1497-zopenalex-snapshot
Differentially expressed gene analysis of Tamarix chinensis provides insights into NaCl-stress response
inferred← citeshttps://doi.org/10.1007/s00468-017-1588-5openalex-snapshot
Transcriptome comparative analysis of two Camellia species reveals lipid metabolism during mature seed natural drying
inferred← citeshttps://doi.org/10.1007/s00468-017-1620-9openalex-snapshot
De novo transcriptome sequencing and identification of genes related to salt stress in Eucommia ulmoides Oliver
inferred← citeshttps://doi.org/10.1007/s00468-018-1783-zopenalex-snapshot
Prospects for the study of genetic variation among Moso bamboo wild-type and variants through genome resequencing
inferred← citeshttps://doi.org/10.1007/s00468-019-01916-4openalex-snapshot
De novo transcriptomic analysis of light-induced flavonoid pathway, transcription factors in the flower buds of Lonicera japonica
inferred← citeshttps://doi.org/10.1007/s00468-020-01979-8openalex-snapshot
Transcripts and ABA-dependent signaling in response to drought stress in Hippophae rhamnoides L
inferred← citeshttps://doi.org/10.1007/s00468-021-02099-7openalex-snapshot
Exogenous melatonin-stimulated transcriptomic alterations of Davidia involucrata seedlings under drought stress
inferred← citeshttps://doi.org/10.1007/s00606-016-1353-zopenalex-snapshot
Genome-wide analysis and characterization of molecular evolution of the HCT gene family in pear (Pyrus bretschneideri)
inferred← citeshttps://doi.org/10.1007/s00709-020-01508-xopenalex-snapshot
Transcriptional analysis reveals sodium nitroprusside affects alfalfa in response to PEG-induced osmotic stress at germination stage
inferred← citeshttps://doi.org/10.1007/s00792-021-01239-8openalex-snapshot
Transcriptomic responses of haloalkalitolerant bacterium Egicoccus halophilus EGI 80432T to highly alkaline stress
inferred← citeshttps://doi.org/10.1007/s10126-018-9798-4openalex-snapshot
Gonad Transcriptome Analysis of the Pacific Oyster Crassostrea gigas Identifies Potential Genes Regulating the Sex Determination and Differentiation Process
inferred← citeshttps://doi.org/10.1007/s10126-019-09903-zopenalex-snapshot
Dynamics of MiRNA Transcriptome in Turbot (Scophthalmus maximus L.) Intestine Following Vibrio anguillarum Infection
inferred← citeshttps://doi.org/10.1007/s10126-021-10061-4openalex-snapshot
A Transcriptome Insight During Early Fish Larval Development Followed by Starvation in Seriola rivoliana
inferred← citeshttps://doi.org/10.1007/s10126-021-10080-1openalex-snapshot
MiRNA-mRNA Integration Analysis Reveals the Regulatory Roles of MiRNAs in Shell Pigmentation of the Manila clam (Ruditapes philippinarum)
inferred← citeshttps://doi.org/10.1007/s10126-021-10083-yopenalex-snapshot
Genome-Wide Differential DNA Methylomes Provide Insights into the Infertility of Triploid Oysters
inferred← citeshttps://doi.org/10.1007/s10126-021-10086-9openalex-snapshot
Full-Length Transcriptome of Red Swamp Crayfish Hepatopancreas Reveals Candidate Genes in Hif-1 and Antioxidant Pathways in Response to Hypoxia-Reoxygenation
inferred← citeshttps://doi.org/10.1007/s10126-023-10201-yopenalex-snapshot
Liver Transcriptome Analysis Reveals Energy Regulation and Functional Impairment of Onychostoma sima During Starvation
inferred← citeshttps://doi.org/10.1007/s10126-023-10234-3openalex-snapshot
Whole Transcriptome Analysis Reveals the Global Molecular Responses of mRNAs, lncRNAs, miRNAs, circRNAs, and Their ceRNA Networks to Salinity Stress in Hong Kong Oysters, Crassostrea hongkongensis
inferred← citeshttps://doi.org/10.1007/s10126-023-10259-8openalex-snapshot
Muscle Transcriptome Sequencing Revealed Thermal Stress–Responsive Regulatory Genes in Farmed Rohu, Labeo rohita (Hamilton, 1822)
inferred← citeshttps://doi.org/10.1007/s10126-023-10261-0openalex-snapshot
Change and Regulation of Nutritional Metabolism in Silver Pomfret During Compensatory Growth
inferred← citeshttps://doi.org/10.1007/s10126-024-10296-xopenalex-snapshot
DNA Methylation Analysis Reveals Potential Mechanism in Takifugu rubripes Against Cryptocaryon irritans Infection
inferred← citeshttps://doi.org/10.1007/s10126-024-10348-2openalex-snapshot
Exploring the Heat-Responsive miRNAs and their Target Gene Regulation in Ruditapes philippinarum Under Acute Heat Stress
inferred← citeshttps://doi.org/10.1007/s10126-024-10384-yopenalex-snapshot
Identification of Key Genes Correlated with Economic Trait Superiorities and Their SNP Screening Through Transcriptome Comparisons, WGCNA and Pearson Correlation Coefficient in the Sea Cucumber Apostichopus Japonicus
inferred← citeshttps://doi.org/10.1007/s10126-025-10454-9openalex-snapshot
Pathological and miRNA-mRNA Analyses Provide New Insights into the Immune Response of Clams to Vibrio Infection
inferred← citeshttps://doi.org/10.1007/s10126-025-10565-3openalex-snapshot
The Effect of High Temperature at the Larval Stage on Sex Ratio and Development of Chinese Shrimp (Fenneropenaeus chinensis)
inferred← citeshttps://doi.org/10.1007/s10142-016-0500-5openalex-snapshot
Deep-sequencing transcriptome analysis of field-grown Medicago sativa L. crown buds acclimated to freezing stress
inferred← citeshttps://doi.org/10.1007/s10142-018-0623-yopenalex-snapshot
Transcriptomic analysis of Aegilops tauschii during long-term salinity stress
inferred← citeshttps://doi.org/10.1007/s10142-019-00682-3openalex-snapshot
High-throughput sequencing reveals microRNAs in response to heat stress in the head kidney of rainbow trout (Oncorhynchus mykiss)
inferred← citeshttps://doi.org/10.1007/s10142-019-00717-9openalex-snapshot
RNA-Seq revealed that infection with white tip nematodes could downregulate rice photosynthetic genes
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