Keywords: AGO; Argonaute; AMY3; alpha-amylase-like 3; APX; ascorbate peroxidase; ARF5/MP; Auxin response factor 5; BAM1; beta-amylase 1; CAT; catalase; CK; control check; COG; Clusters of Orthologous Groups of proteins; DEG; differential expression gene; ERF1; Ethy
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Keywords: Bisphenol A; Pregnancy; Metabolomics; FAAH; Endocannabinoids; 2-AG; 2-arachidonoylglycerol; AMCAA; AMC Arachidonyl Amide; AEA; anandamide; BSTFA; N,O-bis(trimethylsilyl)trifluoroacetamide; eCB; endocannabinoids; FAA; fatty acid amide; FAAH; fatty acid ami
Keywords: Rumen; HF cross; Pfam; Metagenomics; CAZymes; MiSeq;
Keywords: Triticum aestivum; Salt tolerance; qRT-PCR; Transcriptome; qPCR; quantitative polymerase chain reaction; SOM; self-organizing mapping; EST; expressed sequence tag; EMS; ethyl methyl sulfonate; RNA-Seq; RNA-Sequence; CDD; conserved domain database; Pfam; p
Keywords: Germination thermoinhibition; Illumina paired-end sequencing; Lettuce seed; Sodium nitroprusside; Transcriptome; ABA; abscisic acid; DEG; different expression gene; GA; gibberellin; GO; Gene Ontology; KEGG; Kyoto Encyclopedia of Genes and Genomes Pathway
Keywords: APx; ascorbate peroxidase; CcP; cytochrome c peroxidase; Cld; chlorite dismutase; DyP; dye-decolorizing peroxidase; EPO; eosinophil peroxidase; HGT; horizontal gene transfer; HRP; horseradish peroxidase; KatG; catalase-peroxidase; LDS; linoleate diol sy
Keywords: MDA; multi-domain arrangement; SDA; single-domain arrangement; ORA; over-representation analysis; My; million years; Modular protein evolution; Protein domain; Drosophila genome evolution; Pfam; Bioinformatics;
A Model for Manganese interaction with Deinococcus radiodurans proteome network involved in ROS response and defense
Keywords: GO; gene ontology; HMM; hidden markov model; IRRB; ionizing-radiation resistance bacterium; IRSB; ionizing-radiation sensitive bacterium; LBPs; ligand binding patterns; MBP; metal binding pattern; PDB; protein data bank; Pfam; protein family; PPI; protein
Mapping podophyllotoxin biosynthesis and growth-related transcripts with high elevation in Sinopodophyllum hexandrum
Keywords: asl; above sea level; DEGs; differentially expressed genes; DR; down-regulated; GO; gene ontology; KEGG; Kyoto Encyclopedia of Genes and Genomes; KOG; euKaryotic orthologous groups of proteins; NCBI; National Center for Biotechnology Information; NR; non-
Digital gene expression analysis in the gills of Ruditapes philippinarum exposed to short- and long-term exposures of ammonia nitrogen
Keywords: DGE; Digital gene expression technology; UIA; un-ionized ammonia nitrogen; NMDA; N-Methyl-d-aspartic acid; DEG; differentially expressed genes; Nr; NCBI non-redundant protein sequences; Nt; NCBI non-redundant nucleotide sequences; Pfam; Protein family; KO
The pharmacological properties of Ophiocordyceps xuefengensis revealed by transcriptome analysis
Keywords: 2â²-C-3â²-dA; 2â²-carbonyl-3â²-deoxyadenosine; 3â²-AMP; adenosine-3â²-monophosphate; 5â²-ADP; adenosine-5â²-diphosphate; 5â²-P-3â²-dADP; 3â²-deoxyadenosine-5â²-diphosphate; COG; Clusters of Orthologous Group
The splicing of tiny introns of Paramecium is controlled by MAGO
Keywords: EJC; exon junction complex; PTC; premature termination codon; NMD; nonsense-mediated decay; IR; intron retention; BLAST; basic local alignment search tool; dNTPs; deoxynucleotide triphosphates; EDTA; ethylenediaminetetraacetic acid; EEO; electroendosmosis
Transcriptome analysis and identification of genes associated with flower development in Rhododendron pulchrum Sweet (Ericaceae)
Keywords: qRT-PCR; quantitative real-time PCR; FLC; Flowering Locus; FT; Flowering Locus T; DEGs; differentially expressed genes; CO; CONSTANS; SOC1; SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1; LFY; LEAFY; AP1; APETALA1; CAL; CAULOFLOWER; AG; AGAMOUS; PGRs; Plant g
Transcriptome sequencing of Paeonia suffruticosa 'Shima Nishiki' to identify differentially expressed genes mediating double-color formation
Keywords: Transcriptome; Anthocyanins; P. suffruticosa 'Shima Nishiki'; Double-color; Differentially expressed genes (DEGs); HPLC; High-performance liquid chromatography; CHS; Chalcone synthase gene; CHI; Chalcone isomerase gene; F3H; Flavanone 3-hydroxylase ge
Advancing our understanding of the oxygen minimum zone microbial communities by an integrated metatranscriptomics approach
Keywords: OMZs; Oxygen Minimum Zones; GO; Gene Ontology; COG; Clusters of Orthologous Group; PFAM; Protein family; KEGG; Kyoto Encyclopedia of Genes and Genomes; SRA; Sequence Read Archive; dbCAN; DataBase for automated carbohydrate-active enzyme annotation; NGS; N
Genome expression profile analysis of two types of new roots in apple rootstock via Solexa sequencing
Keywords: Apple GFDB database; Apple Gene Function and Gene Family Database; GDR; Genome Database for Rosaceae; Pfam; Protein family; AR; Absorbing roots; GR; Growing roots; GO; Gene Ontology; DGE; Digital gene expression; EST; Expressed sequence tag; Root; Differe
Analyses of long non-coding RNAs and mRNA profiling through RNA sequencing of MDBK cells at different stages of bovine viral diarrhea virus infection
Keywords: BVDV; Bovine viral diarrhea virus; CNCI; Coding-Non-Coding-Index; CPC; Coding Potential Calculator; DMEM; Dulbecco's modified Eagle's medium; FBS; fetal bovine serum; FPKMs; fragments per kilobase of transcript sequences per million base pairs sequenced;
Genome-wide identification and expression analysis of transcription factors in Solanum lycopersicum
Keywords: TF; transcription factor; BLAST; the Basic Local Alignment Search Tool; PFAM; Protein Family; HMM; Hidden Markov Model; ITAG; International Tomato Genome Sequencing Project; TRR; transcriptional regulation region; ITAG; International Tomato Genome Sequenc
The family of berberine bridge enzyme-like enzymes: A treasure-trove of oxidative reactions
Keywords: FAD-Linked oxidases; Alkaloids; Antibiotics; Covalent FAD; Flavoproteins; 6HDNO; 6-hydroxy-d-nicotine oxidase; A40926; teicoplanin homolog; CpADHAPS; alkyldihydroxyacetonephosphate synthase from Cavia porcellus; DdADHAPS; alkyldihydroxyacetonephosphate sy
Genome-wide analysis of long non-coding RNAs and their role in postnatal porcine testis development
Keywords: lncRNA; long non coding RNA; ncRNA; non coding RNA; GO; gene ontology; KEGG; kyoto encyclopedia of genes and genomes; DS; sixty-day-old; DN; ninety-day-old; DT; one hundred and twenty-day-old; DF; one hundred and fifty-day-old; RIN; RNA integrity number;
Transcriptomics provides insight into Mytilus galloprovincialis (Mollusca: Bivalvia) mantle function and its role in biomineralisation
Keywords: RNA-seq; Gene expression; Multi-functional; Pfam; Trinity;
Tunicate pregnane X receptor (PXR) orthologs: Transcript characterization and natural variation
Keywords: AF-1; transcription activation function 1; AR; androgen receptor; BsVDR/PXRα; Botryllus schlosseri VDR/PXR ortholog α; BSA; bovine serum albumin; bp; base pair; CAR; constitutive androstane receptor; CiVDR/PXRα; Ciona intestinalis VDR/PXR ortholog α;
Genome-wide identification and analysis of the MADS-box gene family in apple
Keywords: BLAST; Basic Local Alignment Search Tool; DAA; Day After Anthesis; GWD; Genome-wide duplication; HMM; Hidden Markov model; MEGA; Molecular Evolutionary Genetics Analysis; NJ; Neighbour-joining; Pfam; Protein family; NCBI; National Center for Biotechnology
Drosophila melanogaster as a model system to study long-chain fatty acid amide metabolism
Keywords: ATP; adenosine triphosphate; CoA; coenzyme A; EIC; extracted ion chromatogram; FAAH; fatty acid amide hydrolase; HPLC; high performance liquid chromatography; LC/QTOF-MS; liquid chromatography/quadrupole time-of-flight mass spectrometry; NAE; N-acylethano
Identification of putative and potential cross-reactive chickpea (Cicer arietinum) allergens through an in silico approach
Keywords: BLAST; Basic Local Alignment Search Tool; BLASTp; protein-protein BLAST; IgE; immunoglobulin E; WHO; World Health Organization; IUIS; International Union of Immunological Societies; FAO; Food and Agriculture Organization; Pfam; protein families' datab
Identification of novel phospholipase A2 group IX members in metazoans
Keywords: GIX phospholipase A2; GXIV phospholipase A2; Conserved domain; Pfam09056; PLA2; phospholipase A2; sPLA2; secreted phospholipase A2; GIX PLA2; group IX phospholipase A2; GXII PLA2; group XII phospholipase A2; GXIV PLA2; group XIV phospholipase A2; cd; cons
Genome-wide analysis and identification of stress-responsive genes of the NAM-ATAF1,2-CUC2 transcription factor family in apple
Keywords: Genome-wide analysis; NAC transcription factor; Gene family; Stress-responsive genes; Malus domestica; BLAST; the Basic Local Alignment Search Tool; GWD; genome-wide duplication; HMM; Hidden Markov Model; NAC, NAM, ATAF and CUC; transcription factor; MEGA
An integrated study of grain development of wheat (cv. Hereward)
Keywords: Wheat; Protein; Metabolomics; Cell walls; AX; arabinoxylan; AXAH; arabinoxylan arabinofuranohydrolase; AXOS; arabinoxylan oligosaccharide; BAHD; a family of acyltransferases named after the four first characterised members; β-glucan; (1,3:1,4) β-d-gluca
EuPathDomains: The divergent domain database for eukaryotic pathogens
Keywords: Pathogens; Protein domains; Functional annotations; Pfam; HMMs; Database
The challenge of annotating protein sequences: The tale of eight domains of unknown function in Pfam
Keywords: Sequence homology; Function prediction; Pfam; Domains of unknown function
Prediction of subcellular protein localization based on functional domain composition
Keywords: Protein subcellular localization; Pfam; Nearest Neighbor Algorithm
Druggability of human disease genes
Keywords: Disease genes; Druggability; Drugs; Model organisms; Pfam
A normalised scale for structural genomics target ranking: The OB-Score
Keywords: HTPX; Structural genomics; Target selection; Pfam; Bioinformatics
Searching for hypothetical proteins: Theory and practice based upon original data and literature
Keywords: 2-DE; two-dimensional gel electrophoresis; 3D-PSSM; three-dimensional position-specific scoring matrix; ANN; artificial neural networks; BIND; biomolecular interaction network database; BLAST; basic local alignment search tool; CAMPASS; Cambridge database