Keywords: ANOVA; analysis of variance; CS; cobblestone; KEGG; Kyoto Encyclopedia of Gene and Genomes; MP; microplastics; NMDS; non-metric multidimensional scaling; OTUs; operational taxonomic units; PE; linear low-density polyethylene; PP; polypropylene; STAMP; Sta
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Keywords: NSCs; neural stem cells; RGCs; embryonic radial glia cells; VZ; ventricular zone; GFAP; glial fibrillary acidic protein; GS; glutamine synthase; iPCs; intermediate progenitor cells; SVZ; subventricular zone; SGZ; subgranular zone; CP; cortical plate; GEO;
Keywords: CNV; copy number variation; DEGs; differentially expressed genes; DMSs; differentially methylated sites; DNAm; DNA methylation; FDR; false discovery rate; GO; Gene Ontology; GWAS; genome-wide association studies; KEGG; Kyoto Encyclopedia of Genes and Geno
Keywords: STH; small-tailed Han sheep; RT-PCR; real-time PCR; GO; gene ontology; KEGG; Kyoto Encyclopedia of Genes and Genomes; Transcriptome; Ovary;
Keywords: AI; adequate intake; Cys; cysteine; DNMT, DIO; iodothyronine deiodinase; DNA; methyltransferase; EAR; estimated average requirement; HDAC; histone deacetylase; HSP; heat shock protein; HRM; high-resolution metabolomics; ICP-MS; inductively coupled plasma
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: Akt; serine-threonine kinase; DAG; directed acyclic graph; DnC; sampling time at day  n of a Control explant; DnS; sampling time at day  n of a Stimulated explant; ELF; extremely low frequency; EMF; electromagnetic field; ERKs; extracellular signal-
Keywords: Breast cancer; Pathway-based analysis; PKA pathways; PKA; Protein Kinase A; PDS; Pathway Deregulation Score; ER; Estrogen Receptor; HER2; Epidermal growth factor receptor 2; METABRIC; Molecular Taxonomy of Breast Cancer International Consortium; TIL; Tumo
Keywords: CD 14; cluster determinant 14; TLR; toll like receptor; TNF; tumor necrotic factor; EGFR; epidermal growth factor receptor; ODE; ordinary differential equation; PCA; principal component analysis; NIK; NFκB-inducing kinase; MKK; mitogen kinase kinases; PI
Keywords: BP; biological process; ChIP; Chromatin immunoprecipitation; DMEM; Dulbecco's modified Eagle's medium; EB; embryoid bodies; EGFP; enhanced green fluorescence protein; ESC; Embryonic stem cells; FCS; fetal calf serum; GO; gene ontology; IMDM; Iscove's modi
Keywords: Alzheimer's disease; Biological pathway; Brain atrophy; Epistasis; Gene-gene interaction; GWIA; GWAS; KEGG; MRI; Neuroimaging; Pathway-based analysis;
Combination of iTRAQ proteomics and RNA-seq transcriptomics reveals jasmonate-related-metabolisms central regulation during the process of Jujube witches' broom recovery by tetracycline treatment
Keywords: JA; jasmonic acid; JWB; jujube witches' broom; MTT; month of tetracycline treatment; DEGs; differentially expressed genes; DEPs; differentially expressed proteins; JIPs; jasmonate induced protein-like; ssDNA; Single strand DNA; DNBs; DNA nanoballs; RCR;
Genome-wide identification and analysis of the evolution and expression patterns of the GATA transcription factors in three species of Gossypium genus
Keywords: QTL; quantitative trait locus; FPKM; fragments per kilobase of exon per million fragments mapped; SNP; single nucleotide polymorphisms; qRT-PCR; quantitative real-time PCR; DPA; days post anthesis; SRA; sequence read archive; NCBI; National Center for Bio
Genomic insights of Vibrio harveyi RT-6 strain, from infected “Whiteleg shrimp” (Litopenaeus vannamei) using Illumina platform
Keywords: Vibrio harveyi; Illumina sequencing; Cluster of orthologous; Gene ontology; KEGG; Virulence genes; Prophage regions;
Transcriptome profiling and identification of the functional genes involved in berry development and ripening in Vitis vinifera
Keywords: Early ripening; Transcriptome; Mutant; Sequencing; Vitis vinifera; ABA; abscisic acid; ABF; ABRE binding factor; ACO; ACC oxidase; ACS; ACC synthase; ARF; auxin response factor; CIPK; CBL-interacting protein kinase; DEG; differentially expressed gene; FPK
Circular RNA expression profile of articular chondrocytes in an IL-1β-induced mouse model of osteoarthritis
Keywords: OA; Osteoarthritis; circRNAs; circular RNAs; MACs; mouse articular chondrocytes; IL-1β; interleukin-1β; GO; Gene Ontology; KEGG; Kyoto Encyclopedia of Genes and Genomes; qRT-PCR; quantitative real-time polymerase chain reaction; Circular RNA; Next gener
De novo assembly and functional annotations of the transcriptome of Metorchis orientalis (trematoda: Opisthorchiidae)
Keywords: Metorchis orientalis; Transcriptome; De novo; Next-generation sequencing; M. orientalis; Metorchis orientalis; C. sinensis; Clonorchis sinensis; S. mansoni; Schistosoma mansoni; S. japonicum; Schistosoma japonicum; O felineus; Opisthorchis felineus; O
Identification of genes related to proliferative diabetic retinopathy through RWR algorithm based on protein-protein interaction network
Keywords: PPI; protein-protein interaction; RWR; the random walk with restart; SP; shortest path; MES; maximum enrichment score; MIS; maximum interaction score; GO; gene ontology; KEGG; Kyoto Encyclopedia of Genes and Genomes; Proliferative diabetic retinopathy;
Genomic transcriptional response to 20-hydroxyecdysone in the fat body of silkworm, Bombyx mori
Keywords: GO; Gene ontology; KEGG; Kyoto Encyclopedia of Genes and Genomes; NCBI; National Center of Biotechnology Information; Bombyx mori; 20-hydroxyecdysone; Fat body; Transcriptomic analysis;
Genome-wide identification of the interactions between key genes and pathways provide new insights into the toxicity of bisphenol F and S during early development in zebrafish
Keywords: Bisphenol F; Bisphenol S; KEGG; GSEA; Hub genes; Carcinogenicity;
Comprehensive inbred variation discovery in Bama pigs using de novo assemblies
Keywords: BX pig; Bama Xiang pig; BM pig; Bama mini-pig; SNP; single nucleotide polymorphism; Indel; insertion and deletion; SV; structural variation; CNV; copy number variation; GO; Gene Ontology; KEGG; Kyoto Encyclopedia of Genes and Genomes; ADGRE2; adhesion G p
Modular organization analysis of specific naringin/neoeriocitrin related gene expression induced by UVC irradiation in Drynaria roosii
Keywords: bHLH; basic helix-loop-helix; C3H; p-coumarate 3-hydroxylase; C3'H; p-coumarate 3â²-hydroxylase; C4H; cinnamate 4-hydroxylase; CHI; chalcone isomerase; CHS; chalcone synthase; 4CL; 4-coumarate CoA ligase; CNR; new rhizome; CNRCK; new rhizome treated fo
Lysophosphatidylcholine induces expression of genes involved in cholesterol biosynthesis in THP-1 derived macrophages
Keywords: LPC; lysophosphatidylcholine; PCA; principal component analysis; FFA; free fatty acids; DMSO; dimethyl sulfoxide; FPKM; fragments per kilobase of transcript per million fragments mapped; RT-PCR; reverse transcription polymerase chain reaction; KEGG; Kyoto
Identification of novel and conserved microRNA and their expression in the gray mouse lemur, Microcebus murinus, a primate capable of daily torpor
Keywords: Akt; RAC-alpha serine/threonine-protein kinase; AMPK; AMP-activated protein kinase; ERK; Extracellular signal-regulated kinase; GO; Gene ontology; JNK; c-Jun N-terminal kinase; KEGG; Kyoto encyclopedia of genes and genomes; MAPK; Mitogen-activated protein
Serum miRNAs miR-140-3p and miR-23b-3p as potential biomarkers for osteoporosis and osteoporotic fracture in postmenopausal Mexican-Mestizo women
Keywords: BMD; Bone mineral density; OF; osteoporotic fracture; DXA; Dual-energy X-ray Absorptiometry; miRNA; microRNA; VC; Variation Coefficient; TLDA; TaqMan Low Density Array; SE; Standard error; AUC; Area Under the Curve; BMI; Body Mass Index; ROC; Receiver Ope
Comparative transcriptome analysis of genes involved in Na+ transport in the leaves of halophyte Halogeton glomeratus
Keywords: CDS; coding DNA sequence; COG; Clusters of Orthologous Groups; CS; consensus sequence; DEIs; differentially expressed isoforms; FL; full-length; GO; Gene Ontology; H. glomeratus; Halogeton glomeratus; HgNHX1; H. glomeratus vacuolar Na+/H+ antiporter; Iso-
FGF2 and FAM201A affect the development of osteonecrosis of the femoral head after femoral neck fracture
Keywords: ONFH; osteonecrosis of the femoral head; FNF; femoral neck fracture; DEGs; differentially expressed genes; PPI; protein-protein interaction; VEGF; vascular endothelial growth factor; HIF-1α; hypoxia-inducible factor-1 alpha; OPG; osteoprotegerin; RANK; r
Differentially DNA methylation changes induced in vitro by traffic-derived nanoparticulate matter
Keywords: nPM; nanoparticulate matter; PM; particulate matter; ROS; reactive oxygen species; HUVECs; human umbilical vein endothelial cells; DMP; differential methylated probes; GO; gene ontology; DMGs; differential methylated genes; KEGG; Kyoto encyclopedia of gen
High-throughput gene expression analysis identifies p53-dependent and -independent pathways contributing to the adrenocortical dysplasia (acd) phenotype
Keywords: TPP1; protein encoded by adrenocortical dysplasia gene; Acd; adrenocortical dysplasia gene; acd; adrenocortical dysplasia mutation; p53; transformation related protein 53; DNA; Deoxyribonucleic acid; DC; Dyskeratosis congenita; HHS; Hoyeraal-Hreidarsson s
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
The E. coli S30 lysate proteome: A prototype for cell-free protein production
Keywords: GeLC-MS/MS; Pre-fractionation by 1D-SDS-PAGE coupled with liquid chromatography mass spectrometry; FDR; false discovery rate; ABC-transporters; ATP-binding cassette transporters; CECF; continuous exchange cell-free; CFPS; cell-free protein synthesis; em
De-novo assembly and transcriptome analysis of Odontesthes argentinensis gill tissue, with development of single sequence repeat markers
Keywords: BLAST; Basic Local Alignment Search Tool; bp; base pair(s); CDS; coding sequence; cDNA; DNA complementary to RNA; GO; Gene Ontology; INDEL; insertion or deletion of bases; KEGG; Kyoto Encyclopedia of Genes and Genomes; mRNA; messenger RNA; UTR; untranslat
Members of the neuropeptide transcriptional network in Helicoverpa armigera and their expression in response to light stress
Keywords: H. armigera; Helicoverpa armigera; C. suppressalis; Chilo suppressalis; B. mori; Bombyx mori; D. melanogaster; Drosophila melanogaster; N. lugens; Nilaparvata lugens; A. mellifera; Apis mellifera; T. castaneum; Tribolium castaneum; A. pisum; Acyrthosiphon
A hypothesis-driven approach to assessing significance of differences in RNA expression levels among specific groups of genes
Keywords: GO; gene ontology; HSP; heat shock protein; KEGG; Kyoto Encyclopedia of Genes and Genomes; HSF TF; heat shock factor transcription factor; HSBP; heat shock binding protein; RNA; ribonucleic acid; TE; transposable element; TF; transcription factor; TPM; tr
Global regulation of alternative RNA splicing by the SR-rich protein RBM39
Keywords: ULM; U2AF ligand motif; snRNPs; small nuclear ribonucleoproteins; SR; serine/arginine-rich; RRMs; RNA-recognition motifs; RS domain; arginine- and serine-rich domain; VEGF; vascular endothelial growth factor; PNK; polynucleotide kinase; RPKM; reads per ki
Five pectinase gene expressions highly responding to heat stress in rice floral organs revealed by RNA-seq analysis
Keywords: Rice; High temperature damage; Transcriptome; RNA-seq; Pectinase; CAT; catalase; COG; Clusters of Orthologous Groups; DEGs; differentially expressed genes; FDR; false discovery rate; GO; Gene Ontology; KEGG; Kyoto Encyclopedia of Genes and Genomes; PE; pe
Bioinformatics analyses provide insight into distant homology of the Keap1-Nrf2 pathway
Keywords: ADT; AutoDock Tools; ARE; antioxidant response element; BLAST; Basic Local Alignment Search Tool; DHSP; Distant Homology Search Pipeline; NTMT; NCBI Taxonomy Mapping Tool; HMM; Hidden Markov Model; HMMER3; HMM-based utility version 3; Keap1; Kelch-like EC
Transcriptome analyses to understand effects of the Fusarium deoxynivalenol and nivalenol mycotoxins on Escherichia coli
Keywords: ACN; acetonitrile; AFB1; aflatoxin B1; ATA; alimentary toxic aleukia; DEG; differentially expressed gene; DH; 2Â ppm deoxynivalenol; DL; 0.2Â ppm deoxynivalenol; DON; deoxynivalenol; E. coli; Escherichia coli; F. graminearum; Fusarium graminearum; FB1; fu
VDR primary targets by genome-wide transcriptional profiling
Keywords: 1α,25(OH)2D3; 1α,25-dihydroxyvitamin D3; ChIP; chromatin immunoprecipitation; ChIP-Seq; ChIP-sequencing; DAVID; Database for Annotation, Visualization and Integrated Discovery; FVKM; fragments per virtual kb per million; log2fc; log2 fold change; H3K4me
A practical data processing workflow for multi-OMICS projects
Keywords: ASCII; American Standard Code for Information Interchange; BC-FC; Box-Cox-transformed fold changes; BG; bio-molecule group; CRAN; The Comprehensive R Archive Network; Deucl; Euclidean distance; FC; fold change; GUI; graphical user interface; HCC; hepato
Glyphosate effects on the gene expression of the apical bud in soybean (Glycine max)
Keywords: cDNA; complementary deoxyribonucleic acid; FC; fold change; FDR; false detection rate; GO; gene ontology; KEGG; kyoto encyclopedia of genes and genomes; DGE; digital gene expression tag profiling; 26 DGEs; 26 differentially expressed cross talk genes at t
NEDD4 is overexpressed in colorectal cancer and promotes colonic cell growth independently of the PI3K/PTEN/AKT pathway
Keywords: AKT; v-akt murine thymoma viral oncogene; CRC; colorectal cancer; FDR; false discovery rate; HECT; homologous to E6AP C terminus; KEGG; Kyoto Encyclopedia of Genes and Genomes; mut; mutated; NCBI; National Center for Biotechnology Information; PBS; phosph
Combined CpG and poly I:C stimulation of monocytes results in unique signaling activation not observed with the individual ligands
Keywords: TLRs; Toll-like receptors; CpG; unmethylated CpG oligodeoxynucleotides; poly I:C; polyinosinic-polycytidylic acid; NO; nitric oxide; iNOS; inducible nitric oxide synthase; CREB; cAMP response element-binding protein; NFκB; nuclear factor κB; PRRs; pat
Wnt signaling in liver fibrosis: Progress, challenges and potential directions
Keywords: Liver fibrosis; Wnt signaling; Canonical Wnt signaling pathway; Hepatic stellate cell; Myofibroblastic transdifferentiation; HSCs; hepatic stellate cells; GFAP; glial fibrillary acidic protein; a-SMA; a-smooth muscle actin; TRAIL; tumor necrosis factor-re
Dynamic expression of miR-126â and its effects on proliferation and contraction of hepatic stellate cells
Keywords: miRNA; microRNA; HSC; hepatic stellate cell; VEGF; vascular endothelial growth factor; GO; gene ontology; KEGG; kyoto encyclopedia of genes and genomes; VG; Van Gieson; ECM; extracellular matrix; 3â²UTR; 3â²untranslated region; HE; hematoxylin/eosin; PI
Subtype-specific response to bevacizumab is reflected in the metabolome and transcriptome of breast cancer xenografts
Keywords: Bevacizumab; Xenograft; Breast cancer; Transcriptomics; Metabolomics; PFS; Progression Free Survival; OS; Overall Survival; FDA; Food and Drug Administration; tCHO; total Choline; MRS; Magnetic Resonance Spectroscopy; PCho; Phosphocholine; GPC; Glyceropho
Ubiquitin C-terminal Hydrolase 37, a novel predictor for hepatocellular carcinoma recurrence, promotes cell migration and invasion via interacting and deubiquitinating PRP19
Keywords: 2D; two-dimensional; ABC; avidin-biotin complex; ACN; acetonitrile; AFP; alpha-fetoprotein; BAP1; BRCA1-associated protein-1; BCLC; Barcelona Clinic Liver Cancer; co-IP; co-immunoprecipitation; CT; computed tomography; DAB; diaminobenzidine; DDR; DNA da
Proteomic characterization of larval and adult developmental stages in Echinococcus granulosus reveals novel insight into host-parasite interactions
Keywords: 2D-LC-MS; two dimensional LC-MS; AE; alveolar echinococcosis; Ag5; antigen 5; AGC; automatic gain control; BCA; bicinchoninic acid assay; CE; cystic echinococcosis; CHD; cystic hydatid disease; DB; database; DLC; dynein light chain; EgFABP1; E. granul
Comparative proteomic analysis of seedling leaves of different salt tolerant soybean genotypes
Keywords: AAS; aspartate aminotransferase; ACO; 1-aminocyclopropane-1-carboxylate oxidase; ACC; 1-aminocyclopropane-1-carboxylate; ACS; 1-aminocyclopropane-1-carboxylate synthetase; Ald; aldolase; APX; ascorbate peroxidase; ASD; aspartate-semialdehyde dehydrogenase
Differential gene expression in normal and transformed human mammary epithelial cells in response to oxidative stress
Keywords: HMEC; human mammary epithelial cell; ROS; reactive oxygen species; H-RasV12; oncogenic allele of GTPase H-Ras; GluOx; glucose oxidase; GCRMA; GeneChip Multi-Array Average; KEGG; Kyoto Encyclopaedia of Genes and Genomes; GSH; reduced glutathione; GSSG; oxi