Keywords: CLD; collagen-like domain; CRD; carbohydrate recognition domain; FBD; fibrinogen-like domain; FCN; ficolin; indel; small insertion or deletion; MASP; MBL-associated serine protease; MBL; mannose-binding lectin; miRNA; microRNA; TFBS; transcription factor
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Keywords: Childhood asthma; asthma phenotypes; gene expression profiling; microarray analysis; longitudinal study; ADD3; Adducin 3 (gamma); CAMP; Childhood Asthma Management Program; DE; Differentially expressed; FDR; False discovery rate; GR; Glucocorticoid recept
Keywords: MI; myocardial infarction; LV; left ventricle; EX; exercise-training; SED; sedentary; TFBS; transcription factor binding site; GR; glucocorticoid receptor; FDR; false discovery rate; DE; differentially expressed; Cardiac hypertrophy; Physiological hypertr
Keywords: IRF-1; interferon regulatory factor-1; TF; transcription factor; TFBS; transcription factor binding site; YY1; Ying-Yang 1; STAT; signal transducer and activator of transcription; HS; hypersensitive; CIITA; class II transactivator; MHC; major histocompati
Keywords: Enrichment analysis; TFBS; Mirna; Network motifs; Nucleosomes;
Keywords: TF; transcription factor; TFBS; transcription factor binding sites; GEP; gene expression profiling; NAFLD; nonalcoholic fatty liver disease; NASH; nonalcoholic steatohepatitis; LXR; liver X receptor; PPAR; peroxisome proliferator-activated receptor; HNF;
Association of PARK2 promoter polymorphisms and methylation with colorectal cancer in North Indian population
Keywords: SNP; single nucleotide polymorphism; CRC; colorectal cancer; PARK2; Parkin gene; TSG; tumor suppressor gene; SPSS; Statistical Package of Social Sciences; PCR; polymerase chain reaction; RFLP; restriction fragment length polymorphism; MS; methylation spec
Molecular characterization of the TaWTG1 in bread wheat (Triticum aestivum L.)
Keywords: QTL; Quantitative trait loci; TFBS; transcription factor binding sites; CDS; coding sequences; ESTs; Expression sequence tags; RPKM; Reads per kilobase per million reads; tpm; transcripts per million; Expression pattern; Structure; Transcription factor; S
Assessment of DNA repair susceptibility genes identified by whole exome sequencing in head and neck cancer
Keywords: AAS; Amino Acid Substitution; BAM; Binary Alignment Map; BER; Base Excision Repair; CI; Confidence Interval; CVC; Cross Validation Consistency; dbSNP; Single Nucleotide Polymorphism database; DDG; The predicted free energy change value; DSBR; Double Stran
Long-term evolutionary DNA methylation dynamic of protein-coding genes and its underlying mechanism
Keywords: CDS; coding sequence; mCG; CG methylation; mCHG; CHG methylation; mCHH; CHH methylation; MYA; million years ago; RdDM; RNA-directed DNA methylation; siRNA; small interfering RNA; TAIR; The Arabidopsis Information Resource; TE; transposable element; TF; tr
Molecular cloning, transcriptional profiling, and subcellular localization of signal transducer and activator of transcription 2 (STAT2) ortholog from rock bream, Oplegnathus fasciatus
Keywords: STAT2; signal transducer and activator of transcription 2; JAK; Janus kinase; IL-10; interleukin-10; TYK2; tyrosine kinase 2; IFN; interferon; ISGF3; IFN-stimulated gene factor 3; ISG; IFN-stimulated gene; CREB; cyclic AMP-response element-binding protein
Activity analysis of LTR12C as an effective regulatory element of the RAE1 gene
Keywords: bp; base pairs; LTR; long terminal repeat; NF-Y; nuclear transcription factor Y; PCR; polymerase chain reaction; RAE1; ribonucleic acid export 1; siRNA; small interfering RNA; TFBS; transcription factor-binding site; TRR; tandem repeat region; TSS; transc
Comparative and evolutionary studies of ALDH18A1 genes and proteins
Keywords: Aldehyde dehydrogenases; Bifunctional enzyme; ALDH18A1; Glutamyl kinase; GK; Glutamyl phosphate reductase; GPR; Vertebrates; Invertebrates; Evolution; Phylogeny; Primordial gene; Gene integration; Transcription factor binding sites; CpG islands; ALDH; ald
Drought-responsive genes expressed predominantly in root tissues are enriched with homotypic cis-regulatory clusters in promoters of major cereal crops
Keywords: DREs; dehydrin response elements; TSS; translational start site; TFBS; transcription factor binding sites; HCTs; homotypic cis-clusters; CRMs; cis-regulatory modules; DREs; drought response elements; AuxREs; auxin response elements; MYCREs; MYC response e
Modulation of signaling mechanisms in the heart by thioredoxin 1
Keywords: Akt; protein kinase B; AMPK; Adenosine Monophosphate-activated Protein Kinase; Ang-II; Angiotensin-II; AP1; Activator protein 1 (AP-1); ASK1; Apoptosis Signal-regulating kinase; Atg4; Autophagy related-4; ATP; Adenosine Triphosphate; CDDP; cis-diammine-di
Polymorphisms of CYP2C8, CYP2C9 and CYP2C19 and risk of coronary heart disease in Russian population
Keywords: AA; arachidonic acid; CHD; coronary heart disease; CI; confidence intervals; CVD; cardiovascular disorder; EETs; epoxyeicosatrienoic acids; FDR; false discovery rate; HWE; Hardy-Weinberg equilibrium; LRT; log-likelihood ratio test; OR; odds ratio; PCR; po
Insights into inner ear-specific gene regulation: Epigenetics and non-coding RNAs in inner ear development and regeneration
Keywords: bps; base pairs; DHS; DNase Hypersensitive sites; TFBS; transcription factor binding sites; PTMs; post-translational modifications; HDACs; histone deacetylases; H3K4me3; histone 3 lysine 4 tri-methylation; H3K27me3; histone 3 lysine 27 tri-methylation; Ch
Stratifying melanoma and breast cancer TCGA datasets on the basis of the CNV of transcription factor binding sites common to proliferation- and apoptosis-effector genes
Keywords: BAM; binary alignment/map; BRCA; breast cancer; CNV; copy number variation; SKCM; skin cutaneous melanoma; SNP; simple nucleotide polymorphism; SOM; supporting online material; TB; terabyte; TCGA; the cancer genome atlas; TFBS; transcription factor bindin
Data in support of FSH induction of IRS-2 in human granulosa cells: Mapping the transcription factor binding sites in human IRS-2 promoter
Keywords: IRS-2; TFBS; FSH; SP1; ChIP
Single cell genomics reveals activation signatures of endogenous SCAR's networks in aneuploid human embryos and clinically intractable malignant tumors
Keywords: Human endogenous stem cell-associated retroviruses (SCARs); Human-specific regulatory sequences; Human embryos; LTR7/HERVH; Therapy-resistant cancers; Cancer stem cells; HERV; human endogenous retroviruses; hESC; human embryonic stem cells; LINE; long int
Intermittent hypoxia confers pro-metastatic gene expression selectively through NF-κB in inflammatory breast cancer cells
Keywords: ADAM19; a disintegrin and metalloproteinase 19; AP-1; activator protein-1; ARE; antioxidant response element; BSP; bisulfite sequencing PCR; CA9; carbonic anhydrase IX; CIH; chronic intermittent hypoxia; COX-2; cyclooxygenase-2; DCF; 2',7'-dichlorofluores
Variable reproducibility in genome-scale public data: A case study using ENCODE ChIP sequencing resource
Keywords: ENCODE; encyclopaedia of DNA elements; TFBS; transcription factor binding site; ChIP; chromatin immunoprecipitation; ChIP-seq; ChIP followed by massively parallel sequencing; UV; ultraviolet; FAANG; functional annotation of animal genomes; UCSC; Universit
Identification of microRNAs and their targets in Finger millet by high throughput sequencing
Keywords: GO, gene ontology; miRNA, microRNA; TF, transcription factor; TSS, transcription start site; TFB, transcription factor binding site; NB-ARC, nucleotide binding domain with ARC motifcis-regulatory motifs; GO analysis; RT-qPCR; RISC; TFBs; TSS
GCDCA down-regulates gene expression by increasing Sp1 binding to the NOS-3 promoter in an oxidative stress dependent manner
Keywords: Cholestatic liver disease; Endothelial nitric oxide synthase; Oxidative stress; Transcription factor Sp1; Glycochenodeoxycholic acid; ADHP; 0-acetyl-3, 7-dihydroxyphenoxazine; ALT; alanine aminotransferase; AST; aspartate aminotransferase; BDL; bile duct
Toll-like receptor 7 variations are associated with the susceptibility to HCV infection among Chinese females
Keywords: HCV; hepatitis C virus; TLR7; Toll-like receptor 7; SNP; single nucleotide polymorphism; HCC; hepatocellular carcinoma; PRR; pattern recognition receptor; PAMP; pathogen associated molecular pattern; ssRNA; single strand RNA; HIV; human immunodeficiency v
The high-mobility group I-Y transcription factor is involved in cerebral ischemia and modulates the expression of angiogenic proteins
Keywords: ANGPT-1; angiopoietin 1; CCA; common carotid arteries; ChIP; chromatin immunoprecipitation; DAPI; 4â²,6-diamidino-2-phenylindole; GFAP; glial fibrillary acidic protein; HMGIY/HMGA1; high-mobility group I-Y protein; MTT; 3-(4,5-dimethylthiazol)-2,5-diphen
Association study of CRP gene polymorphism and hypertension in Han Chinese population
Keywords: BMI; body mass index; Ï2; Chi-square; CHB; Chinese population in Beijing; CRP; C-reactive protein; CRPP1; C-reactive protein pseudogene 1; DBP; diastolic blood pressure; EDTA; ethylenediamine tetraacetic acid; ET-1; endothelin 1; GLM; general linear mode
Computational interrogation of cis-regulatory elements of genes that are common targets of luteotropin and luteolysin in the primate corpus luteum
Keywords: CL; corpus luteum; TFBS; transcription factor binding sites; PG; prostaglandin; LH; luteinizing hormone; P4; progesterone; hCG; human chorionic gonadotropin; GEO; Gene Expression Omnibus; SCARB1; scavenger receptor class B type I; SCD; stearoyl-CoA desatu
Genome-wide characterization of the relationship between essential and TATA-containing genes
Keywords: NENT; non-essential non-TATA; NET; non-essential TATA; ENT; essential non-TATA; ET; essential TATA; CAI; codon adaptation index; Fop; frequency of optimal codon; EL; mRNA expression level; Degree; degree in protein interaction network; TFBS; the number of
Distinct tissue expression profiles of chicken Lpin1-α/β isoforms and the effect of the variation on muscle fiber traits
Keywords: fld; fatty liver dystrophic; PAP; phosphatidic acid phosphohydrolase; qPCR; real-time quantitative RT-PCR; FLR; flanking region; TFBS; transcription factor binding sites; MNLP; multiple-nucleotide length polymorphism; BFS; breast muscle fiber density; BFA
The role of classical and non-classical HLA class I antigens in human tumors
Keywords: APM; antigen processing machinery; β2-m; β2-microglobulin; CALR; calreticulin; CANX; calnexin; CTL; cytotoxic T lymphocyte; DAC; 5-aza-2â²-deoxycytidine; ER; endoplasmic reticulum; ERAP; ER aminopeptidase associated with antigen processing; HC; heavy c
Differential expression of the Gstp2 gene between the aboriginal species Mus spretus and the laboratory mouse Mus musculus
Keywords: GST; Glutathione S-transferase; GST-Pi; Pi class of GST enzymes; GSH; reduced glutathione; Mm; Mus musculus; Ms; Mus spretus; MmGstp2; Gstp2 gene of M. musculus; MsGstp2; Gstp2 gene of M. spretus; TF; transcription factor; TFBS; transcription factor bindi
Towards the elucidation of the regulatory network guiding the insulin producing cells' differentiation
Keywords: NGN3 (NEUROG3); neurogenin3; ESCs; Embryonic Stem Cells; TFBS; Transcription Factor Binding Sites; TFs; Transcription Factors; AP4 (TFAP4); Activating enhancer-binding Protein 4 (Transcription Factor AP-4); WISP1; WNT-Induced Secreted Protein 1; CTGF; Con
AT1 receptor Gαq protein-independent signalling transcriptionally activates only a few genes directly, but robustly potentiates gene regulation from the β2-adrenergic receptor
Keywords: AT1R, angiotensin II type 1 receptor; Ang II, angiotensin II; SII Ang II, [Sar1, Ile4, Ile8] Ang II; Iso, isoproterenol; Forsk, forskolin; 7TMR, seven-transmembrane receptor; TELIS, transcription element listening system based on the Jasper database; TFBS
Identification and analysis of transcription factor family-specific features derived from DNA and protein information
Keywords: Transcription factor; TF family-specific features; TF–TFBS interaction; Multi-class classification; TFBS; Feature selection
An efficient computational method for screening functional SNPs in plants
Keywords: Functional analysis; Computational; In silico screening; Waxy protein; Ns coding; Non-synonymous coding; UTRs; Untranslated regions; TF; Transcriptional factors; TFBS; Transcriptional factor binding site;
Identification of phylogenetically conserved enhancer elements implicated in pancreas development in the WISP1 and CTGF orthologs
Keywords: TFBS; transcription factor binding site; CTGF; connective tissue growth factor; ESC; embryonic stem cell; RT-PCR; reverse transcription polymerase chain reaction; EST; expressed sequence tag; IGF; insulin-like growth factor; TSS; transcription starting si
Identification of the minimal promoter region of the mouse NKX5-3, a transcription factor implicated in eye development
Keywords: EMSA; electrophoretic mobility shift assay; cDNA; DNA complementary to RNA; PCR; polymerase chain reaction; DMEM; Dulbecco's modified Eagle's medium; PBS; phosphate-buffered saline; AP-2; activator protein 2; Sp1; specificity protein 1; SV40; simian virus
Promoter analysis of TCDD-inducible genes in a thymic epithelial cell line indicates the potential for cell-specific transcription factor crosstalk in the AhR response
Keywords: 1AhR; aryl hydrocarbon receptor; DRE; dioxin response element; E2; 17β-estradiol; ER; estrogen receptor; HIF; hypoxia inducible factor; HRE; hypoxia response elements; PAX-4; paired box gene 4; PPARγ; peroxisome proliferative activated receptor, gamma;
Genome-wide effects of acute progressive feed restriction in liver and white adipose tissue
Keywords: Feed restriction; Energy metabolism; Peripheral rhythms; Food entrainment; Microarrays; RT-PCR; APFR; acute progressive feed restriction; WAT; white adipose tissue; TFBS; transcription factor binding site; TSS; transcription start site; SRE; sterol respon
Comparative Analysis of Regulatory Motif Discovery Tools for Transcription Factor Binding Sites
Keywords: motif; TFBS; non-coding DNA sequence; computational algorithm; motif discovery tool
Elucidating effects of long-term expression of HIV-1 Nef on astrocytes by microarray, promoter, and literature analyses
Keywords: CNS; central nervous system; CD; cluster of differentiation; GO; gene ontology; G418; Geneticin; GTPase; guanidin triphosphatase; NCBI; National Center for Biotechnology Information; HIV-1; Human Immunodeficiency Virus-1; rev, nef, tat; HIV-1 encoded regu
Overview of computational methods for the inference of gene regulatory networks
Keywords: cis-Regulatory networks; GRN; Binding site discovery; TFBS; Systems biology;