A5006229200- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Biomedical Text Mining and Ontologies
- Molecular Biology Techniques and Applications
- Effects and risks of endocrine disrupting chemicals
- Cancer therapeutics and mechanisms
- Metabolomics and Mass Spectrometry Studies
- Carcinogens and Genotoxicity Assessment
- Computational Drug Discovery Methods
- Synthesis and Biological Evaluation
- Genetics, Bioinformatics, and Biomedical Research
- Bioactive Compounds and Antitumor Agents
- RNA modifications and cancer
- Mitochondrial Function and Pathology
- Scientific Computing and Data Management
- Semantic Web and Ontologies
- Drug Transport and Resistance Mechanisms
- RNA and protein synthesis mechanisms
- Air Quality and Health Impacts
- Nutrition, Genetics, and Disease
- Pharmacogenetics and Drug Metabolism
- Animal testing and alternatives
- Fibromyalgia and Chronic Fatigue Syndrome Research
- Retinoids in leukemia and cellular processes
- Research Data Management Practices
National Institute of Environmental Health Sciences
2009-2021
Triangle
2006-2018
National Institutes of Health
2006-2017
Research Triangle Park Foundation
1983-2016
National Cancer Institute
2006-2010
Center for Cancer Research
2006-2010
SRA International (United States)
2009-2010
Lockheed Martin (United States)
2005-2008
National Institute for Environmental Studies
2007
Hi-Z Technology (United States)
2006
The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies provide a representation biomedical knowledge from Open Biological Ontologies (OBO) project adds ability this was derived. We here state several applications using it, such as adding semantic expressivity existing databases, building data entry forms,...
Experimental descriptions are typically stored as free text without using standardized terminology, creating challenges in comparison, reproduction and analysis. These difficulties impose limitations on data exchange information retrieval.
Cancer stem cells are presumed to have virtually unlimited proliferative and self-renewal abilities be highly resistant chemotherapy, a feature that is associated with overexpression of ATP-binding cassette transporters. We investigated whether prolonged continuous selection for drug resistance enriches cultures cancer stem-like cells.Cancer were defined as CD44+/CD24⁻ could self-renew (ie, generate the tumorigenic phenotype), differentiate, invade, form tumors in vivo. used...
The propensity of compounds to produce adverse health effects in humans is generally evaluated using animal-based test methods. Such methods can be relatively expensive, low-throughput, and associated with pain suffered by the treated animals. In addition, differences species biology may confound extrapolation human effects.The National Toxicology Program Institutes Health Chemical Genomics Center are collaborating identify a battery cell-based screens prioritize for further toxicologic...
ABSTRACT Enzymes in the ergosterol-biosynthetic pathway are targets of a number antifungal agents including azoles, allylamines, and morpholines. In order to understand response Saccharomyces cerevisiae perturbations ergosterol pathway, genome-wide transcript profiles following exposure targeting biosynthesis (clotrimazole, fluconazole, itraconazole, ketoconazole, voriconazole, terbinafine, amorolfine) were obtained. These compared strains containing deletions one late-stage genes: ERG2 ,...
Abstract Motivation: The generation of large amounts microarray data and the need to share these bring challenges for both management annotation highlights standards. MIAME specifies minimum information needed describe a experiment Microarray Gene Expression Object Model (MAGE-OM) resulting MAGE-ML provide mechanism standardize representation exchange, however common terminology is support Results: Here we MGED Ontology (MO) developed by Working Group Data (MGED) Society. MO provides terms...
Abstract The U.S. Tox21 program has screened a library of approximately 10,000 (10K) environmental chemicals and drugs in three independent runs for estrogen receptor alpha (ERα) agonist antagonist activity using two types ER reporter gene cell lines, one with an endogenous full length ERα (ER-luc; BG1 line) the other transfected partial consisting ligand binding domain (ER-bla; β-lactamase line), quantitative high-throughput screening (qHTS) format. ability assays to correctly identify...
CEBS (Chemical Effects in Biological Systems) is an integrated public repository for toxicogenomics data, including the study design and timeline, clinical chemistry histopathology findings microarray proteomics data. contains data derived from studies of chemicals genetic alterations, compatible with environmental studies. designed to permit user query using conditions, subject responses then, having identified appropriate set subjects, move module carry out gene signature pathway analysis....
Understanding the mechanisms of multidrug resistance (MDR) could improve clinical drug efficacy. Multidrug is associated with ATP binding cassette (ABC) transporters, but factors that regulate their expression at clinically relevant concentrations are poorly understood. We report a single-step selection low doses anti-cancer agents, similar to reported in vivo, induces MDR mediated exclusively by ABCG2. selected breast, ovarian and colon cancer cells (MCF-7, IGROV-1 S-1) after exposure 14 or...
Nrf2 is an essential transcription factor for protection against oxidant disorders. However, its role in organ development and neonatal disease has received little attention. Therapeutically administered oxygen been considered to contribute bronchopulmonary dysplasia (BPD) prematurity. The current study was performed determine Nrf2-mediated molecular events during saccular-to-alveolar lung maturation, the of pathogenesis hyperoxic injury using newborn Nrf2-deficient (Nrf2(-/-)) wild-type...
Nrf2 is a key transcription factor that regulates cellular redox and defense responses. However, permanent activation in human lung carcinomas promotes pulmonary malignancy chemoresistance. We tested the hypothesis has cell survival properties lack of suppresses chemically-induced neoplasia by treating Nrf2(+/+) Nrf2(-/-) mice with urethane. Airway inflammation injury were assessed bronchoalveolar lavage analyses histopathology, tumors analyzed gross histologic analysis. used transcriptomics...
The Chemical Effects in Biological Systems database (CEBS) is a comprehensive and unique toxicology resource that compiles individual summary animal data from the National Toxicology Program (NTP) testing program other depositors into single electronic repository. CEBS has undergone significant updates recent years currently contains over 11 000 test articles (exposure agents) 8000 studies including all available NTP carcinogenicity, short-term toxicity genetic studies. Study provided to are...
Abstract Background The use of gene expression profiling in both clinical and laboratory settings would be enhanced by better characterization variance due to individual, environmental, technical factors. Meta-analysis microarray data from untreated or vehicle-treated animals within the control arm toxicogenomics studies could yield useful information on baseline fluctuations expression, although animal has not been available a scale form best served for data-mining. Results A dataset was...
This article summarizes the motivation for, and proceedings of, first ISA-TAB workshop held December 6–8, 2007, at EBI, Cambridge, UK. exploratory workshop, organized by members of Microarray Gene Expression Data (MGED) Society's Reporting Structure for Biological Investigations (RSBI) working group, brought together a group developers range collaborative systems to discuss use common format address pressing need reporting communicating data metadata from biological, biomedical,...
The genotoxicity testing battery is highly sensitive for detection of chemical carcinogens. However, it features a low specificity and provides only limited mechanistic information required risk assessment positive findings. This especially important in case findings the vitro chromosome damage assays, because may be also induced secondarily to cell death. An increasing body evidence indicates that toxicogenomic analysis cellular stress responses an insight into mechanisms action...
DNA topoisomerases, a class of enzymes that change the topological structure DNA, have been shown to be target many therapeutic agents, including antibacterial agents (quinolones) and anticancer agents. These drugs inhibit enzyme in unique way so is converted into cellular poison. Candida albicans Aspergillus niger are two major opportunistic fungal pathogens. Our results show these fungi high levels both type I II topoisomerases (with minimum 5 x 10(5) ATP-independent relaxation units 2 P-4...
To gain understanding of the molecular basis chronic fatigue syndrome (CFS) through gene expression analysis using a large microarray data set in conjunction with clinically administrated questionnaires.Data from Wichita (KS, USA) CFS Surveillance Study was used, comprising 167 participants two self-report questionnaires (multidimensional inventory [MFI] and Zung depression scale [Zung]), data, empiric classification, others. Microarray analyzed bioinformatics tools ArrayTrack.Correspondence...
The effects of human papillomavirus type 18 (HPV-18) E6 and E7 proteins on global patterns host gene expression in primary keratinocytes grown organotypic raft culture system were assessed. Primary infected with retroviruses that express the wild-type HPV-18 genes from native differentiation-dependent HPV enhancer-promoter. Total RNA was isolated cultures used to generate probes for querying Affymetrix U95A microarrays, which contain >12,500 sequences. Quadruplicate arrays each...
The nucleotide sequence of the gpt coding for enzyme xanthine guanine phosphoribosyl transferase has been determined. gene codes a protein molecular weight 16,950. construction deletions in which can be used genetic analysis mutations gene, is described.
With the increasing use of metabolomics as a means to study large number different biological research questions, there is need for minimal set reporting standards that allow scientific community evaluate, understand, repeat, compare and re-investigate studies. Here we propose, first draft requirements effectively describe context studies involve microbial or in vitro subjects. This recommendation has been produced by microbiology biology working subgroup Metabolomics Standards Initiative...