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Progress in Nucleic Acid Research and Molecular Biology, Volume 48
Subject alert. Receive exclusive offers and updates from Oxford Academic. More on this topic The Radiation Hybrid Database. The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. MetaboAnalyst 4. Related articles in Web of Science Google Scholar. Saliva microbiome in primary Sjogren's syndrome reveals distinct set of disease associated microbes. Crystal structure of peptide-bound neprilysin reveals key binding interactions.
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Bre akpoint profiles of can cer genomes. C ancer c ell m etabolism g ene d ata b ase. Conserved e lements from g enomic a lignments. Da tabase of h uman s mall non-coding R NA. D ata b ase of m onoallelic gene e xpression. A d ata b ase of super -enhancers. Deciphering the m echanisms of d evelopmental d isorder.
Flo we r ing i nteractive d atabase.
H orizontally t ransferred genes identified by tree -based methods. H uman p an- m icrobial c ommunities d atabase. H uman p luripotent s tem c ell reg istry. I nformation c ommons for r ice. Exon-exon junc tion d ata b ase. Me tabolic gene ra pid v isualizer. Open te ratoma in vestigation: images. P oly c ystic o vary s yndrome k nowledge b ase. Plant D Nase I- h ypersensitive S ites.
R NA m odification data base. R ibosome p ro f iling database. S tructurally a nnotated t herapeutic p eptides. Systems b iology r epository for hematopoietic cells. S uper e nhancer a rchive. Quorum sensing sig nalling mol ecules. Sig naling n etwork o pen r esource. Universal e volutionary t race: protein motifs important for function. We ighted g ene co- e xpression t ool. A scidian n etwork for i n s itu e xpression and e mbryological d ata. Thus, the finding that cell-free circulating DNA in the plasma of cancer patients has characteristics of tumor DNA has produced much interest.
In fact, in the last few years, more than publications on this topic have appeared in the literature. In the s, early studies showed that increased quantities of DNA could be found in the plasma of patients suffering from different malignancies 1. Later it was reported that this circulating extracellular DNA exhibits tumor-related alterations, such as decreased strand stability 2 , Ras or p53 mutations, microsatellite alterations, aberrant promoter hypermethylation of tumor suppressor genes, rearranged immunoglobulin heavy-chain DNA, mitochondrial DNA mutations, and tumor-related viral DNA 3.
This very active group has been able, for example, to quantify the amount of Epstein-Barr virus DNA in the serum of patients with nasopharyngeal cancer. It is possible to predict by measuring the amount of free Epstein-Barr virus DNA the patients who are likely to relapse several months before the clinical appearance of a tumor. A recent development in this new field is the finding of tumor-related RNA in the plasma or serum of cancer patients 5.
The work on circulating RNA markers is particularly promising because the percentage of detectable tumors seems higher than that found with DNA markers.
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Telomerase RNA seems to be a promising marker because it can be found in the serum of patients with small, still-undifferentiated breast tumors without any metastasized nodes. In their study, 8 of 9 plasma samples from colorectal cancer patients and 9 of 9 plasmas from patients with lymphoma were positive for human telomerase reverse transcriptase, whereas all 10 healthy controls were negative.
Moreover, tumor size and proliferative index were associated with the presence of mammaglobin, CK19, or both RNAs in plasma 8. The article by Ng et al. They found that glyceraldehyde 3-phosphate dehydrogenase GAPDH mRNA concentrations were significantly higher in patients with hepatocellular carcinoma than in healthy controls. Although there was some overlap between a subset of patients with low GAPDH mRNA concentrations and healthy controls with higher concentrations, it seems that the majority of the patients could have been detected by measuring the quantity of mRNA in the plasma.
Nevertheless, this simple and robust method might be used as a very easy and useful assay for follow-up after surgery or therapy. This article also brings new insights on the biological problem concerning the origin of circulating nucleic acids. Indeed, before RNA extraction, the authors submitted the plasma samples to different centrifugation or filtration techniques Plasma samples from each individual were either filtered through different-sized filters 5—0. These particles are of different sizes and could be apoptotic bodies, which would explain why the circulating RNA is protected in the plasma.
The field of circulating nucleic acids is becoming more exciting. The use of plasma DNA and RNA may provide opportunities to establish noninvasive tests for detecting cancer, in addition to their use in prenatal detection 16 , and may open new and largely unexplored biological pathways. Skip to main content. Assembly: a resource for assembled genomes at NCBI. Dousse A. CEGA-a catalog of conserved elements from genomic alignments. Chorev M.
JuncDB: an exon-exon junction database. Khan A. Wei Y. SEA: a super-enhancer archive. Dowen J. Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes. Hospital A. Finn R. The Pfam protein families database: towards a more sustainable future. Dinkel H. ELM - data update and new functionality of the eukaryotic linear motif resource. Zheng Z. Nucleotide binding database NBDB - a collection of sequence motifs with specific protein-ligand interactions.
Lua R. UET: A database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures. Olexiouk V. Vizcaino J. Huang K. Velankar S. Pancsa R. Hrabe T. PDBFlex: exploring flexibility in protein structures. Sud M. Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools.
Kersey P. Ensembl Genomes more genomes, more complexity. BacDive — The Bacterial Diversity metadatabase. Lasker K. CauloBrowser: a systems biology resource for Caulobacter crescentus. Winsor G. Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database. Michna R. SubtiWiki 2. Wilke A. Mitchell A. EBI Metagenomics in - an expanding and evolving resource for the analysis and archiving of metagenomic data. Greuter D. Forster S.
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HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes. Ruan Z. BacWGSTdb, a database for genotyping and source tracking bacterial pathogens. Yin C. InsectBase: a resource for insect genomes and transcriptomes. Brozovic M. Brandl H. PlanMine - a mineable resource of planarian biology and biodiversity. Wilson R. Deciphering the mechanisms of developmental disorders: phenotype analysis of embryos from mutant mouse lines. Savova V.
Autosomal monoallelic expression: genetics of epigenetic diversity. Siramshetty V. Kuhn M. Gilson M. BindingDB in a public database for medicinal chemistry, computational chemistry and systems pharmacology. Gazzo A. DIDA: A curated and annotated digenic diseases database. Kim S. PubChem Substance and Compound databases. Hastings J.