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Open Mass Spectrometry Search Algorithm (OMSSA)
Probe Database Debut
New Structure Link from Protein
BLAST Download Update
New Microbial Genomes in GenBank
Nucleotide Database Splits
NCBI 4-Pack Course
RefSeq Release 14
New Organisms in UniGene
GenBank Passes 100 Gigabases
New BLAST Formatter
Splign Alignment Tool
GenBank Release 150
New Genome Builds
Submission Corner
Masthead
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The Probe Database Makes its Debut in Entrez
Nucleic acid probes are molecules that complement or hybridize to a specific mRNA or DNA sequence and are designed to target a gene so that information about its location, structure and function can be obtained. Probes are important reagents used in a wide range of biomolecular studies. In many cases, however, the molecular probe sequences have not been deposited in primary nucleotide sequence databases such as GenBank because these sequences are derived from longer sequences already present in the database. Moreover, many important details about the probes, such as experimental application, the efficacy of the probe in that application, and information on obtaining these reagents are not normally available in traditional sequence records. A number of high-throughput genome analysis projects, among them ENCODE, HapMap, and GENSAT, are producing large numbers of molecular probes that have been used in a variety of experimental applications. The information obtained from these and other molecular studies will have a profound impact in the areas of functional genomics, diagnostic medicine, and agriculture. In order for researchers to have access to these and other molecular probes, NCBI has established the Probe database as a public repository for probe reagents.
Probe contains sequences of oligonucleotide probes and results from a wide variety of applications and technologies, including gene silencing experiments (RNAi), gene expression assays, variation analysis, genome mapping, nucleic acid detection, and genotyping studies. Currently, more than one million records are in the Probe database and include reagents and results for experiments in human, mouse, rat, fruit fly, and C. elegans.
Querying the Database
The Probe database is now searchable as a part of the Entrez database system at NCBI
As with all other Entrez databases, search terms can be restricted to a specific field and combined using Boolean logic. A list of terms indexed under each field can be found by going to the Preview/Index tab on the Entrez Probe home page, selecting the appropriate search field and clicking "Index". For example, the following Entrez Probe query find probes that have been used to study the gene mutated in ataxia telangiectasia, ATM.
ATM [gene name]
This search returns a list of probes shown in Figure 1. The returned results contain probes designed for expression, gene silencing and variation studies. Results are easily filtered by application using the "Expression", "Silencing", or "Variation" tabs at the top of the display. Clicking on the probe ID displays an Entrez Probe summary report. Depending on the application or technology, the report includes the sense and/or antisense probe sequence, a link to order the probe from the manufacturer, supporting literature references with links to PubMed and a list of other potentially cross-reacting probes in the database, their location on the target mRNA and the experimental results.
Figure 1. Summary results for a search for probes specific to the ATM gene.
An expression probe for ATM, #196090, was used in an in situ hybridization study of gene expression in the developing mouse brain These data are part of the Gene Expression Nervous System SAtlas (GENSAT) database reported in the May 2005 NCBI News. The summary for probes such as #196090 from GENSAT contains previews of corresponding in situ hybridization images in Entrez GENSAT (Figure 2 A). The gene silencing probes for ATM are RNA interference (RNAi) reagents used in sequence specific gene silencing experiments. These include small-hairpin (shRNA) and small interfering (siRNA) probes which target the ATM gene in human. An RNAi Homepage is also available for researchers interested in gene silencing.
Figure 2. Samples of probe reports. A) a portion of the report for an expression probe for the ATM gene used in the GenSat project (above). The summary shows an image of an in situ hybridization experiment using this probe to label a whole mouse embryo section. B) A summary of the RSA probes that cover the exons of the human ATM gene (below).
Queries on this page return only gene silencing reagents. The RNAi home page also contains LinkOuts to supporting references and reviews on RNAi technology, RNAi projects, probe design tools, companies specializing in RNAi technology, and recent primary literature and reviews from PubMed.
The remaining probes retrieved for ATM are used to study sequence variation. Probe #1274377 is a resequencing amplicon (RSA) - a set of primers designed for PCR amplification and resequencing of the exons of human genes. The RSA probes are intended for use in SNP discovery and are available for a large fraction of human genes. The summary for #1274377 shows the alignment of all RSA probes for the ATM gene and its transcript variants and includes a link to select and download primers (Figure 2 B). Another class of variation probes are those associated with the human haplotype mapping projects (HapMap).These are not directly associated with specific genes and are not found by searching for ATM in the probe database. HapMap probes that map to ATM region are easily found by searching for the ATM gene in the Entrez SNP database and following the links to Entrez Probe.
Researchers who wish to submit their unpublished or published data to the probe database should send an email request to
Specific guidelines for submitting the results from RNAi studies are available online:
Questions regarding Entrez Probe should be sent to
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