NCBI Entrez Research Articles

Annokey: an annotation tool based on key term search of the NCBI Entrez Gene database

BackgroundThe NCBI Entrez Gene and PubMed databases contain a wealth of high-quality information about genes for many different organisms. The NCBI Entrez online web-search interface is convenient for simple manual search for a small number of genes but impractical for the kinds of outputs seen in typical genomics projects.ResultsWe have developed an efficient open source tool implemented in Python called Annokey, which annotates gene lists with the results of a keyword search of the NCBI Entrez Gene database and linked Pubmed article information. The user steers the search by specifying a ranked list of keywords (including multi-word phrases and regular expressions) that are correlated with their topic of interest. Rank information of matched terms allows the user to guide further investigation.We applied Annokey to the entire human Entrez Gene database using the key-term “DNA repair” and assessed its performance in identifying the 176 members of a published “gold standard” list of genes established to be involved in this pathway. For this test case we observed a sensitivity and specificity of 97% and 96%, respectively.ConclusionsAnnokey facilitates the identification of genes related to an area of interest, a task which can be onerous if performed manually on a large number of genes. Annokey provides a way to capitalize on the high quality information provided by the Entrez Gene database allowing both scalability and compatibility with automated analysis pipelines, thus offering the potential to significantly enhance research productivity.

MMDB and VAST+: tracking structural similarities between macromolecular complexes

The computational detection of similarities between protein 3D structures has become an indispensable tool for the detection of homologous relationships, the classification of protein families and functional inference. Consequently, numerous algorithms have been developed that facilitate structure comparison, including rapid searches against a steadily growing collection of protein structures. To this end, NCBI’s Molecular Modeling Database (MMDB), which is based on the Protein Data Bank (PDB), maintains a comprehensive and up-to-date archive of protein structure similarities computed with the Vector Alignment Search Tool (VAST). These similarities have been recorded on the level of single proteins and protein domains, comprising in excess of 1.5 billion pairwise alignments. Here we present VAST+, an extension to the existing VAST service, which summarizes and presents structural similarity on the level of biological assemblies or macromolecular complexes. VAST+ simplifies structure neighboring results and shows, for macromolecular complexes tracked in MMDB, lists of similar complexes ranked by the extent of similarity. VAST+ replaces the previous VAST service as the default presentation of structure neighboring data in NCBI’s Entrez query and retrieval system. MMDB and VAST+ can be accessed via http://www.ncbi.nlm.nih.gov/Structure.

Abstract 2900: Phylogenetic classification, structural evolution, and functional divergence of the Ras superfamily of GTPases as tracked by the Conserved Domain Database (CDD)..

Abstract The Conserved Domain Database (CDD, http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml) is part of NCBI's Entrez query and retrieval system and is a collection of annotated multiple sequence alignment (MSA) models representing ancient conserved protein domains, basic units of protein function and protein evolution.These MSA models are available as position specific score matrices (PSSMs) for fast identification of conserved domains in protein sequences via Reverse Position Specific -BLAST (RPS-BLAST), a variation of the commonly used PSI-BLAST. The domain models can be viewed and examined interactively using NCBI's CDTree/Cn3D software applications. Conserved functional annotations such as key catalytic and ligand-binding sites are displayed on protein structures sharing significant homology to the query, thereby inferring the underlying mechanism(s) of the protein domain family. Here, we present the current, functionally annotated, evolutionary classification of the Ras GTPase superfamily, including the circularly permuted Ras-like domain, and its downstream effectors such as RasGAP and RasGEF. Using CDTree/Cn3D tools, subfamilies in diverse organisms were inferred from the MSAs, phylogenetic trees, and domain architectures of the Ras superfamily. Furthermore, several subfamilies comprising of only uncharacterized protein sequences have their functions annotated by inference from the molecular and cellular functions of known related proteins having 3D structure, and based on the available literature. We demonstrate the utility of CDTree/Cn3D in studying molecular evolution of protein domain families, and in accelerating the pace of biological discovery by enabling researchers to obtain valuable clues regarding as-yet-unidentified molecular properties and mechanisms. CDTree/Cn3D software is freely available for download via the CDD website. Citation Format: James S. Song, Narmada Thanki, Myra K. Derbyshire, Marc Gwadz, Noreen R. Gonzales, Aron Marchler-Bauer, Stephen H. Bryant. Phylogenetic classification, structural evolution, and functional divergence of the Ras superfamily of GTPases as tracked by the Conserved Domain Database (CDD). [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2900. doi:10.1158/1538-7445.AM2013-2900

Co-infection of tuberculosis and parasitic diseases in humans: a systematic review

Co-infection of tuberculosis and parasitic diseases in humans is an important public problem in co-endemic areas in developing countries. However, there is a paucity of studies on co-infection and even fewer reviews. This review examines 44 appropriate papers by PRISMA from 289 papers searched in PubMed via the NCBI Entrez system (no grey literature) up to December 2012 in order to analyze the factors that influence epidemic and host’s immunity of co-infection. The limited evidence in this review indicates that most common parasite species are concurrent with Mycobacterium tuberculosis in multiple organs; socio-demographics such as gender and age, special populations with susceptibility such as renal transplant recipients, patients on maintenance haemodialysis, HIV positive patients and migrants, and living in or coming from co-endemic areas are all likely to have an impact on co-infection. Pulmonary tuberculosis and parasitic diseases were shown to be risk factors for each other. Co-infection may significantly inhibit the host’s immune system, increase antibacterial therapy intolerance and be detrimental to the prognosis of the disease; in addition, infection with parasitic diseases can alter the protective immune response to Bacillus Calmette-Guerin vaccination against Mycobacterium tuberculosis.

CDD: conserved domains and protein three-dimensional structure

CDD, the Conserved Domain Database, is part of NCBI’s Entrez query and retrieval system and is also accessible via http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml. CDD provides annotation of protein sequences with the location of conserved domain footprints and functional sites inferred from these footprints. Pre-computed annotation is available via Entrez, and interactive search services accept single protein or nucleotide queries, as well as batch submissions of protein query sequences, utilizing RPS-BLAST to rapidly identify putative matches. CDD incorporates several protein domain and full-length protein model collections, and maintains an active curation effort that aims at providing fine grained classifications for major and well-characterized protein domain families, as supported by available protein three-dimensional (3D) structure and the published literature. To this date, the majority of protein 3D structures are represented by models tracked by CDD, and CDD curators are characterizing novel families that emerge from protein structure determination efforts.

GenBank

GenBank® (http://www.ncbi.nlm.nih.gov) is a comprehensive database that contains publicly available nucleotide sequences for almost 260 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI home page: www.ncbi.nlm.nih.gov.

A semantic collaborative system for the management of translational research projects

A semantic collaborative system for the management of translational research projects

SpliceAid-F: a database of human splicing factors and their RNA binding sites

Motivations. The pre-mRNA sequences of eukaryotes harbour multiple information layers in addition to the one specifying the aminoacid sequence. Indeed, specific signals regulating the splicing process, RNA folding, capping, polyadenylation, stability and nuclear export, overlap each other and with the coding information. Mutagenesis experiments have highlighted that splicing regulatory elements are scattered in the entire pre-mRNA sequence and that all nucleotide positions are potentially involved in the generation of the specific splicing pattern through the specific interaction with trans-acting RNA-binding proteins. In particular, the identification of cis-regulatory motifs in exonic regions, such as exonic splicing enhancers (ESEs) or silencers (ESSs), superimposed on the coding sequence of the gene can be driven by the observation of purifying selection occurring at synonymous codons [5]. The coordinated binding of combinations of regulatory proteins to their binding sites modulate the expression of specific transcript isoforms in a cell/tissue type-, development stage-, disease- and/or other condition-specific manners and may also promote or repress the formation of the spliceosome, the large (~60S) RNA-protein machinery that catalyzes intron removal. A growing list of mammalian protein factors involved in splicing regulation and their target sites in the pre-mRNA has been reported in the literature [2]. In order to establish a curated and retrievable repository of splicing regulatory factors and target sites for human genes we have recently created SpliceAid [4] that can also be used to find putative regulatory motifs in user submitted sequences. As a further evolution of SpliceAid, we present here SpliceAid-F, a database compilation of splicing regulatory factors and their experimentally validated target RNAs extracted from an exhaustive hand-curated literature search. Methods. For each known splicing factor, cross-links to gene (NCBI Entrez) and protein (Uniprot) IDs, as well as information on the structure of the RNA binding domain, the protein-defect associated disease (MIM), and the interacting proteins (from STRING and IntAct) have been collected. Moreover, we have extracted from the literature the relevant information on the genome coordinates of RNA binding sites (or experimentally validated non-binding sites), type of binding assay, gene information and the context-specific splicing effects of splicing factor binding in terms of exonization or intronization. Furthermore, binding site information have been also reported in the transcript view of ASPicDB [1,3]. Results. SpliceAid-F, currently collects 68 records for splicing regulatory factors and 2489 records for their related binding sites and can be retrieved through a web interface. SpliceAid-F collects in a unique resource heterogeneous information about splicing regulatory proteins, related RNA binding sites and context-specific activity of their interaction. Our database may be a useful resource to retrieve and visualize experimentally known splicing factor binding sites in a gene and to investigate their context where additional binding sites may establish a potential competition or co-regulation. All these information may help to explain the observed splicing pattern as well as the effect of mutations, which if located in functional regulatory elements may generate an aberrant and possibly pathological splicing pattern. This resource can also be useful to develop a new generation of prediction software taking into account all the splicing regulatory element and so allowing to attain a more accurate prediction of splicing patterns. Availability http://www.caspur.it/SpliceAidF

GenBank

GenBank® is a comprehensive database that contains publicly available nucleotide sequences for more than 250 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI home page: www.ncbi.nlm.nih.gov.

PubChem's BioAssay Database

PubChem (http://pubchem.ncbi.nlm.nih.gov) is a public repository for biological activity data of small molecules and RNAi reagents. The mission of PubChem is to deliver free and easy access to all deposited data, and to provide intuitive data analysis tools. The PubChem BioAssay database currently contains 500 000 descriptions of assay protocols, covering 5000 protein targets, 30 000 gene targets and providing over 130 million bioactivity outcomes. PubChem's bioassay data are integrated into the NCBI Entrez information retrieval system, thus making PubChem data searchable and accessible by Entrez queries. Also, as a repository, PubChem constantly optimizes and develops its deposition system answering many demands of both high- and low-volume depositors. The PubChem information platform allows users to search, review and download bioassay description and data. The PubChem platform also enables researchers to collect, compare and analyze biological test results through web-based and programmatic tools. In this work, we provide an update for the PubChem BioAssay resource, including information content growth, data model extension and new developments of data submission, retrieval, analysis and download tools.

MMDB: 3D structures and macromolecular interactions

Close to 60% of protein sequences tracked in comprehensive databases can be mapped to a known three-dimensional (3D) structure by standard sequence similarity searches. Potentially, a great deal can be learned about proteins or protein families of interest from considering 3D structure, and to this day 3D structure data may remain an underutilized resource. Here we present enhancements in the Molecular Modeling Database (MMDB) and its data presentation, specifically pertaining to biologically relevant complexes and molecular interactions. MMDB is tightly integrated with NCBI's Entrez search and retrieval system, and mirrors the contents of the Protein Data Bank. It links protein 3D structure data with sequence data, sequence classification resources and PubChem, a repository of small-molecule chemical structures and their biological activities, facilitating access to 3D structure data not only for structural biologists, but also for molecular biologists and chemists. MMDB provides a complete set of detailed and pre-computed structural alignments obtained with the VAST algorithm, and provides visualization tools for 3D structure and structure/sequence alignment via the molecular graphics viewer Cn3D. MMDB can be accessed at http://www.ncbi.nlm.nih.gov/structure.

PubChem promiscuity: a web resource for gathering compound promiscuity data from PubChem

Promiscuity counts allow for a better understanding of a compound's assay activity profile and drug potential. Although PubChem contains a vast amount of compound and assay data, it currently does not have a convenient or efficient method to obtain in-depth promiscuity counts for compounds. PubChem promiscuity fills this gap. It is a Java servlet that uses NCBI Entrez (eUtils) web services to interact with PubChem and provide promiscuity counts in a variety of categories along with compound descriptors, including PAINS-based functional group detection. http://chemutils.florida.scripps.edu/pcpromiscuity southern@scripps.edu

Searching NCBI Databases Using Entrez

One of the most widely used interfaces for the retrieval of information from biological databases is the NCBI Entrez system. Entrez capitalizes on the fact that there are pre-existing, logical relationships between the individual entries found in numerous public databases. The existence of such natural connections, mostly biological in nature, argued for the development of a method through which all the information about a particular biological entity could be found without having to sequentially visit and query disparate databases. Two basic protocols describe simple, text-based searches, illustrating the types of information that can be retrieved through the Entrez system. An alternate protocol builds upon the first basic protocol, using additional, built-in features of the Entrez system, and providing alternative ways to issue the initial query. The support protocol reviews how to save frequently issued queries. Finally, Cn3D, a structure visualization tool, is also discussed.

Searching NCBI databases using Entrez.

One of the most widely used interfaces for the retrieval of information from biological databases is the NCBI Entrez system. Entrez capitalizes on the fact that there are pre-existing, logical relationships between the individual entries found in numerous public databases. The existence of such natural connections, mostly biological in nature, argued for the development of a method through which all the information about a particular biological entity could be found without having to sequentially visit and query disparate databases. Two basic protocols describe simple, text-based searches, illustrating the types of information that can be retrieved through the Entrez system. An alternate protocol builds upon the first basic protocol, using additional, built-in features of the Entrez system, and providing alternative ways to issue the initial query. The support protocol reviews how to save frequently issued queries. Finally, Cn3D, a structure visualization tool, is also discussed.

A Combination of Biochemical and Proteomic Analyses Reveals Bx-LEC-1 as an Antigenic Target for the Monoclonal Antibody 3-2A7-2H5-D9-F10 Specific to the Pine Wood Nematode

Pine wilt disease (PWD) is one of the most devastating forest diseases in Asia and Europe. The pine wood nematode, Bursaphelenchus xylophilus, has been identified as the pathogen underlying PWD, although the pathology is not completely understood. At present, diagnosis and confirmation of PWD are time consuming tasks that require nematode extraction and microscopic examination. To develop a more efficient detection method for B. xylophilus, we first generated monoclonal antibodies (MAbs) specific to B. xylophilus. Among 2304 hybridoma fusions screened, a hybridoma clone named 3-2A7-2H5 recognized a single protein from B. xylophilus specifically, but not those from other closely related nematodes. We finally selected the MAb clone 3-2A7-2H5-D9-F10 (D9-F10) for further studies. To identify the antigenic target of MAb-D9-F10, we analyzed proteins in spots, fractions, or bands isolated from SDS-PAGE, two-dimensional electrophoresis, anion exchange chromatography, and immunoprecipitation via nano liquid chromatography electrospray ionization quadrupole ion trap mass spectrometry (nano-LC-ESI-Q-IT-MS). Peptides of galactose-binding lectin-1 of B. xylophilus (Bx-LEC-1) were commonly detected in several proteomic analyses, demonstrating that this LEC-1 is the antigenic target of MAb-D9-F10. The localization of MAb-D9-F10 immunoreactivities at the area of the median bulb and esophageal glands suggested that the Bx-LEC-1 may be involved in food perception and digestion. The Bx-LEC-1 has two nonidentical galactose-binding lectin domains important for carbohydrate binding. The affinity of the Bx-LEC-1 to D-(+)-raffinose and N-acetyllactosamine were much higher than that to L-(+)-rhamnose. Based on this combination of evidences, MAb-D9-F10 is the first identified molecular biomarker specific to the Bx-LEC-1.

Bioinformatic analysis for allergenicity assessment of Bacillus thuringiensis Cry proteins expressed in insect-resistant food crops

The novel proteins introduced into the genetically modified (GM) crops need to be evaluated for the potential allergenicity before their introduction into the food chain to address the safety concerns of consumers. At present, there is no single definitive test that can be relied upon to predict allergic response in humans to a new protein; hence a composite approach to allergic response prediction is described in this study. The present study reports on the evaluation of the Cry proteins, encoded by cry1Ac, cry1Ab, cry2Ab, cry1Ca, cry1Fa/cry1Ca hybrid, being expressed in Bt food crops that are under field trials in India, for potential allergenic cross-reactivity using bioinformatics search tools. The sequence identity of amino acids was analyzed using FASTA3 of AllergenOnline version 10.0 and BLASTX of NCBI Entrez to identify any potential sequence matches to allergen proteins. As a step further in the detection of allergens, an independent database of domains in the allergens available in the AllergenOnline database was also developed. The results indicated no significant alignment and similarity of Cry proteins at domain level with any of the known allergens revealing that there is no potential risk of allergenic cross-reactivity.

GenBank

GenBank® is a comprehensive database that contains publicly available nucleotide sequences for more than 380 000 organisms named at the genus level or lower, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system that integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. To access GenBank and its related retrieval and analysis services, begin at the NCBI Homepage: www.ncbi.nlm.nih.gov.

A method to track dataset reuse in biomedicine: Filtered GEO accession numbers in PubMed Central

Reusing research data has important potential benefits: generative science and efficient resource use. Tracking the reuse of research datasets would allow us to understand whether the potential benefits are indeed realized, enable recognition of investigators who produce, annotate, and share useful data, and inform data sharing and reuse initiatives, tools, and policies. Unfortunately, the lack of clear attribution practices for data make automated tracking of data reuse difficult. I present a method for tracking research data reuse that takes advantage of the community norms around gene expression microarray data sharing and the rich NCBI Entrez resources. Specifically, the full-text of papers stored in PubMed Central are queried for accession numbers of datasets archived in NCBI's Gene Expression Omnibus (GEO) repository. Studies known to have created microarray data are excluded through automated filters and guided manual curation. MeSH terms attached to the data creation and data reuse studies provide additional information for analysis. Finally, I extrapolate the findings to all of PubMed. Automated portions of this method have been implemented in python and are openly available. Although imperfect, this dataset is a valuable initial resource for research into patterns of data reuse.

Abstract B5: Sequence analysis of HSP90-encoding genes in breast tumor tissue identifies a novel 9 bp deletion in HSP90AB1

Abstract The 90 kDa heat-shock protein (HSP90) functions as a ubiquitous cellular chaperone in cells, and is required for the function and stability of many client proteins such as ERBB2, EGFR, BCR-ABL, MET, androgen and estrogen receptors, BRAF and HIF-1α.1 There are four primary genes that encode for HSP90 in humans: HSP90AA1 and HSP90AB1 (cytosolic), HSP90B1 (endoplasmic reticulum) and TRAP1 (mitochondrial). Increased HSP90 expression has been associated with poor prognosis in cancer, and inhibiting HSP90 can lead to degradation of many oncogenic client proteins via the proteasome pathway.1 HSP90 has been the subject of intense drug discovery activities, with several therapeutics under clinical investigation.2 However, the data on single nucleotide polymorphisms (SNPs) and potential somatic mutations within the HSP90-encoding genes in tumor tissue is limited. Target allelic variation can alter drug binding and therapeutic response, as demonstrated by Iressa™'s reported specific efficacy in EGFR-mutant non-small cell lung cancer patients.3 Therefore, it is critical to understand target allelic variance as part of a drug development program. To facilitate drug development efforts around HSP90, we investigated allelic variation within the coding regions of HSP90AA1 (second isoform) and HSP90AB1 genes in 49 formalin-fixed paraffin- embedded human breast tumor samples. Sample SNP data were compared to control data from the NCBI Entrez SNP database. We observed four synonymous changes within HSP90AA1, and two synonymous changes within HSP90AB1. Intriguingly, we also observed a heterozygous 9-base deletion in exon 1 of HSP90AB1 within one breast tumor patient sample. This deletion results in an alanine>valine substitution at amino acid 22 and a loss of amino acid 23-25 (glutamine, leucine, methionine). The deleted region includes one turn of a 3-turn alpha helix, located within the N-terminal domain structure of the HSP90AB1 protein. Full details of HSP90 allelic variance within breast tumor tissue, and a discussion of the potential functional significance of the deletion, will be provided.

The 19-Amino Acid Insertion in the Tumor-associated Splice Isoform Rac1b Confers Specific Binding to p120 Catenin

The Rac1b splice isoform contains a 19-amino acid insertion not found in Rac1; this insertion leads to decreased GTPase activity and reduced affinity for GDP, resulting in the intracellular predominance of GTP-bound Rac1b. Here, using co-precipitation and proteomic methods, we find that Rac1b does not bind to many common regulators of Rho family GTPases but that it does display enhanced binding to SmgGDS, RACK1, and p120 catenin (p120(ctn)), proteins involved in cell-cell adhesion, motility, and transcriptional regulation. We use molecular modeling and structure analysis approaches to determine that the interaction between Rac1b and p120(ctn) is dependent upon protein regions that are predicted to be unstructured in the absence of molecular complex formation, suggesting that the interaction between these two proteins involves coupled folding and binding. We also find that directed cell movement initiated by Rac1b is dependent upon p120. These results define a distinct binding functionality of Rac1b and provide insight into how the distinct phenotypic program activated by this protein may be implemented through molecular recognition of effectors distinct from those of Rac1.