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PubMed1992

Workshop on two-dimensional gel protein databases.

A workshop on two-dimensional gel electrophoresis (2-DE) protein database, organized by the Committee on Data for Science and Technology (CODATA) of the International Council of Scientific Unions Task Group on Biological Macromolecules, was held at the CODATA Secretariat in Paris on March 9, 1992. Eleven scientists from eight different countries represented various aspects of 2-DE analysis--namely, cellular protein database development and protein microsequencing methodologies. The purpose of the workshop was to explore means of integrating the rapidly expanding body of information on 2-DE resolved proteins from different laboratories. A major proposal emanating from the workshop was the establishment of an intermediary or "relational" 2-DE gel protein database. This intermediary database, which would catalogue pertinent information on 2-DE resolved proteins (experimental source, 2-DE loci, biological information, etc.) could be an adjunct to, and accessed through, the existing international protein sequence databanks. It would function as a pointer for researchers to the individual 2-DE protein databases where primary and more specialized 2-DE data would be housed.

Databases, Factual↗
PubMed1994

The human keratinocyte two-dimensional protein database (update 1994): towards an integrated approach to the study of cell proliferation, differentiation and skin diseases.

The master two-dimensional (2-D) gel database of human keratinocytes currently lists 3087 cellular proteins (2168 isoelectric focusing, IEF; and 919 none-quilibrium pH gradient electrophoresis, NEPHGE), many of which correspond to posttranslational modifications, 890 polypeptides have been identified (protein name, organelle components, etc.) using one or a combination of procedures that include (i) comigration with known human proteins, (ii) 2-D gel immunoblotting using specific antibodies (iii) microsequencing of Coomassie Brilliant Blue stained proteins, (iv) mass spectrometry and (v) vaccinia virus expression of full length cDNAs. These are listed both in alphabetical order and with increasing SSP number, together with their M(r), pI, cellular localization and credit to the investigator(s) that aided in the identification. Furthermore, we list 239 microsequenced proteins recorded in the database. We also report a database of proteins recovered from the medium of noncultured, unfractionated keratinocytes. This database lists 398 polypeptides (309 IEF; 89 NEPHGE) of which 76 have been identified. The aim of the comprehensive databases is to gather, through a systematic study of keratinocytes, qualitative and quantitative information on proteins and their genes that may allow us to identify abnormal patterns of gene expression and, ultimately, to pinpoint signaling pathways and components affected in various skin diseases, cancer included.

Amino Acid Sequence↗
PubMed1996

High-performance human myocardial two-dimensional electrophoresis database: edition 1996.

The master gel of the human myocardial two-dimensional electrophoresis (2-DE) gel database contains about 3300 protein spots characterized in terms of isoelectric point (pI) and molecular mass. A high-performance technique was applied, using large gels (23 x 30 cm). Isoelectric focusing with anodic sample preparation and nonequilibrium running conditions (NEPHGE) was combined with sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) in 15% acrylamide gels in the second dimension. The range of pI extends from pH 4.5 to 9.6. Seventy proteins were identified by combinations of amino acid analysis, N-terminal and internal sequencing, immunostaining, matrix assisted laser desorption/ionization-mass spectrometry (MALDI-MS) peptide mass fingerprinting, post-source decay MALDI-MS and ladder sequencing by carboxypeptidase P. The identification of additional proteins, not found in the master gel, was achieved by immunoblotting. Unequivocal identification with high sensitivity and good yield was obtained by combining internal sequencing and MALDI-MS. In-gel digestion, the concentration and purification of peptides in a peptide collecting device, and the improved FRAGMOD program for peptide mass fingerprinting have added to the security and sensitivity of identification. The high-performance human myocardial 2-DE database was built up with proteins detected by the TOPSPOT program. Spots within six sections of the whole pattern are clickable. Protein description includes detailed information about identification, characterization, and links to the related SWISS-PROT, other 2-DE databases and Medline entries. The database is constructed in accordance with four of the rules for a federated database.

Computer Communication Networks↗
PubMedDate not supplied

Towards design and comparison of World Wide Web-accessible myocardial two-dimensional gel electrophoresis protein databases.

In addition to the recently published HEART-2DPAGE--a myocardial World Wide Web-accessible 2-DE gel protein database--the usage and installation of software tools are described with regard to the hard- and software environments. Further, access to the HEART-2DPAGE from other two-dimensional electrophoresis (2-DE) databases using name or accession code of a protein is now available. Moreover, database images, published in the myocardial HSC-2DPAGE and HEART-2DPAGE databases are compared. Using the warping tool of the common image processing system Khoros the database images are matched and added in order to visualize the effects of warping. The application of such image processing tools is aimed at improving the comparability of protein spot patterns of different gel images available through the net.

Computer Communication Networks↗
PubMed1997

Dilated cardiomyopathy-associated proteins and their presentation in a WWW-accessible two-dimensional gel protein database.

High resolution two-dimensional electrophoresis (2-DE) and computer-assisted image analysis were used to screen 13 patients suffering from dilated cardiomyopathy (DCM) versus 15 control patients for quantitative and qualitative differences in their myocardial protein expression. Right atrial tissue samples were obtained from end-stage failing explanted hearts and control hearts. Fifty-two spots differed significantly in average intensity between the DCM and the control groups. Myosin light chain 2, ventricular (MLC2) and heat shock protein HSP 27 were identified by protein microsequencing and gel map comparison with other databases. These proteins were found to be characteristic protein markers for DCM in the right atrium. In DCM patients, the spot intensity (protein abundance) of MLC2 is increased to 336% and HSP 27 is decreased to 59%, compared to the control group. The HEART-2DPAGE, a World Wide Web-accessible 2-DE database, was used and extended for the presentation of these disease-associated proteins. Retrievable via Internet we present a list of disease-associated proteins, their altered level of expression in DCM, and their position on a right atrial protein pattern. The accession number to protein sequence databases confers a connection to databases like SWISS-PROT to obtain a detailed functional and structural description of disease-associated proteins. New DCM-associated proteins are detected and their presentation in a 2-DE gel protein database is described.

Cardiomyopathy, Dilated↗
PubMed1998

Database searching using mass spectrometry data.

Large-scale DNA sequencing is creating a sequence infrastructure of great benefit to protein biochemistry. Concurrent with the application of large-scale DNA sequencing to whole genome analysis, mass spectrometry has attained the capability to rapidly, and with remarkable sensitivity, determine weights and amino acid sequences of peptides. Computer algorithms have been developed to use the two different types of data generated by mass spectrometers to search sequence databases. When a protein is digested with a site-specific protease, the molecular weights of the resulting collection of peptides, the mass map or fingerprint, can be determined using mass spectrometry. The molecular weights of the set of peptides derived from the digestion of a protein can then be used to identify the protein. Several different approaches have been developed. Protein identification using peptide mass mapping is an effective technique when studying organisms with completed genomes. A second method is based on the use of data created by tandem mass spectrometers. Tandem mass spectra contain highly specific information in the fragmentation pattern as well as sequence information. This information has been used to search databases of translated protein sequences as well as nucleotide databases such as expressed sequence tag (EST) sequences. The ability to search nucleotide databases is an advantage when analyzing data obtained from organisms whose genomes are not yet completed, but a large amount of expressed gene sequence is available (e.g., human and mouse). Furthermore, a strength of using tandem mass spectra to search databases is the ability to identify proteins present in fairly complex mixtures.

Animals↗
PubMed2002

Data mining of public SNP databases for the selection of intragenic SNPs.

Different strategies to search public single nucleotide polymorphism (SNP) databases for intragenic SNPs were evaluated. First, we assembled a strategy to annotate SNPs onto candidate genes based on a BLAST search of public SNP databases (Intragenic SNP Annotation by BLAST, ISAB). Only BLAST hits that complied with stringent criteria according to 1) percentage identity (minimum 98%), 2) BLAST hit length (the hit covers at least 98% of the length of the SNP entry in the database, or the hit is longer than 250 base pairs), and 3) location in non-repetitive DNA, were considered as valid SNPs. We assessed the intragenic context and redundancy of these SNPs, and demonstrated that the SNP content of the dbSNP and HGBASE/HGVbase databases are highly complementary but also overlap significantly. Second, we assessed the validity of intragenic SNP annotation available on the dbSNP and HGVbase websites by comparison with the results of the ISAB strategy. Only a minority of all annotated SNPs was found in common between the respective public SNP database websites and the ISAB annotation strategy. A detailed analysis was performed aiming to explain this discrepancy. As a conclusion, we recommend the application of an independent strategy (such as ISAB) to annotate intragenic SNPs, complementary to the annotation provided at the dbSNP and HGVbase websites. Such an approach might be useful in the selection process of intragenic SNPs for genotyping in genetic studies. Hum Mutat 20:162-173, 2002.

DNA↗
PubMed2002

The human SHOX mutation database.

The human SHOX database has recently been established to provide clinicians and scientists access to a central source of information about all known SHOX mutations associated with short stature phenotypes such as idiopathic short stature, Lèri-Weill dyschondrosteosis, Langer syndrome, and Turner syndrome. So far, the database contains 29 unique intragenic mutations of the SHOX gene. These mutations were detected in a total of 39 patients from different families. Fourteen of these mutations have been found from the SHOX research group at the Institute of Human Genetics in Heidelberg, Germany; 25 mutations are from data reported in the literature. Not included in this database are complete SHOX gene deletions which represent the majority of all detectable SHOX mutations [Rappold et al., 2002]. The database is accessible via the website www.shox.uni-hd.de. It contains general information about the SHOX gene, and allows remote users to search the data and to submit new mutations to the database.

Base Sequence↗
PubMed2003

eMelanoBase: an online locus-specific variant database for familial melanoma.

A proportion of melanoma-prone individuals in both familial and non-familial contexts has been shown to carry inactivating mutations in either CDKN2A or, rarely, CDK4. CDKN2A is a complex locus that encodes two unrelated proteins from alternately spliced transcripts that are read in different frames. The alpha transcript (exons 1alpha, 2, and 3) produces the p16INK4A cyclin-dependent kinase inhibitor, while the beta transcript (exons 1beta and 2) is translated as p14ARF, a stabilizing factor of p53 levels through binding to MDM2. Mutations in exon 2 can impair both polypeptides and insertions and deletions in exons 1alpha, 1beta, and 2, which can theoretically generate p16INK4A-p14ARF fusion proteins. No online database currently takes into account all the consequences of these genotypes, a situation compounded by some problematic previous annotations of CDKN2A-related sequences and descriptions of their mutations. As an initiative of the international Melanoma Genetics Consortium, we have therefore established a database of germline variants observed in all loci implicated in familial melanoma susceptibility. Such a comprehensive, publicly accessible database is an essential foundation for research on melanoma susceptibility and its clinical application. Our database serves two types of data as defined by HUGO. The core dataset includes the nucleotide variants on the genomic and transcript levels, amino acid variants, and citation. The ancillary dataset includes keyword description of events at the transcription and translation levels and epidemiological data. The application that handles users' queries was designed in the model-view-controller architecture and was implemented in Java. The object-relational database schema was deduced using functional dependency analysis. We hereby present our first functional prototype of eMelanoBase. The service is accessible via the URL www.wmi.usyd.edu.au:8080/melanoma.html.

Computer Security↗
PubMed2003

The UMD-p53 database: new mutations and analysis tools.

The tumor suppressor gene TP53 (p53) is the most extensively studied gene involved in human cancers. More than 1,400 publications have reported mutations of this gene in 150 cancer types for a total of 14,971 mutations. To exploit this huge bulk of data, specific analytic tools were highly warranted. We therefore developed a locus-specific database software called UMD-p53. This database compiles all somatic and germline mutations as well as polymorphisms of the TP53 gene which have been reported in the published literature since 1989, or unpublished data submitted to the database curators. The database is available at www.umd.necker.fr or at http://p53.curie.fr/. In this paper, we describe recent developments of the UMD-p53 database. These developments include new fields and routines. For example, the analysis of putative acceptor or donor splice sites is now automated and gives new insight for the causal role of "silent mutations." Other routines have also been created such as the prescreening module, the UV module, and the cancer distribution module. These new improvements will help users not only for molecular epidemiology and pharmacogenetic studies but also for patient-based studies. To achieve theses purposes we have designed a procedure to check and validate data in order to reach the highest quality data.

Databases, Genetic↗
PubMed2001

Go!Poly: A gene-oriented polymorphism database.

Human genome polymorphisms play a key role in defining the molecular basis of phenotypic differences between individuals in aspects such as disease susceptibility and drug responses. The database requirements for supporting the study of human genetic variation have been well recognized. In order to meet these needs, several generalized databases have been built. However, it is still hard for users to find gene-related variation data from these huge and sophisticated databases. In its role as a gene-oriented directory of polymorphism data, Go!Poly (Gene Oriented Polymorphism Database; http://61.139.84.5/gopoly/) utilizes two new highly curated and non-redundant resources, LocusLink (http://www.ncbi.nlm.nih.gov/LocusLink/) and RefSeq (http://www.ncbi.nlm.nih.gov/LocusLink/refseq.html), as the standard for identifying and positioning nucleotide variations. As a generalized polymorphism database, Go!Poly extracts human gene-linked sequence variations of all common types (SNP, insertion-deletion, simple tandem repeat, and complex nucleotides variations) from various public resources including scientific journals and internet resources, such as HGBASE (http://hgbase.cgr.ki.se) and dbSNP (http://www.ncbi.nlm.nih.gov/SNP/). The polymorphism data are then categorized into different gene loci, and the reference sequences given by LocusLink are used as positioning references. Through close integration with LocusLink, Go!Poly also provides facilitated connections among sequence data, gene name, and related biological information. This feature also makes Go!Poly easy to search and navigate. Future automated annotations and internal consistency checking may also benefit from this. Extensive efforts are being taken to make the polymorphism information generated by the Chinese scientific community available from this resource.

China↗
PubMed2004

The CDKN2A database: Integrating allelic variants with evolution, structure, function, and disease association.

In this report, we introduce the CDKN2A Database, an online database of germline and somatic variants of the CDKN2A tumor suppressor gene recorded in human disease through the year 2002, annotated with evolutionary, structural, and functional information. The CDKN2A Database improves upon existing resources by: 1) including both somatic mutations and germline variants, thereby adding the perspective of somatic cell carcinogenesis to that of hereditary cancer predisposition; 2) including information that assists with the interpretation of allelic variants, such as other primary data (sequences, structures, alignments, functional measurements, and literature references) and annotations (extensive text, figures, and a tree-based phylogenetic classification); and 3) providing the information in a format that allows a user to either download the database or to easily manipulate it online. We describe the database structure, content, current uses, and potential implications (http://biodesktop.uvm.edu/perl/p16).

Alleles↗
PubMed2006

The UMD TP53 database and website: update and revisions.

Mutation of the p53 gene is the most frequent genetic alteration found in human cancer, but it is also the most frequently reported with more than 22,000 mutations published in 2,000 papers. In 1991, we developed a database and software to handle and analyze all this information. The database has been widely used for clinical analysis and molecular epidemiology. We have expanded the scope of the database by integrating structural, phylogenetic and biological information on wild-type (wt) and mutant TP53. Integration of the TP53 mutant activity database provides unique information that will be useful to both clinicians and scientists. All of this information is available from a new website (www.umd.be:2072/) that will generate a detailed informative page for every TP53 mutant in the database. New tools to check TP53 mutations and minimize errors found in the literature are also available.

DNA Mutational Analysis↗
PubMed2007

The interactive Factor H-atypical hemolytic uremic syndrome mutation database and website: update and integration of membrane cofactor protein and Factor I mutations with structural models.

Atypical hemolytic uremic syndrome (aHUS) is a disease of hemolytic anemia, thrombocytopenia, and renal failure associated with defective alternative pathway (AP) complement control. Previously, we presented a database (www.FH-HUS.org) focusing on aHUS mutations in the Factor H gene (CFH). Here, new aHUS mutations are reported for the complement regulatory proteins Factor H (FH), Factor I (FI), and membrane cofactor protein (MCP). Additional mutations or polymorphisms within CFH have been associated with membranoproliferative glomerulonephritis (MPGN) and age-related macular degeneration (AMD). Accordingly, the database now includes substitutions that predispose to aHUS, MPGN, and AMD. For this, structural models for the domains in MCP and FI were developed using homology modeling. With this new database, patients with mutations in more than one gene can be displayed and interpreted in a coherent manner. The database also includes SNP polymorphisms in CFH, MCP, and IF. There are now a total of 167 genetic alterations, including 100 in CFH, 43 in MCP, and 24 in IF. The mutations characterize clinical outcomes that vary from several AMD-associated polymorphisms to those associated with aHUS, MPGN, or FI deficiency. A consensus short complement regulator (SCR) domain structure facilitated the interpretations of aHUS mutations. Specific locations within this consensus domain often correlate with the occurrence of clinical phenotypes. The AMD Tyr402His polymorphism is structurally located at a hotspot for several aHUS mutations. The database emphasizes the causative role of the alternative pathway of complement in disease and provides a repository of knowledge to assist future diagnosis and novel therapeutic approaches.

Amino Acid Sequence↗
PubMed2007

HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update.

HbVar (http://globin.bx.psu.edu/hbvar) is a locus-specific database (LSDB) developed in 2001 by a multi-center academic effort to provide timely information on the genomic sequence changes leading to hemoglobin variants and all types of thalassemia and hemoglobinopathies. Database records include extensive phenotypic descriptions, biochemical and hematological effects, associated pathology, and ethnic occurrence, accompanied by mutation frequencies and references. In addition to the regular updates to entries, we report significant advances and updates, which can be useful not only for HbVar users but also for other LSDB development and curation in general. The query page provides more functionality but in a simpler, more user-friendly format and known single nucleotide polymorphisms in the human alpha- and beta-globin loci are provided automatically. Population-specific beta-thalassemia mutation frequencies for 31 population groups have been added and/or modified and the previously reported delta- and alpha-thalassemia mutation frequency data from 10 population groups have also been incorporated. In addition, an independent flat-file database, named XPRbase (http://www.goldenhelix.org/xprbase), has been developed and linked to the main HbVar web page to provide a succinct listing of 51 experimental protocols available for globin gene mutation screening. These updates significantly augment the database profile and quality of information provided, which should increase the already high impact of the HbVar database, while its combination with the UCSC powerful genome browser and the ITHANET web portal paves the way for drawing connections of clinical importance, that is from genome to function to phenotype.

DNA Mutational Analysis↗
PubMed2006

Association of Clinical Cytogeneticists chorion villus sampling database 1987-2000.

OBJECTIVES: To produce a fully searchable Microsoft Access database of mosaic and non-mosaic cytogenetic abnormalities, detected during diagnostic chorionic villi sampling (CVS) to aid laboratories in predicting pregnancy outcome, in particular differentiating between cases of likely genuine fetal cytogenetic abnormalities and those likely to represent confined placental mosaicism (CPM). METHODS: Retrospective collection of referral data, initial karyotype data, follow-up karyotype data and pregnancy outcome data from almost all cytogenetically abnormal diagnostic CVS, processed in UK National Health Service laboratories, between 1987 and 2000. Collection of similar data from a published series of CVS and individual case reports. RESULTS: A fully searchable database of abnormal CVS cases, containing over 5000 entries, has been produced. This is available to download at http://www.ncl.ac.uk/cvs/. CONCLUSIONS: Following detection of a cytogenetic abnormality during prenatal diagnosis using CVS, use of this database allows rapid access to comparable cases from the United Kingdom and the literature. This database will improve the speed of availability and quality of information available to clinicians and patients for pregnancy management and counselling purposes. The database has been designed with future data collection in mind, and can be developed for wider research use, through more detailed registries of individual chromosome abnormalities.

Chorionic Villi Sampling↗
PubMed2005

A pilot study to build a database on seven anti-hypertensive drugs.

PURPOSE: In Japan, all patients are able to see freely any clinics or hospitals. So clinical data of all patients have been stored at clinics, hospitals and medical institutes respectively. These patients' clinical course data stocks have not been combined with one another. There is no large-scale database, which has been available and has played its role in complementing spontaneous adverse drug reaction (ADR) reporting system. We tried to build an original database using anti-hypertensive drugs' data from Drug Use Investigation conducted for the Japanese Drug Re-examination application by every pharmaceutical manufacturer in conformity with Japanese Pharmaceutical Affairs Law and Related Regulation. METHODS: The 43 565 case data of seven anti-hypertensive drugs (one Ca-antagonist, one alpha-blocker, two beta-blockers, three ACE inhibitors) were kindly offered from seven manufacturers who were members of RAD-AR Council, Japan. After examining the data items and categories, they were standardized into common codes based on Japanese Drug Category Classification (JDCC), International Classification of Diseases 9 (ICD-9) and Japanese Adverse Drug Reaction Terminology (J-ART). As each manufacturer had a different coding method in accordance to manufacturer's own practice of data management, the original forms were divided into several datasets. The data processing and statistical analysis were conducted using Statistical Analysis System (SAS). RESULTS: (1) Technology and know-how to combine data coded by different methods were established for building a database that had never been tried in Japan. (2) The following are the by-products of the study: a) Onset of ADR concentrated in the early stage but onset of some disorders prevailed equally throughout the investigation period. b) Although the number of collected cases of anti-hypertensive drugs was 43 565, total number of administrated anti-hypertensive drugs reached to 70 714 because additional anti-hypertensive drugs were often used with subject drugs. CONCLUSION: There is no large-scale database of patients' clinical course in Japan. However, since the Japanese Drug Re-examination System started in 1979, almost eight million cases of Drug Use Investigation on about 700 drugs have been collected with enormous human power and huge expenditure for Japanese Drug Re-examination application by pharmaceutical manufacturers. New and more appropriate information will be detected by the database, built using Drug Use Investigation data that were collected only for the Japanese Drug Re-examination application.

Adverse Drug Reaction Reporting Systems↗
PubMed2001

Privacy considerations in the context of an Australian observational database.

Observational databases are increasingly acknowledged for their value in clinical investigation. Australian general practice in particular presents an exciting opportunity to examine treatment in a natural setting. The paper explores issues such as privacy and confidentiality--foremost considerations when conducting this form of pharmacoepidemiological research. Australian legislation is currently addressing these exact issues in order to establish clear directives regarding ethical concerns. The development of a pharmacoepidemiological database arising from the integration of computerized Australian general practice records is described in addition, to the challenges associated with creating a database which considers patient privacy. The database known as 'Medic-GP', presently contains more than 950,000 clinical notes (including consultations, pathology, diagnostic imaging and adverse reactions) over a 5-year time period and relates to 55,000 patients. The paper then details a retrospective study which utilized the database to examine the interaction between antibiotic prescribing and patient outcomes from a community perspective, following a policy intervention. This study illustrates the application of computerized general practice records in research.

Australia↗