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General sites | Specific 2D gel databases | Special Interest Groups
2D GEL DATABASES WORLD-WIDE |
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| An overview at this Web site with hypertext links to the Web about on-line collaboration in 2D Gel electrophoresis: bridging the gap between genomes and gene products | ||
GENERAL INFORMATION & LISTS |
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| Index of Federated 2D gel databases on University of Geneva ExpaSy Server | ||
| Catalog of 2D gel images (meta database contains information about other databases) found in Wb databases at NCIFCRF, USA. The 2DWG database is a organized as a spreadsheet table with each gel image represented by a row. Data for each gel includes tissue, species, cell-line, image URL, database URL, gel protocol, organization URL, image properties, map URL if it exists. | ||
| Compilation of 2D Databases: Links at Harefield Hospital Web Site | ||
| This document contains lists of items of interest to the 2D electrophetic protein gel research community including a list of 2D protein gel databases or related sites. It also contains Mailing and E-mail list for researchers attending the 1994 Siena conference "2D Electrophoresis: from protein maps to genomes" to facilitate collaboration. (at NCIFCRF) | ||
| Image analysis of 2D protein gels using QUEST II, Links to 2D gel protein databases searchable via gel images, Information on other 2D gel protein databases, Other databases and useful offerings at major WWW servers, Electrophoresis tank for 2nd dimension of 2D PAGE, Protein structure, Molecular biology Software. | ||
| 2D Gel images on the ExPASy server (Geneva, Switzerland) | ||
| Databases at University of Chicago (USA) | ||
| Cold Spring Harbor Laboratory on Long Island. A facility for the construction and analysis of Protein Databases. Data is generated by 2D PAGE electrophoresis. It's located at the Cold Spring Harbor Laboratory on Long Island, New York. Their goal is the construction of protein databases for scientific investigations. Quest offers software from its site for use with the World Wide Web (for example for generating "clickable" image maps of gels for on-line interrogation of individual spots). | ||
| Databases and other tools at the Large Scale Biology (LSB) company (USA). Includes Rabbit Psoas muscle, Rat and Mouse liver, Human liver and plasma, Corn and Wheat | ||
| The Proteome Company. Library access to YPD™ -- The Yeast Proteome Handbook provides the researcher with convenient access to the complete proteome of Saccharomyces cerevisiae. Scientists need access to YPD™ in their academic and corporate libraries. | ||
| Open access WWW database engine at NCIFCRF, USA) | ||
| Comparing images across the Internet (at NCIFCRF, USA) | ||
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Proteomics & Improving the resolution of electrophoresis in protein separation At present, electrophoresis is the choice method to analyze complex protein mixtures. However, still we cannot analyze total protein species in a cell, since the number should be above several thousands. Then, we are working on the improvement of two-dimensional gel electrophoresis and capillary electrophoresis, which exert the best resolution for protein/DNA analysis within electrophoretic techniques. In the field of two-dimensional gel electrophoresis (2-D PAGE), we developed a technique of micro 2-D PAGE in native conditions. This technique was applied for the analysis of human serum/plasma proteins and animal serum/plasma proteins. Also, we developed a technique of micro 2-D PAGE in denaturing conditions and applied this for the analysis of polypeptides in human leukemic cell HL-60. @In the field of capillary electrophoresis, we have established the conditions for high-resolution capillary electrophoresis of native proteins . These conditions have been successfully applied for the analysis of human plasma/serum proteins. Further, we also established capillary electrophoretic conditions for separating DNA sequencing fragments and for separating SDS-protein complexes . | |
SPECIFIC DATABASES |
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| The Danish Centre for Human Genome Research's 2-D PAGE Databases at the University of Aarhus contain data on proteins identified on various reference maps. You can display protein names and information on specific protein spots by clicking on the image in which you are interested. Also, you can search by protein name, keywords, Mr and pI or organelle or cellular component. Protein files contain extensive links to other databases or Web sites. The databases are being constructed for the study of global cell regulation, skin biology and bladder cancer. Procedures are illustrated with still images and videos. Paginated list output. Clickable image of human fibroblast proteins run in immobilized pH gradients. (Modified after Bjellqvist, B., Basse, B., Olsen, E. and Celis, J. E. Electrophoresis, 15, 529-539, 1994. All gels in the gallery will be labeled with Mr and pI. January 14, 1997 Major software upgrade applying to all databases (show images in basic-acidic and acidic-basic orientation; search by Mr and pI; list all proteins; display Mr and pI grid). | ||
| 2D heart muscle database at the German Heart Institute, University of Berlin, Germany | ||
| 2D Heart protein databases at the Heart
Science Centre, Harefield Hospital , UK are maintained by the Protein Biochemistry Group. You can peruse individual Harefield 2D-gel protein databases, search all Harefield 2D-gel protein databases, or browse other 2D-gel protein databases available on the Web. You can retrieve spots from individual databases. This includes facilities to select spots from the gel image, perform sophisticated searches and obtained sorted spot listings. The following databases are available: Human Heart (Ventricle) (last updated 7 Jan 97) Human endothelial cell (EA.hy 926) (last updated 7 Jan 97) Rat Heart (Ventricle) (last updated 7 Jan 97) Dog heart (ventricle) (last updated 7 Jan 97) This server and its associated data and services are for research purposes only, not for clinical or commercial use. It is a non-profit service to the scientific community. |
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| NIMH-NCI Protein Disease Database, USA (This is an ftp server site) | ||
| Joint Protein Structure Laboratory, University of Melbourne / Ludwig Institute for Cancer Research, Melbourne, Australia A database of bladder squamous cell carcinomas (IEF) has been included. To illustrate the power of 2D gel electrophoresis to analyze knock-outs we have included IEF 2D gels of [35S]-methionine labeled externalized proteins from primary kidney cells (overnight culturing) of ß2-microglobulin knockout and normal mice. Additional names have been added in several of the databases. Additional protein sequences have been entered in the keratinocyte IEF and NEPHGE databases. | ||
| E.coli Gene-Protein Database Project (NCBI-NLM, USA) | ||
| Lundberg Lab, Göteborg University, Sweden. This is a 2D-PAGE protein database containing information about 2D-PAGE resolved proteins from a number of species of yeast, however, the main focus will be on Saccharomyces cerevisiae. The database will display information about the identity and expression profile of resolved proteins. | ||
| Databases at the Proteome company, USA | ||
| At L' Institut de Biochimie et Génétique Cellulaires, Bordeaux, France | ||
| Bacillus subtilis database at University of Greifswald | ||
| Mitochondrial proteins (LMMB-NCIFCRF, USA). This database is dedicated to the nuclear genes specifying the enzymes, structural proteins, and other proteins, many still not identified, involved in mitochondrial biogenesis and function. MitoDat highlights predominantly human nuclear-encoded mitochondrial proteins, although we are including proteins from other animals in addition to those currently known only from yeast and other fungal mitochondria, as well as from plant mitochondria. The database consolidates information from various biological databases, eg., GenBank, SwissPro, Genome Data Base (GDB), Online Mendelian Inheritance in Man (OMIM), et al. Because the mitochondrion has a central role in cellular metabolism, it is involved in many human diseases. This database should help us in studying these diseases. It is also hyperlinked to the report of the committee on human mitochondrial DNA, maintained by the Wallace group at Emory http://infinity.gen.emory.edu/mitomap.html. It can be accessed here and also from the results when searching mitoDat for mitochondrially encoded genes. The Report of the committee on human mitochondrial DNA is currently the most comprehensive source of information on mitochondrial DNA mutations, other defects, and disorders in which the mitochondrial DNA deficiencies have been associated. | ||
| Immunobiology Department, University of Edinburgh, UK Molecular control of hematopoietic commitment, differentiation and self renewal. One approach is use transgenesis to perturb/redirect/enhance hematopoietic commitment. However, although studies using retroviral transgenesis of cell lines and isolated hematopoietic stem cells (HSC) have begun to shed light on the molecular control of differentiation of HSC into more committed progeny, the transformed nature of cell lines, and the difficulties of retroviral infection of slowly cycling stem cell populations have limited their usefulness. Commitment to the hematopoietic lineage could be studied by transgenesis and gene knock out in whole animals, but transgenesis that affects hematopoiesis often has pleiotropic effects, not the least of which is common embryo lethality. An alternate approach to the study of commitment and differentiation which would allow facile transgenesis, use primary tissue and allow reproducible and quantifiable commitment of mesoderm to the hematopoietic lineage is indicated. In vitro differentiation of embryonal stem (ES) cells satisfies these criteria. | ||
| Database at University of
Southern California, San Francisco. This server presents information on proteins
identified following isolation by two dimensional polyacrylamide gel electrophoresis (2D
PAGE). The proteins have been rapidly identified through extensive use of the mass
spectrometry based peptide sequencing power of the UCSF Mass Spectrometry Facility,
directed by Professor Alma L. Burlingame in the Department of Pharmaceutical Chemistry at
the University of California San Francisco (UCSF). Collaboration with Dr. Lois B. Epstein's Tumor Immunolgy and Interferon Research Laboratory in the Cancer Research Institute and the Department of Pediatrics at UCSF has led to identification of proteins present in malignant human cell lines. Of particular interest are proteins which are either induced or suppressed by Interferon-gamma and/or Tumor Necrosis Factor as the identified proteins may mediate the anti-tumor or immunomodulatory functions of the two cytokines. |
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| A rat neuronal gel database | ||
| The data base is at INRA, France | ||
| At the Karolinska Institute, Stockholm | ||
| Phosphoprotein database at NCIFCRF, USA | ||
| Clickable 2-D Gel Protein Map TIG-3, a normal human diploid fibroblast line established in our institute, is used as a model of cellular aging in this database. The cell line shows the finite life span around 70-80 population doubling levels (PDL). Cellular proteins were separated by two-dimensional gel electrophoresis in combination of immobilized pH-gradient isoelectric focusing and vertical gel slab SDS-PAGE. The clickable 2-D gel protein map was prepared by silver staining | ||
| Proteins and ageing: at the Tokyo Metropolitan Gerontology Institute | ||
| Cyano2Dbase | Cyanobacteria Proteome - at Kazusa, Japan | |
| Aberdeen | University of Aberdeen, Scotland: H. influenzae and N. meningitidis databases | |
SPECIAL INTEREST GROUPS |
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British Electrophoresis
Society The British Electrophoresis Society is a registered charity and aims to advance the science of electrophoresis |
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| American Electrophoresis society There are some updates here (1997) |
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| The French Electrophoresis Society (of ICES) | ||
| The Swiss Electrophoresis Society | ||
| The Japanese Electrophoresis Society | ||
