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General sites | Specific 2D gel databases | Special Interest Groups

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2D GEL DATABASES WORLD-WIDE

OVERVIEW

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

WORLD-2DPAGE

Index of Federated 2D gel databases on University of Geneva ExpaSy Server

2DW Image Meta-Database

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.

Harefield list

Compilation of 2D Databases: Links at Harefield Hospital Web Site

Two-Dimensional Gel Electrophoresis Databases

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)

Cambridge 2DPAGE

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.

SWISS-2DPAGE

2D Gel images on the ExPASy server (Geneva, Switzerland)

Argonne protein mapping group

Databases at University of Chicago (USA)

QUEST Protein Database Center

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).

Large Scale Biology

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

Proteome

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.

dbEngine

Open access WWW database engine at NCIFCRF, USA)

FLICKER

Comparing images across the Internet (at NCIFCRF, USA)

Laboratory of Analytical Biochemistry Ehime University, Japan

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

Human protein 2D gels at Biobase

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).

German Heart- 2DPAGE

2D heart muscle database at the German Heart Institute, University of Berlin, Germany

Harefield Heart 2D-PAGE

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.

PDD

NIMH-NCI Protein Disease Database, USA (This is an ftp server site)

Human Colon Carcinoma 2D PAGE

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.

ECO2DBASE

E.coli Gene-Protein Database Project (NCBI-NLM, USA)

YEAST 2D-PAGE

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.

Yeast Protein Database (YPD)

Databases at the Proteome company, USA

Yeast Protein Map (YPM)

At L' Institut de Biochimie et Génétique Cellulaires, Bordeaux, France

Sub2D

Bacillus subtilis database at University of Greifswald

MitoDat

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.

Embryonal Stem Cells (ES)

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.

UCSF 2DPAGE (A375 cell line)

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.

Cambridge NEURON 2D PAGE

A rat neuronal gel database

Maize Genome Database

The data base is at INRA, France

Drosophila

At the Karolinska Institute, Stockholm

PPDB

Phosphoprotein database at NCIFCRF, USA

TIG-3

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

TMIG

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

BES

 

British Electrophoresis Society
The British Electrophoresis Society is a registered charity and aims to advance the science of electrophoresis

AES

American Electrophoresis society
There are some updates here (1997)

ICES

The French Electrophoresis Society (of ICES)

CHEL

The Swiss Electrophoresis Society

JES

The Japanese Electrophoresis Society

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