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  • 1
    Electronic Resource
    Electronic Resource
    Protein Indexing in Leukemias and Lymphomas (1984)
    Oxford, UK : Blackwell Publishing Ltd
    Annals of the New York Academy of Sciences 428 (1984), S. 0 
    Details
    ISSN: 1749-6632
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Natural Sciences in General
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1749-6632.1984.tb12293.x
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  • 2
    Electronic Resource
    Electronic Resource
    Human leukemias: A preliminary 2-D electrophoretic analysisPresented at the Second International Argonne-Mayo Symposium on Technical Advances in Two-dimensional Electrophoresis and Clinical Applications, Argonne National Laboratory, Argonne, IL 60439, USA, August 29 to September 1, 1982. (1982)
    Weinheim : Wiley-Blackwell
    Electrophoresis 3 (1982), S. 364-375 
    Details
    ISSN: 0173-0835
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: We have investigated the qualitative and quantitative differences in the two-dimensional (2-D) gel fluorographic patterns of biosynthetically pulse-labeled cellular proteins from the malignant cells of patients with various leukemias (acute myelogenous, acute lymphoblastic, chronic lymphocytic, and hairy cell). Significant similarities and differences between the major types of leukemias were found. An initial small data base was constructed using our GELLAB computer analysis system for 2-D gels in order to define methods for data base definition, normalization, and visual verification of results. Search strategies to find significant spot differences, both qualitative and quantitative, between currently accepted classes of leukemias were explored. Potential methods of expressing in a summary statistic the overall similarities and differences between gels were also investigated. A series of proteins whose relative synthetic rates may serve as potential markers of states of differentiation in human leukemias were identified in this initial data base and are reported here.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/elps.1150030612
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    Paper (German National Licenses)
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  • 3
    Electronic Resource
    Electronic Resource
    Database and search techniques for two-dimensional gel protein data: A comparison of paradigms for exploratory data analysis and prospects for biological modeling (1989)
    Weinheim : Wiley-Blackwell
    Electrophoresis 10 (1989), S. 122-140 
    Details
    ISSN: 0173-0835
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Two-dimensional (2-D) polyacrylamide gel electrophoresis can detect thousands of polypeptides, separating them by apparent molecular weight (Mr) and isoelectric point (pI). Thus it provides a more realistic and global view of cellular genetic expression than any other technique. This technique has been useful for finding sets of key proteins of biological significance. However, a typical experiment with more than a few gels often results in an unwieldy data management problem. In this paper, the GELLAB-II system is discussed with respect to how data reduction and exploratory data analysis can be aided by computer data management and statistical search techniques. By encoding the gel patterns in a “three-dimensional” (3-D) database, an exploratory data analysis can be carried out in an environment that might be called a “spread sheet for 2-D gel protein data”. From such databases, complex parametric network models of protein expression during events such as differentiation might be constructed. For this, 2-D gel databases must be able to include data from other domains external to the gel itself. Because of the increasing complexity of such databases, new tools are required to help manage this complexity. Two such tools, object-oriented databases and expert-system rule-based analysis, are discussed in this context. Comparisons are made between GELLAB and other 2-D gel databases analysis systems to illustrate some of the analysis paradigms common to these systems and where this technology may be heading.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/elps.1150100207
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  • 4
    Electronic Resource
    Electronic Resource
    A fast spot segmentation algorithm for two-dimensional gel electrophoresis analysis (1993)
    Weinheim : Wiley-Blackwell
    Electrophoresis 14 (1993), S. 1351-1356 
    Details
    ISSN: 0173-0835
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: An important issue in the automation of two-dimensional gel electrophoresis image analysis is the detection and quantification of protein spots. A spot segmentation algorithm must detect, define the extent of, and measure the integrated density of spots under a wide variety of actual gel image conditions. Besides these functions, the algorithm must be memory efficient to be able to process very large gel images and do this in a reasonable amount of computation time on low-cost computers, such as workstations and personal computers. We have developed a fast spot segmentation algorithm, extending the GELLAB-II segmenter, which extracts spots in a single raster scanning pass through the gel image. The performance analysis of the algorithm will be given in the paper as well as a discussion of the algorithm.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/elps.11501401208
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  • 5
    Electronic Resource
    Electronic Resource
    2-D Electrophoresis gel data base analysis: Aspects of data structures and search strategies in GELLABPresented at the Second International Argonne-Mayo Symposium on Technical Advances in Two-dimensional Electrophoresis and Clinical Applications, Argonne National Laboratory, Argonne, IL 60439, USA, August 29 - September 1, 1982 (1983)
    Weinheim : Wiley-Blackwell
    Electrophoresis 4 (1983), S. 71-81 
    Details
    ISSN: 0173-0835
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Search strategies for finding spot differences among multiple two-dimensional (2-D) polyacrylamide electrophoresis gels are discussed in the context of the GELLAB spot data base management system. A 2-D gel experiment should have a well-defined biological experimental and preparation protocol reflecting the hypotheses of the problem. So too should the analysis of its corresponding 2-D gel computer spot data base have a protocol. This protocol is heavily influenced by the nature of the biological experiment as well as 2-D gel preparation considerations including the realities of artifactual and systematic noise. It is further influenced by constraints due to computational considerations. The search strategy is that part of the analysis protocol in which an experimenter iteratively defines tests to find significant spot differences. One goal of designing a well thought out search protocol is to reduce the number of search iterations required. Aspects of some requirements and constraints for useful search strategies are discussed.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/elps.1150040110
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  • 6
    Electronic Resource
    Electronic Resource
    High resolution comparison of Plasmodium knowlesi clones of different variant antigen phenotypes by two-dimensional gel electrophoresis and computer analysis (1983)
    Weinheim : Wiley-Blackwell
    Electrophoresis 4 (1983), S. 420-427 
    Details
    ISSN: 0173-0835
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Antigenic variation of the schizont-infected cell agglutination-antigen on erythrocytes infected by Plasmodium knowlesi is due to the expression of different malarial proteins. Here we examined whether antigenic variation is accompanied by multiple phenotypic changes in the proteins synthesized by P. knowlesi. The malarial proteins of two clones, one of which was produced by antigenic variation from the other clone in vivo, were labeled by [3H]isoleucine uptake during in vitro parasite growth. The proteins were separated by two-dimensional gel electrophoresis, detected by fluorography and compared using the GELLAB computer system. In the molecular weight range 35 000 to 230 000 and pH range 4.55 to 6.10, we found only four qualitative differences and two robust quantitative differences among approximately 500 proteins characterizing the protein phenotype of these clones. One clone exhibited four minor protein spots absent from the other. We conclude that antigenic variation in P. knowlesi represents the differential expression of a very small number of malarial genes.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/elps.1150040610
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    Paper (German National Licenses)
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  • 7
    Electronic Resource
    Electronic Resource
    The protein disease database (1995)
    Weinheim : Wiley-Blackwell
    Electrophoresis 16 (1995), S. 1175-1175 
    Details
    ISSN: 0173-0835
    Keywords: Protein disease dazabase ; World-Wide Web ; Database ; Internet ; Body fluids ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/elps.11501601194
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  • 8
    Electronic Resource
    Electronic Resource
    A World Wide Web (WWW) server database engine for an organelle database, MitoDat (1996)
    Weinheim : Wiley-Blackwell
    Electrophoresis 17 (1996), S. 566-572 
    Details
    ISSN: 0173-0835
    Keywords: Mitochrondrial proteins ; World Wide Web Internet ; Two-dimensional polyacrylamide gel wis ; Databases ; Chromosome idiograms ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: We describe a simple database search engine “dbEngine” which may be used to quickly create a searchable database on a World Wide Web (WWW) server. Data may be prepared from spreadsheet programs (such as Excel, etc.) or from tables exported from relational database systems. This Common Gateway Interface (CGI-BIN) program is used with a WWW server such as available commercially, or from National Center for Supercomputer Algorithms (NCSA) or CERN. Its capabilities include: (i) searching records by combinations of terms connected with ANDs or ORs; (ii) returning search results as hypertext links to other WWW database servers; (iii) mapping lists of literature reference identifiers to the full references; (iv) creating bidirectional hypertext links between pictures and the database. DbEngine has been used to support the MitoDat database (Mendelian and non-Mendelian inheritance associated with the Mitochondrion) on the WWW.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/elps.1150170327
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  • 9
    Electronic Resource
    Electronic Resource
    The 2DWG meta-database of two-dimensional electrophoretic gel images on the Internet (1997)
    Weinheim : Wiley-Blackwell
    Electrophoresis 18 (1997), S. 2759-2773 
    Details
    ISSN: 0173-0835
    Keywords: World Wide Web ; Internet ; Two-dimensional polyacrylamide gel electrophoresis ; Databases ; Meta-database ; Proteins ; Genetics ; Image analysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: The 2DWG meta-database is a searchable database of two-dimensional (2-D) electrophoretic gel images found on the Internet. A meta-database contains information about locating data in other databases - but not that data itself. This database was constructed because of a need for an enriched set of World Wide Web (WWW) locations (URLs) of 2-D gel images on the Internet. These gel images are used in conjunction with the National Cancer Institute (NCI) Flicker Server to manipulate and visually compare 2-D gel images across the Internet. User's gels may also be compared with those in the database. The 2DWG is organized as a spreadsheet table with each gel image being represented by a row sorted by tissue type. Data for each gel includes tissue type, species, cell-line, image URL, database URL, gel protocol, organization URL, image properties, map URL if it exists, etc. The 2DWG may be searched to find relevant subsets of gels. Searching is done using the dbEngine - a WWW database search engine which accesses selected rows of gels from the full 2DWG table. The 2DWG meta-database is accessible on the WWW at http://www-lecb.ncifcrf.gov/2dwgDB/ and the NCI Flicker server at http://www-lecb.ncifcrf.gov/flicker/.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/elps.1150181510
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  • 10
    Electronic Resource
    Electronic Resource
    Comparing two-dimensional electrophoretic gel images across the Internet (1997)
    Weinheim : Wiley-Blackwell
    Electrophoresis 18 (1997), S. 461-470 
    Details
    ISSN: 0173-0835
    Keywords: Image comparison ; World Wide Web ; Java ; Internet ; Two-dimensional polyacrylamide electrophoresis ; Databases ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Scientists around the world often work on similar data so the need to share results and compare data arises periodically. We describe a method of comparing two two-dimensional (2-D) protein gels of similar samples created in different laboratories to help identify or suggest protein spot identification. Now that 2-D gels and associated databases frequently appear on the Internet, this opens up the possibility of visually comparing one's own experimental 2-D gel image data with data from another gel in a remote Internet database. In general, there are a few ways to compare images: (i) slide one gel (autoradiograph or stained gel) over the other while back-illuminated, or (ii) build at 2-D gel computer database from both gels after scanning and analyzing these gels. These are impractical since in the first case the gel from the Internet database is not locally available. In the second, the costs of building a multi-gel database solely to answer the question of whether a spot is the same spot may be excessive if only a single visual comparison is needed. We describe a distributed gel comparison program (URL: www-lmmb.ncifcrf.gov/flicker) which runs on any World Wide Web (WWW) connected computer and is invoked from a Java-capable web browser. One gel image is read from any Internet 2-D gel database (e.g. SWISS-2DPAGE) and the other may reside on the investigator's computer. Images may be more easily compared by first applying spatial warping or other transforms interactively on the user's computer. First, regions of interest are “landmarked” with several corresponding points in each gel image, then one gel image is warped to the geometry of the other. As the two gels are rapidly alternated, or flickered, in the same window, the user can slide one gel past the other to visually align corresponding spots by matching local morphology. This flicker-comparison technique may be applied to analyzing other types of one-dimensional and 2-D biomedical images.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/elps.1150180321
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