The REF52 protein database. Methods of database construction and analysis using the QUEST system and characterizations of protein patterns from proliferating and quiescent REF52 cells
The construction and analysis of protein databases using the QUEST system is described, and the REF52 protein database is presented. A protein database provides the means to store and compare quantitative and descriptive data for up to 2000 proteins from many experiments that employ computer-analyze...
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| Veröffentlicht in: | The Journal of biological chemistry 1989-03, Vol.264 (9), p.5283-5298 |
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| creator | J I Garrels B R Franza, Jr |
| description | The construction and analysis of protein databases using the QUEST system is described, and the REF52 protein database is
presented. A protein database provides the means to store and compare quantitative and descriptive data for up to 2000 proteins
from many experiments that employ computer-analyzed two-dimensional gel electrophoresis. The QUEST system provides the tools
to manage, analyze, and communicate these data. The REF52 database contains experiments with normal and transformed rat cell
lines. In this report, many of the proteins on the REF52 map are identified by name, by subcellular localization, and by mode
of post-translational modification. The quantitative experiments analyzed and compared here include 1) a study of the quantitative
reproducibility of the analysis system, 2) a study of the clonal reproducibility of REF52 cells, 3) a study of growth-related
changes in REF52 cells, and 4) a study of the effects of labeling cells for varying lengths of time. Of the proteins analyzed
from REF52 cells, 10% are nuclear, 6% are phosphoproteins, and 4% are mannose-labeled glycoproteins. The mannose-labeled proteins
are more prominent in patterns from quiescent cells, while the synthesis of cytoskeletal proteins is generally repressed at
quiescence. A small set of proteins, selected for elevated rates of synthesis is generally repressed at quiescence. A small
set of proteins, selected for elevated rates of synthesis in quiescent versus proliferating cells includes one of the tropomyosin
isoforms, a myosin light chain isoform, and several prominent glycoproteins. These proteins are thought to be characteristic
of the differentiated state of untransformed REF52 cells. Proteins induced early versus late after refeeding quiescent cells
show very different patterns of growth regulation. These studies lay the foundations of the REF52 database and provide information
needed to interpret the experiments with transformed REF52 cells, which are reported in the accompanying paper (Garrels, J.,
and Franza, B. R., Jr. (1989) J. Biol. Chem. 264, 5299-5312). |
| format | Article |
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presented. A protein database provides the means to store and compare quantitative and descriptive data for up to 2000 proteins
from many experiments that employ computer-analyzed two-dimensional gel electrophoresis. The QUEST system provides the tools
to manage, analyze, and communicate these data. The REF52 database contains experiments with normal and transformed rat cell
lines. In this report, many of the proteins on the REF52 map are identified by name, by subcellular localization, and by mode
of post-translational modification. The quantitative experiments analyzed and compared here include 1) a study of the quantitative
reproducibility of the analysis system, 2) a study of the clonal reproducibility of REF52 cells, 3) a study of growth-related
changes in REF52 cells, and 4) a study of the effects of labeling cells for varying lengths of time. Of the proteins analyzed
from REF52 cells, 10% are nuclear, 6% are phosphoproteins, and 4% are mannose-labeled glycoproteins. The mannose-labeled proteins
are more prominent in patterns from quiescent cells, while the synthesis of cytoskeletal proteins is generally repressed at
quiescence. A small set of proteins, selected for elevated rates of synthesis is generally repressed at quiescence. A small
set of proteins, selected for elevated rates of synthesis in quiescent versus proliferating cells includes one of the tropomyosin
isoforms, a myosin light chain isoform, and several prominent glycoproteins. These proteins are thought to be characteristic
of the differentiated state of untransformed REF52 cells. Proteins induced early versus late after refeeding quiescent cells
show very different patterns of growth regulation. These studies lay the foundations of the REF52 database and provide information
needed to interpret the experiments with transformed REF52 cells, which are reported in the accompanying paper (Garrels, J.,
and Franza, B. R., Jr. (1989) J. Biol. Chem. 264, 5299-5312).</description><identifier>ISSN: 0021-9258</identifier><identifier>EISSN: 1083-351X</identifier><identifier>PMID: 2925693</identifier><identifier>CODEN: JBCHA3</identifier><language>eng</language><publisher>Bethesda, MD: American Society for Biochemistry and Molecular Biology</publisher><subject>Analytical biochemistry: general aspects, technics, instrumentation ; Analytical, structural and metabolic biochemistry ; Animals ; biochemistry ; Biological and medical sciences ; Cell Division ; Cell Line ; computer aided analysis ; cytology ; Cytoskeletal Proteins - isolation & purification ; data bases ; Electrophoresis, Gel, Two-Dimensional - methods ; Fundamental and applied biological sciences. Psychology ; Information Systems - instrumentation ; Information Systems - organization & administration ; Information Systems - standards ; Interphase ; mathematical models ; Mitochondria - analysis ; Nuclear Proteins - isolation & purification ; Phosphates ; Protein Biosynthesis ; proteins ; Proteins - isolation & purification ; Proteins - standards ; QUEST ; Rats ; REF52 ; Reference Standards ; Reproducibility of Results ; Software - methods ; Subcellular Fractions - analysis ; Terminology as Topic</subject><ispartof>The Journal of biological chemistry, 1989-03, Vol.264 (9), p.5283-5298</ispartof><rights>1989 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=7311707$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/2925693$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>J I Garrels</creatorcontrib><creatorcontrib>B R Franza, Jr</creatorcontrib><title>The REF52 protein database. Methods of database construction and analysis using the QUEST system and characterizations of protein patterns from proliferating and quiescent REF52 cells</title><title>The Journal of biological chemistry</title><addtitle>J Biol Chem</addtitle><description>The construction and analysis of protein databases using the QUEST system is described, and the REF52 protein database is
presented. A protein database provides the means to store and compare quantitative and descriptive data for up to 2000 proteins
from many experiments that employ computer-analyzed two-dimensional gel electrophoresis. The QUEST system provides the tools
to manage, analyze, and communicate these data. The REF52 database contains experiments with normal and transformed rat cell
lines. In this report, many of the proteins on the REF52 map are identified by name, by subcellular localization, and by mode
of post-translational modification. The quantitative experiments analyzed and compared here include 1) a study of the quantitative
reproducibility of the analysis system, 2) a study of the clonal reproducibility of REF52 cells, 3) a study of growth-related
changes in REF52 cells, and 4) a study of the effects of labeling cells for varying lengths of time. Of the proteins analyzed
from REF52 cells, 10% are nuclear, 6% are phosphoproteins, and 4% are mannose-labeled glycoproteins. The mannose-labeled proteins
are more prominent in patterns from quiescent cells, while the synthesis of cytoskeletal proteins is generally repressed at
quiescence. A small set of proteins, selected for elevated rates of synthesis is generally repressed at quiescence. A small
set of proteins, selected for elevated rates of synthesis in quiescent versus proliferating cells includes one of the tropomyosin
isoforms, a myosin light chain isoform, and several prominent glycoproteins. These proteins are thought to be characteristic
of the differentiated state of untransformed REF52 cells. Proteins induced early versus late after refeeding quiescent cells
show very different patterns of growth regulation. These studies lay the foundations of the REF52 database and provide information
needed to interpret the experiments with transformed REF52 cells, which are reported in the accompanying paper (Garrels, J.,
and Franza, B. R., Jr. (1989) J. Biol. Chem. 264, 5299-5312).</description><subject>Analytical biochemistry: general aspects, technics, instrumentation</subject><subject>Analytical, structural and metabolic biochemistry</subject><subject>Animals</subject><subject>biochemistry</subject><subject>Biological and medical sciences</subject><subject>Cell Division</subject><subject>Cell Line</subject><subject>computer aided analysis</subject><subject>cytology</subject><subject>Cytoskeletal Proteins - isolation & purification</subject><subject>data bases</subject><subject>Electrophoresis, Gel, Two-Dimensional - methods</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Information Systems - instrumentation</subject><subject>Information Systems - organization & administration</subject><subject>Information Systems - standards</subject><subject>Interphase</subject><subject>mathematical models</subject><subject>Mitochondria - analysis</subject><subject>Nuclear Proteins - isolation & purification</subject><subject>Phosphates</subject><subject>Protein Biosynthesis</subject><subject>proteins</subject><subject>Proteins - isolation & purification</subject><subject>Proteins - standards</subject><subject>QUEST</subject><subject>Rats</subject><subject>REF52</subject><subject>Reference Standards</subject><subject>Reproducibility of Results</subject><subject>Software - methods</subject><subject>Subcellular Fractions - analysis</subject><subject>Terminology as Topic</subject><issn>0021-9258</issn><issn>1083-351X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1989</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkV2L1TAQhoso63H1JwhBxLtKPpo2uZTlrAorop4F78o0nW4j_TibSZHjH_Pvme7Wvd1AyPDOM--8kCfZTnCjcqXFz6fZjnMpciu1eZ69IPrF0ymsOMvOZBJLq3bZ30OP7Pv-Ukt2DHNEP7EWIjRA-J59wdjPLbG5exCZmyeKYXHRzxODqU0XhhN5Ygv56YbF5Pftev_jwOhEEcc7xvUQwEUM_g-sg3eW__cdIaZO0rowj6s6-A5D4pLbOny7eCSHU9xyOhwGepk962AgfLW959n15f5w8Sm_-vrx88WHq7xXsoh52SGY1vAKy1RUUnNVaGXANEWjClPqiqfCOodtqRthmxa4UlC06ConO1Dn2bt735TrdkGK9ehpTQATzgvVlTFGWWMfBaXWwoqyfBQUWpZc2iqBrzdwaUZs62PwI4RTvf1d6r_d-kAOhi7A5Dw9YJUSouKrzZt7rPc3_W8fsG787Hoca1kWta21NEr9A_DasX8</recordid><startdate>19890325</startdate><enddate>19890325</enddate><creator>J I Garrels</creator><creator>B R Franza, Jr</creator><general>American Society for Biochemistry and Molecular Biology</general><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>7QL</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>M81</scope><scope>P64</scope><scope>7SC</scope><scope>JQ2</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>7X8</scope></search><sort><creationdate>19890325</creationdate><title>The REF52 protein database. Methods of database construction and analysis using the QUEST system and characterizations of protein patterns from proliferating and quiescent REF52 cells</title><author>J I Garrels ; B R Franza, Jr</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-h324t-6fea8d807e6ea8725034538a8b4b34865704b39cced65b19bda033a4dec7c2fa3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>1989</creationdate><topic>Analytical biochemistry: general aspects, technics, instrumentation</topic><topic>Analytical, structural and metabolic biochemistry</topic><topic>Animals</topic><topic>biochemistry</topic><topic>Biological and medical sciences</topic><topic>Cell Division</topic><topic>Cell Line</topic><topic>computer aided analysis</topic><topic>cytology</topic><topic>Cytoskeletal Proteins - isolation & purification</topic><topic>data bases</topic><topic>Electrophoresis, Gel, Two-Dimensional - methods</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Information Systems - instrumentation</topic><topic>Information Systems - organization & administration</topic><topic>Information Systems - standards</topic><topic>Interphase</topic><topic>mathematical models</topic><topic>Mitochondria - analysis</topic><topic>Nuclear Proteins - isolation & purification</topic><topic>Phosphates</topic><topic>Protein Biosynthesis</topic><topic>proteins</topic><topic>Proteins - isolation & purification</topic><topic>Proteins - standards</topic><topic>QUEST</topic><topic>Rats</topic><topic>REF52</topic><topic>Reference Standards</topic><topic>Reproducibility of Results</topic><topic>Software - methods</topic><topic>Subcellular Fractions - analysis</topic><topic>Terminology as Topic</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>J I Garrels</creatorcontrib><creatorcontrib>B R Franza, Jr</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>Biochemistry Abstracts 3</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Computer and Information Systems Abstracts</collection><collection>ProQuest Computer Science Collection</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>MEDLINE - Academic</collection><jtitle>The Journal of biological chemistry</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>J I Garrels</au><au>B R Franza, Jr</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The REF52 protein database. Methods of database construction and analysis using the QUEST system and characterizations of protein patterns from proliferating and quiescent REF52 cells</atitle><jtitle>The Journal of biological chemistry</jtitle><addtitle>J Biol Chem</addtitle><date>1989-03-25</date><risdate>1989</risdate><volume>264</volume><issue>9</issue><spage>5283</spage><epage>5298</epage><pages>5283-5298</pages><issn>0021-9258</issn><eissn>1083-351X</eissn><coden>JBCHA3</coden><abstract>The construction and analysis of protein databases using the QUEST system is described, and the REF52 protein database is
presented. A protein database provides the means to store and compare quantitative and descriptive data for up to 2000 proteins
from many experiments that employ computer-analyzed two-dimensional gel electrophoresis. The QUEST system provides the tools
to manage, analyze, and communicate these data. The REF52 database contains experiments with normal and transformed rat cell
lines. In this report, many of the proteins on the REF52 map are identified by name, by subcellular localization, and by mode
of post-translational modification. The quantitative experiments analyzed and compared here include 1) a study of the quantitative
reproducibility of the analysis system, 2) a study of the clonal reproducibility of REF52 cells, 3) a study of growth-related
changes in REF52 cells, and 4) a study of the effects of labeling cells for varying lengths of time. Of the proteins analyzed
from REF52 cells, 10% are nuclear, 6% are phosphoproteins, and 4% are mannose-labeled glycoproteins. The mannose-labeled proteins
are more prominent in patterns from quiescent cells, while the synthesis of cytoskeletal proteins is generally repressed at
quiescence. A small set of proteins, selected for elevated rates of synthesis is generally repressed at quiescence. A small
set of proteins, selected for elevated rates of synthesis in quiescent versus proliferating cells includes one of the tropomyosin
isoforms, a myosin light chain isoform, and several prominent glycoproteins. These proteins are thought to be characteristic
of the differentiated state of untransformed REF52 cells. Proteins induced early versus late after refeeding quiescent cells
show very different patterns of growth regulation. These studies lay the foundations of the REF52 database and provide information
needed to interpret the experiments with transformed REF52 cells, which are reported in the accompanying paper (Garrels, J.,
and Franza, B. R., Jr. (1989) J. Biol. Chem. 264, 5299-5312).</abstract><cop>Bethesda, MD</cop><pub>American Society for Biochemistry and Molecular Biology</pub><pmid>2925693</pmid><tpages>16</tpages></addata></record> |
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| ispartof | The Journal of biological chemistry, 1989-03, Vol.264 (9), p.5283-5298 |
| issn | 0021-9258 1083-351X |
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| source | MEDLINE; Alma/SFX Local Collection; EZB Electronic Journals Library |
| subjects | Analytical biochemistry: general aspects, technics, instrumentation Analytical, structural and metabolic biochemistry Animals biochemistry Biological and medical sciences Cell Division Cell Line computer aided analysis cytology Cytoskeletal Proteins - isolation & purification data bases Electrophoresis, Gel, Two-Dimensional - methods Fundamental and applied biological sciences. Psychology Information Systems - instrumentation Information Systems - organization & administration Information Systems - standards Interphase mathematical models Mitochondria - analysis Nuclear Proteins - isolation & purification Phosphates Protein Biosynthesis proteins Proteins - isolation & purification Proteins - standards QUEST Rats REF52 Reference Standards Reproducibility of Results Software - methods Subcellular Fractions - analysis Terminology as Topic |
| title | The REF52 protein database. Methods of database construction and analysis using the QUEST system and characterizations of protein patterns from proliferating and quiescent REF52 cells |
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