The proteome is the entire set of protein s expressed by a genome, cell, tissue or organism. More specifically, it is the set of expressed proteins in a given type of cells or an organism at a given time under defined conditions. The term is a portmanteau of proteins and genome . The term has been applied to several different types of biological systems. A cellular proteome is the collection of proteins found in a particular cell biology cell type under a particular set of environmental conditions such as exposure to hormone hormone stimulation . It can also be useful to consider an organism s complete proteome , which can be conceptualized as the complete set of proteins from all of the various cellular proteomes. This is very roughly the protein equivalent of the genome . The term proteome has also been used to refer to the collection of proteins in certain sub cellular biological systems. For example, all of the proteins in a virus can be called a viral proteome. The proteome is larger than the genome , especially in eukaryota eukaryotes , in the sense that there are more protein s than gene s. This is due to alternative splicing of genes and post translational modification s like glycosylation or phosphorylation . Moreover the proteome has at least two levels of complexity lacking in the genome. When the genome is defined by the sequence of nucleotide s, the proteome cannot be limited to the sum of the sequences of the proteins present. Knowledge of the proteome requires knowledge of 1 the protein structure structure of the proteins in the proteome and 2 the functional interaction between the proteins. Proteomics , the study of the proteome, has largely been practiced through the separation of proteins by two dimensional gel electrophoresis . In the first dimension, the proteins ... Plant Proteome Database Transcriptome References Reflist External links http bioinformatics.oupjournals.org Bioinformatics Journal http www.grid.org content about us Grid Computing of the Human Proteome ... more details
italictitle Infobox journal title Journal of Proteome Research cover File Jpr cover.jpg 150 px editor William S. Hancock discipline Proteomics abbreviation J. Proteome Res. publisher American Chemical Society country United States frequency once every two months history 2002 present openaccess license impact 5.132 impact year 2009 website http pubs.acs.org journal jprobs link1 link1 name link2 link2 name RSS http pubs.acs.org action showFeed?ui 0&mi qjmolc&ai 53h&jc jprobs&type etoc&feed rss atom JSTOR OCLC LCCN CODEN jprobs ISSN 1535 3893 eISSN 1535 3907 boxwidth The Journal of Proteome Research is a Peer review peer reviewed scientific journal , published since 2002 by the American Chemical Society . ref http pubs.acs.org American Chemical Society ref The current editor in chief is William S. Hancock . ref http pubs.acs.org page jprobs profile.html Editor profile ref In 2008, the journal had an impact factor of 5.684. Abstracting and indexing The journal is abstracted and indexed in EBSCO Publishing EBSCOhost , PubMed , Scopus , Web of Science . References Reflist DEFAULTSORT Journal Of Proteome Research Category American Chemical Society academic journals Category Monthly journals Category English language journals Category Chemistry journals Category Publications established in 2002 fr Journal of Proteome Research ... more details
The Human Proteome Folding Project HPF is a collaborative effort between New York University Richard Bonneau Bonneau Lab , the Institute for Systems Biology ISB and the University of Washington Baker Lab , using the Rosetta software developed by the Rosetta Commons. The HPF project is currently in Phase 2, which is running exclusively on the World Community Grid . Phase 1 ran on two distributed computing grids the World Community Grid , an IBM philanthropic initiative, and on United Devices grid.org . The Institute for Systems Biology designed the Human Proteome Folding project for World Community Grid and will use the results within its larger research efforts. Image Screensaver HUMAN PROTEOME FOLDING Phase2.png right thumb 250px World Community Grid WCG screensaver , Human Proteome Folding Project Phase2, running under United Devices UD client software Current project status HPF Phase 1 applied Rosetta v4.2x software on the human genome and 89 others, starting in November 2004. Phase 1 ended in July 2006. HPF Phase 2 HPF2 applies the Rosetta v4.8x software in higher resolution, full atom refinement mode, concentrating on cancer biomarkers proteins found at dramatically increased levels in cancer tissues , human secreted proteins and malaria. Publications Citation last Malmstr m first Lars author link last2 Riffle first2 Michael author2 link last3 Strauss first3 Charlie E. M. author3 link last4 Chivian first4 Dylan author4 link last5 Davis first5 Trisha N. author5 link last6 Baker first6 David author6 link title Superfamily Assignments for the Yeast Proteome through Integration ... Scientists and Research Technology Data Visualization and Analysis Human Proteome Folding Project Human Proteome Folding at ISB Category Berkeley Open Infrastructure for Network Computing projects Category Proteomics Category Protein structure de Human Proteome Folding Project es Proyecto del Plegado del Proteoma Humano it Human Proteome Folding fi Human Proteome Folding Project ... more details
Orphan date February 2009 The Plant Proteome Database is an National Science Foundation funded project to determine the biological function of each protein in plant s ref Sun Q, Zybailov B, Majeran W, Friso G, Olinares PD, van Wijk KJ. 2008 PPDB, the Plant Proteomics Database at Cornell. Nucleic Acids Res. 2 Oct ref . It includes data for two plants that are widely studied in molecular biology , Arabidopsis thaliana and maize Zea mays . Initially the project was limited to plant plastids, under the name of the Plastid PDB, but was expanded and renamed Plant PDB in November 2007 ref PPDB Home Page http ppdb.tc.cornell.edu ref . See also Proteome References references External links http ppdb.tc.cornell.edu Plant Proteome Database home page http www.arabidopsis.org TAIR The Arabidopsis Information Resource http groups.yahoo.com group Plastids Plastid Mailing List Category Plant physiology ... more details
The Human Proteome Organization HUPO is an international consortium of national proteomics research associations, government researchers, academic institutions, and industry partners. HUPO was founded in June 2001 and it promotes the development and awareness of proteomics research, advocates on behalf of proteomics researchers throughout the world, and facilitates scientific collaborations between HUPO members and Initiatives. Ultimately, it is organized to gain a better and more complete understanding of the human proteome . Key Members Past and Present Rolf Apweiler Samir Hanash Matthias Mann Gil Omenn Young Ki Paik See also Human Genome Organisation HUGO Human Genome Organisation , Human Genome Project Proteomics Standards Initiative PSI Proteomics Standards Initiative References L.A. Huber Is Proteomics Heading in the Wrong Direction? 2003 Nature Reviews Molecular Cell Biology External links http www.ushupo.org US HUPO http www.aohupo.org Asia Oceania HUPO http www.lahupo.org Latin American HUPO http www.khupo.org Korea HUPO KHUPO Category Research projects sci org stub pl Human Proteome Organization ... more details
Unreferenced date February 2008 Orphan date December 2007 Sequenceome is the totality of polymer sequences on Earth. Sequences in biology such as genome and proteome are the major components. Sequenceome is effectively a large database . Category Polymers ko ... more details
Marc Wilkins may refer to Marc Wilkins baseball , former Major League Baseball pitcher Marc Wilkins geneticist , geneticist credited with the concept of the proteome See also Mark Wilkins disambiguation hndis name Wilkins, Marc ... more details
HPR may mean Harvard Political Review Hawaii Public Radio Heartland Public Radio Flight dynamics Heading, Pitch, Roll High Power Rocketry Holding Period Return Human Proteome Resource program Host plant resistance Home Page Reader an Aural Browser and Screen Reader from IBM HPR Foreign Trade Co. Hobby & Toys Importer located Istanbul Turkey Homiletic and Pastoral Review monthly Catholic journal disambig it HPR ... more details
Unreferenced stub auto yes date December 2009 Orphan date December 2009 Stem cell proteomics is a omics that analyzes the proteome s of stem cell s. Comparing different stem cell proteomes can reveal protein s that are important for cell differentiation stem cell differentiation . See also Stem cell genomics DEFAULTSORT Stem Cell Proteomics Category Stem cells Category Proteomics Cell biology stub ... more details
Notability date November 2007 Structural proteomics is an international collaboration project for solving 3D protein structures at a proteome scale. It is similar to structural genomics project. See also Proteomics Structural genomics Omics External links http www.uhnres.utoronto.ca centres proteomics University of Toronto Structural Proteomics Category Genomics Category Proteins Category Proteomics ... more details
Mycoplasma genitalium pmid 7498152 volume 7 pages 1090 94 issue 7 ref ref cite book title Proteome ... Proteome Analysis Facility, ref name MacquarieUniversityCSIRO http www.ics.mq.edu.au industry ... Government in 1995 as the world s first dedicated proteome research centre. ref name Newlab In 1997 he co edited the first book on proteomics , Proteome Research New Frontiers in Functional .... ref of Australia s largest proteomics company Proteome Systems Ltd. It was established in January ... at Proteome Systems Inc, now renamed as Tyrian Diagnostics, ref http www.tyriandx.com 2008 11 06 new name for proteome systems New Name for Proteome Systems , Tyrian Diagnostics website press release ... , Scientific American April 2002 . http www.proteome.org.au The Australian Proteome Analysis Facility APAF Ltd http www.tyriandx.com Tyrian Diagnostics formerly Proteome Systems Ltd, up to 6 November ... more details
Gilbert Omenn , M.D., Ph.D is Professor of Internal Medicine , Human Genetics , and Public Health at the University of Michigan . He is the director of the UM Center for Computational Medicine & Biology and the Proteomics Alliance for Cancer Research. He served as Executive Vice President for Medical Affairs and as Chief Executive Officer of the University of Michigan Health System from 1997 to 2002. He was formerly Dean of the School of Public Health, and Professor of Medicine and Environmental Health, University of Washington , Seattle. He served as Associate Director, Office of Science and Technology Policy , and Associate Director, Office of Management and Budget, in the Executive Office of the President in the Carter Administration . He is a longtime director of Amgen Inc. and of Rohm & Haas Company http www.rohmhaas.com . He is a member of the Council and leader of the http www.hupo.org research hppp Plasma Proteome Project for the international Human Proteome Organization http www.hupo.org . He is Chairman of the Board 2006 2007 of the American Association for the Advancement of Science AAAS . He is also on the advisory board of NextServices http www.nextservices.net . DEFAULTSORT Omenn, Gilbert Category Living people Category Proteomics ... more details
Multiple issues wikify December 2010 orphan February 2009 COI February 2008 In proteomics , GPM stands for Global Proteome Machine . It is a web based, open source user interface for analyzing and displaying protein identification data. It was originally designed by Rob Craig and Ron Beavis. ref R. Craig, J.P. Cortens and R.C. Beavis, Open source system for analyzing, validating, and storing protein identification data, J. Proteome Res. 2004 Nov Dec 3 6 1234 42. http www.ncbi.nlm.nih.gov pubmed 15595733?dopt Abstract ref The interface creates a series of web browser page views of tandem mass spectrometry data that has been assigned to protein sequences. The underlying data documents are stored in BIOML ref D. Fenyo, The Biopolymer Markup Language, Bioinformatics. 1999 Apr 15 4 339 40 http www.ncbi.nlm.nih.gov pubmed 10320402?dopt Abstract ref format files. References Reflist External links http www.thegpm.org index.html GPM project website DEFAULTSORT Gpm Proteomics Category Proteomics ... more details
Orphan date February 2009 Membranome is the set of biological membranes existing in a specific organism. The term was proposed by British biologist Thomas Cavalier Smith ref Membranome and Membrane Heredity in Development and Evolution by Thomas Cavalier Smith , in Organelles, Genomes and Eukaryote Phylogeny An Evolutionary Synthesis in the Age of Genomics Editors Robert P. Hirt David S. Horner ISBN 978 0 415 29904 6 http books.google.com books?id RpOO3VlVjNYC&pg RA1 PA335&lpg RA1 PA335&dq membranome Cavallier&source bl&ots P6oX22UltG&sig 5rZ9zqvwuIaLhZs1cp V4QJTYs&hl en&ei AAknS7TwDovmMezt1YoM&sa X&oi book result&ct result&resnum 1&ved 0CAwQ6AEwAA v onepage&q &f false ref to discuss epigenetics of biological membranes. The term was also used to define the entire set of membrane proteins ref Ghosh D, Beavis RC, Wilkins JA, The identification and characterization of membranome components, JOURNAL OF PROTEOME RESEARCH Volume 7 Issue 4 Pages 1572 1583. ref or a combination of membrane proteome and lipidome . References references Category Membrane biology Category Omics ja ... more details
The Proteomics Standards Initiative PSI is a working group of Human Proteome Organization HUPO . It aims to define Specification data standards for proteomics in order to facilitate data comparison, exchange and verification ref cite web url http www.psidev.info title HUPO Proteomics Standards Initiative home page work HUPO Proteomics Standards Initiative accessdate 2008 12 06 ref . PSI focuses on the following subjects MIAPE , Minimum Information About a Proteomics Experiment, defines the metadata that should be provided along with a proteomics experiment. Data Markup language Markup Languages for encoding the data and metadata. Ontology information science Ontologies for consistent annotation and representation. References references Further reading Cite journal volume 10 issue 2 pages 145 151 first Chris F. last Taylor coauthors Henning, Hermjakob, Randall K. Julian Jr., John S. Garavelli, Ruedi Aebersold, Rolf Apweiler title The Work of the Human Proteome Organisation s Proteomics Standards Initiative HUPO PSI journal OMICS accessdate 2008 12 06 date 2006 doi 10.1089 omi.2006.10.145 url http www.liebertonline.com doi abs 10.1089 omi.2006.10.145 pmid 16901219 bioinformatics stub Category Bioinformatics software ... more details
Unreferenced date November 2006 Orphan date November 2007 The term lipidome comprises the totality of lipids in Cell biology cells . Lipids are one of the four major molecular components of biological organisms, along with proteins , sugar s and nucleic acid s. Lipidome is a new term coined in the context of omics in modern biology , within the field of lipidomics . See also Genome Proteome Glycome References Quehenberger, O. et al. Lipidomics reveals a remarkable diversity of lipids in human plasma. J. Lipid Res. 29 July 2010 . doi 10.1194 jlr.M009449 http www.lipidmaps.org update 2010 101001 full lipidmaps.2010.28.html Category Lipids Molecular cell biology stub ... more details
JPR may stand for J. P. R. Williams , a Welsh rugby player Jefferson Public Radio , a regional public radio broadcasting network headquartered in Ashland, Oregon Journal of Peace Research , an academic journal targeted toward peace studies, conflict resolution, and international security Journal of Plankton Research Journal of Population Research , a peer reviewed academic journal targeted toward demographic issues Journal of Psychosomatic Research Journal of Proteome Research , a multidisciplinary journal that focuses on the function of proteins in biological systems. disambig fr JPR it JPR ja JPR ... more details
Src family kinase is a family of non receptor tyrosine kinase s that includes nine members Src gene Src , YES1 Yes , FYN Fyn , and FGR gene Fgr , forming the SrcA subfamily, Lck , HCK Hck , Blk, and Lyn Src family Kinase Lyn in the SrcB subfamily, and FRK gene Frk in its own subfamily. Frk has homologs in invertebrate s such as flies and worms, and Src homologs exist in organisms as diverse as unicellular choanoflagellate s, but the SrcA and SrcB subfamilies are specific to vertebrates. Src family kinases interact with a variety of cellular cytosolic, nuclear and membrane proteins, modifying these proteins by phosphorylation of tyrosine residues. A number of substrates have been discovered for these enzyme s. ref Amanchy R, Zhong J, Hong R, Kim JH, Gucek M, Molina H, Pandey A. Identification of c Src tyrosine kinase substrates in PDGF receptor signaling pathway. Molecular Oncology DOI 10.1016 j.molonc.2009.07.001 Amanchy R, Iwahori A, Molina H, Kalume DE, Gronborg M, Joore J, Cope L, Pandey A. Identification of c Src tyrosine kinase substrates using mass spectrometry and peptide microarrays Journal of Proteome Research. 2008 Sep 7 9 3900 10. Luo W, Slebos RJ, Hill S, Li M, Br bek J, Amanchy R, Chaerkady R, Pandey A, Ham AL and Hanks SK. Global impact of oncogenic Src on a phosphotyrosine proteome Journal of Proteome Research. 2008 Aug 7 8 3447 60. ref Tyrosine kinases References reflist Category Enzymes of known structure Category Better category needed Enzyme stub ... more details
Phenotype s Genetics Physiome Physiomics Physiology of an organism Proteome Proteomics Protein s Molecular ... of the proteome consisting of proteins actively exported from cells ref cite journal author Dov Greenbaum ..., from Proteome to Secretome Oming in on Function journal Genome Research url http genome.cshlp.org ... Exome ORFeome Transcriptome Proteome Kinome Secretome Pharmacogenomics Pharmacogenome Phenome Regulome Interactome Metagenome Moleculome Glycome Ionome Lipidome Metabolome Metallome Proteome Physiome ... more details
Unreferenced date November 2006 orphan date November 2009 Orfeome or Orfome is the totality of open reading frames ORF in biology. ORFs are the most important genetic elements in genomes. They code for proteins. Determining ORFs are done by computer programs such as GENSCAN . The computer algorithms are produced by bioinformatists. As ORFs are produced by computer programs, ORFeome s are prediction results by definition. Therefore, ORFeome is a bioinformatics concept. This is the case for genomes, as genomes are also finalized by computer algorithms. On the other hand, a proteome that includes ORFeome is mostly from experimental data generated by techniques such as mass spectrometry . The term ORFeome reflects a new trend in biology that can be succinctly summarized as omics . DEFAULTSORT Orfeome Category Molecular genetics ar ORFeome ... more details
Multiple issues unreferenced August 2009 orphan November 2007 context September 2009 The totality of human speech components such as phoneme which is the smallest contrastive unit in the sound system of a language . Speechome is different from common biological omes such as genome , proteome , and expressome in that it is not biological. However, speechome reflects the omics trend in biology and science in general. Academic researchers in speech and hearing science and machine produced speech from Massachusetts, according to a CNN news story from March 2011, used complex recording devices and microphones to record every aspect of the evolution of their son s speech over the time span of three years with the use of complex algorithms this enabled them to trace the development and context of individual words and phrases across that time. Category Linguistics Ling stub ... more details
Infobox Journal title Proteomics cover Image proteomics cover.gif discipline Biology abbreviation publisher John Wiley & Sons Wiley VCH country Germany frequency bimonthly history 2006 present impact 4.426 impact year 2009 openaccess website http www3.interscience.wiley.com cgi bin jhome 76510741 ISSN 1615 9853 eISSN1615 9861 Proteomics is a Peer review peer reviewed scientific journal covering topics including whole proteome analysis of organisms, protein expression profiling, disease, pharmaceutical, agricultural and biotechnological applications, and analysis of cellular systems, organelles and protein complexes. The 2009 impact factor was 4.426. biology journal stub Category Biology journals Category Publications established in 2006 Category English language journals Category Bimonthly journals ... more details
Context date October 2009 Immobilized pH gradient IPG gel s are the acrylamide gel matrix Polymerization co polymerized with the pH gradient, which result in completely stable gradients except the most alkaline 12 pH values. The immobilized pH gradient is obtained by the continuous change in the ratio of Immobilines . ref Barnes et al., Electrophoresis in Practice A Guide to theory and Practice. Page 44. VCH Publishers Inc, 1993 USA ref This alternative method eliminats the problems of gradient instability and poor sample loading capacity associated with carrier ampholyte pH gradient. ref Wilkins et al., Proteome Research New Frontiers in Functional Genomics. Page 14. Springer, 1997 Germany ref Commercial precast IPG gels are available. An Immobiline is a weak acid or Base chemistry base defined by its pK value. References references Category Acid base chemistry ... more details
Summary Summary Non free use rationale Description JPR journal cover Source Journal website see below Portion all Article Journal of Proteome Research Low resolution It is a low resolution version of the journal cover. Purpose The image will be used for identification and critical commentary in the journal article and possibly other articles in which a visual identification of the journal will serve an educational purpose. Replaceability As the official journal cover, there is no known free alternative available. If a free alternative is found, this image should be Wikipedia Images and media for deletion nominated for deletion as obsolete. other information The use is purely for non profit reasons, and to educate users on the journal in question. Its use does not limit the copyright owner s rights to sell or market related products or the journal itself in any way. Licensing Non free magazine cover Category Academic journal covers ... more details
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