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. While 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 ... Ion physics ion s produced. History Marc Wilkins geneticist Marc Wilkins coined the term proteome ... Bioinformatics List of omics topics in biology Plant Proteome Database Transcriptome References ... content about us Grid Computing of the Human Proteome Dead link Databases PIR Swissprot Pfam Protein ... more details
refimprove date February 2012 The Human Proteome Project ref Legrain, P. et al. The human proteome project Current state and future direction. Mol Cell Proteomics. 10 M111.009993 2011 . ref HPP is a collaborative effort coordinated by the Human Proteome Organization ref HUPO Human Proteome Organization 1st World Congress. Mol Cell Proteomics. 9 651 752 2002 . ref HUPO . Its stated goal is to experimentally observe all of the proteins produced by the sequences translated from the human genome . History http www.hupo.org HUPO has served as a coordinating body for many long running proteomics research projects associated with specific human tissues of clinical interest, such as blood plasma , ref Omenn, G.S. et al. Overview of the HUPO Plasma Proteome Project. Proteomics. 5, 3226 45 2005 . ref liver , ref He, F. Human liver proteome project plan, progress, and perspectives. Mol Cell Proteomics. 4, 1841 8 2005 . ref brain ref Hamacher, M. et al. HUPO Brain Proteome Project toward a code of conduct. Mol Cell Proteomics. 7, 457 2008 . ref and urine . ref Yamamoto, T., Langham, R.G., Ronco, P., Knepper, M.A. & Thongboonkerd, V. Towards standard protocols and guidelines for urine proteomics. Proteomics. 8, 2156 9 2008 . ref It has also been responsible for projects associated with specific ... has debated in the scientific literature. ref Archakov A, et al. The Moscow HUPO Human Proteome ... human proteome project the next big thing in basic and clinical proteomics. Curr Opin Mol Ther. 2009 11 600 2 2009 . ref ref Editorial, The call of the human proteome. Nat Methods. 7 661 2010 . ref ref Rabilloud T., et al. Is a gene centric human proteome project the best way for proteomics to serve biology? Proteomics. 10 3067 72 2010 . ref ref Editorial. A Gene centric Human Proteome Project. Mol ... of two sub projects, C HPP and B D HPP. ref Paik, Y K., et al. A Chromosome Centric Human Proteome ... genome projects Category Proteome projects ... more details
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 Bimonthly history 2002 present openaccess license impact 5.460 impact year 2010 website http pubs.acs.org journal jprobs link1 link1 name link2 link2 name JSTOR OCLC 47082747 LCCN 2001211122 CODEN JPROBS ISSN 1535 3893 eISSN 1535 3907 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 Abstracting and indexing The journal is abstracted and indexed in EBSCO Publishing EBSCOhost , PubMed , Scopus , and the Web of Science . According to the Journal Citation Reports , the journal has a 2010 impact factor of 5.460. ref name WoS cite web url http isiwebofknowledge.com title Web of Science year 2011 accessdate 2011 06 15 ref References Reflist External links Official http pubs.acs.org journal jprobs DEFAULTSORT Journal Of Proteome Research Category American Chemical Society academic journals Category Bimonthly 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 Reflist 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 Category Government databases in the United States Category Biological databases ... 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 ref cite pmid 12511871 ref . 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 reflist 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 polymer stub 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 Hydraulic Power Reversible pack or unit as accumulator 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
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
cite book title Proteome Research New Frontiers in Functional Genomics year 1997 editor Wilkins, MR ... fellow in the Australian Proteome Analysis Facility, ref name MacquarieUniversityCSIRO http www.ics.mq.edu.au ... by the Australian 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 ... 19 January 2009. ref of Australia s largest proteomics company Proteome Systems Ltd. It was established ... of Bioinformatics 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 ... Rule , 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
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 EC 2.7.1 Enzyme stub ... more details
An immunoreceptor tyrosine based inhibition motif ITIM , is a conserved sequence of amino acid s S I V LxYxxI V L that is found in the cytoplasm ic tails of many inhibitory immune receptor receptors of the immune system . After ITIM possessing inhibitory receptors interact with their ligand, their ITIM motif becomes phosphorylation phosphorylated by enzyme s of the Src gene Src family kinases Src of kinase s, allowing them to recruit other enzymes such as the phosphotyrosine phosphatase s SHP 1 and SHP 2 , or the inositol phosphatase called SHIP. These phosphatases decrease the activation of molecules involved in cell signaling. ref cite journal author Barrow A, Trowsdale J title You say ITAM and I say ITIM, let s call the whole thing off the ambiguity of immunoreceptor signaling journal Eur J Immunol volume 36 issue 7 pages 1646 53 year 2006 pmid 16783855 doi 10.1002 eji.200636195 ref A list of human candidate ITIM containing proteins has been generated by proteome wide scans. ref cite journal author Staub E, Rosenthal A, Hinzmann B title Systematic identification of immunoreceptor tyrosine based inhibitory motifs in the human proteome journal Cell Signal volume 16 issue 4 pages 435 456 year 2004 pmid 14709333 ref References reflist Category Immune system protein stub immunology stub sr Imunoreceptorski tirozin bazirani inhibitorni motiv ... 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 cite journal pages 1234 42 doi 10.1021 pr049882h title Open Source System for Analyzing, Validating, and Storing Protein Identification Data year 2004 last1 Craig first1 Robertson last2 Cortens first2 John P. last3 Beavis first3 Ronald C. journal Journal of Proteome Research volume 3 issue 6 pmid 15595733 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 cite journal pages 339 40 doi 10.1093 bioinformatics 15.4.339 title The Biopolymer Markup Language year 1999 last1 Fenyo first1 D journal Bioinformatics volume 15 issue 4 pmid 10320402 ref format files. References Reflist External links http www.thegpm.org index.html GPM project website DEFAULTSORT Gpm Proteomics Category Proteomics ... 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. Ling stub Category Linguistic units ... 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
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
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 doi 10.1089 omi.2006.10.145 ref 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 bioinformatics stub Category Bioinformatics software ... more details
The channelome , sometimes ion channelome , is an expression used to describe the complete set of ion channels expressed in a biological Tissue biology tissue or organism. It is analogous to the genome , the metabolome describing metabolites , the proteome describing general protein expression , the microbiome etc. Characterization of the ion channelome can be performed by a wide variety of ion channel studying techniques channelomics including patch clamp electrophysiology , PCR and immunohistochemistry . References Citation style date September 2009 Barrett Jolley, R., R. Lewis, et al. 2010 . The Emerging Chondrocyte Channelome. Frontiers in Membrane Physiology and Biophysics. http www.frontiersin.org membrane physiology and biophysics 10.3389 fphys.2010.00135 abstract Cite doi 10.1016 S0896 6273 03 00472 0 Cite doi 10.1016 j.phrs.2006.03.005 Cite doi 10.1007 s10162 007 0082 y Cite doi 10.1007 978 1 4020 4896 8 15 Category Ion channels Category Channelopathy chemistry stub ... more details
or Bruton s Disease Prolidase Deficiency autosomal recessive Proteins The Human Proteome Project HPP has been initiated by Human Proteome Organization HUPO aims to sequence the entire human proteome ... with open sharing of proteome datasets. The proteome sequencing has been initiated with a chromosome centric and gene centric approach. Sequencing of chromosome 19 proteome will be coordinated by Prof ... www.tsbvi.edu Outreach seehear spring01 lebers.htm Human Proteome Project Launch website http www.hupo.org ... more details
In biochemistry , a protein ligand is an atom , a molecule or an ion which can bind to a specific site the binding site on a protein. Alternative names used to mean a protein ligand are affinity reagents or protein binders. To date, antibodies are the most widely used protein ligands in life science investigations, however, other molecules such as Scaffold protein protein scaffolds , nucleic acids , peptides are also being used. ref Taussig MJ et al, 2007. ProteomeBinders planning a European resource of affinity reagents for analysis of the human proteome. Nat Methods. 2007 Jan 4 1 13 7. ref Main methods to study protein ligand interactions are principal hydrodynamic and calorimetric techniques, and principal spectroscopic and structural methods such as Fourier transform spectroscopy Raman spectroscopy Fluorescence spectroscopy Circular dichroism Nuclear magnetic resonance Mass spectrometry Atomic force microscope Paramagnetic probes Dual Polarisation Interferometry Other techniques include fluorescence intensity, bimolecular fluorescence complementation, FRET fluorescent resonance energy transfer FRET quenching surface plasmon resonance, Bio Layer Interferometry , Coimmunopreciptation indirect ELIS, equilibrium dialysis, gel electrophoresis, far western blot, fluorescence polarization anisotropy, electron paramagnetic resonance, Microscale Thermophoresis The dramatically increased computing power of supercomputers and personal computers has made it possible to study protein ligand interactions also by means of computational chemistry . For example, a worldwide grid of well over a million ordinary PCs was harnessed for cancer research in the project grid.org , which ended in April 2007. Grid.org has been succeeded by similar projects such as World Community Grid , Human Proteome Folding Project , Compute Against Cancer and Folding Home . References references DEFAULTSORT Protein Ligand Category Biomolecules Category Chemical bonding Category Proteins ... more details
unreferenced date October 2011 Infobox Company company name Institute for Systems Biology company type non profit foundation 2000 founder Leroy Hood , Alan Aderem , Ruedi Aebersold location city Seattle, Washington location area 65,000 square foot location country United States location origins key people President Leroy Hood, MD, PhD, President br John Aitchison, PhD Senior Vice President and Executive Director for Integrative Biology br Nitin Baliga, PhD Director for Integrative Biology area served Systems Biology industry Biology products revenue operating income net income num employees 315 num faculty members and their laboratory groups 12 parent subsid owner company slogan homepage http www.systemsbiology.org footnotes Image InstituteForSystemsBiologyAsViewedFromLakeUnion.jpg thumb right Institute for Systems Biology green windows as viewed from a sailboat on Lake Union. Institute for Systems Biology ISB is a non profit research institution, located in Seattle, Washington , United States . Leroy Hood co founded the Institute with Alan Aderem and Ruedi Aebersold in 2000. cn date October 2011 As its name suggests, the ISB concentrates on systems biology , the study of relationships and interactions between various parts of biological systems. ISB is also notable for advocating an interdisciplinary approach to biological research. cn date October 2011 ISB has been involved in several high profile research projects, including the NHLBI Seattle Proteome Center and the Center for Inquiry Science . cn date October 2011 In late 2005, the ISB began to emphasize the application of systems biology to P4 medicine predictive, preventive, personalized, participatory , the development of techniques for predicting and preventing disease, possibly before the patient knows they are sick. . cn date October 2011 See also List of systems sciences organizations External links http www.systemsbiology.org ISB website http www.proteomecenter.org Seattle Proteome Center Category Organi ... more details
Gilbert Omenn is Professor of Internal Medicine , Human Genetics , and Public Health at the University of Michigan . ref name UM http www.umich.edu mmgmed faculty bios omenn.htm faculty page at the University of Michigan ref 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 . ref http www.mlive.com business ann arbor index.ssf 2009 03 former um health system ceo he.html Former U M Health System CEO Health care reform will come this year , MLive.com, March 31, 2009 ref He is a member of the Council and leader of the Plasma Proteome Project for the international Human Proteome Organization . He is Past President 2005 2006 and Past Chairman of the Board 2006 2007 of the American Association for the Advancement of Science AAAS . He is a longtime director of Amgen Inc. and of Rohm & Haas Company. He is also on the advisory board of NextServices. He received a B.A. from Princeton University , an M.D. from Harvard Medical School and a Ph.D. in genetics from the University of Washington . ref name UM References references Persondata Metadata see Wikipedia Persondata . NAME Omenn, Gilbert ALTERNATIVE NAMES SHORT DESCRIPTION Professor DATE OF BIRTH PLACE OF BIRTH DATE OF DEATH PLACE OF DEATH DEFAULTSORT Omenn, Gilbert Category Living people Category University of Michigan faculty Category Princeton University alumni Category Harvard Medical School alumni Category University of Washington alumni ... more details
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