Human Proteinpedia enables sharing of human protein data.
Suresh Mathivanan,Suresh Mathivanan,Mukhtar Ahmed,Natalie G. Ahn,Hainard Alexandre,Ramars Amanchy,Philip C. Andrews,Joel S. Bader,Brian M. Balgley,Marcus Bantscheff,Keiryn L. Bennett,Erik Björling,Blagoy Blagoev,Ron Bose,Samir K. Brahmachari,Alma S Burlingame,Xosé R. Bustelo,Gerard Cagney,Greg T. Cantin,Helene L. Cardasis,Julio E. Celis,Raghothama Chaerkady,Feixia Chu,Philip A. Cole,Catherine E. Costello,Robert J. Cotter,David K. Crockett,James P. DeLany,Angelo M. De Marzo,Leroi V. DeSouza,Eric W. Deutsch,E. Dransfield,Gerard Drewes,Arnaud Droit,Michael J. Dunn,Kojo S.J. Elenitoba-Johnson,Rob M. Ewing,Jennifer E. Van Eyk,Vitor M. Faça,Jayson A. Falkner,Xiangming Fang,Catherine Fenselau,Daniel Figeys,Pierre Gagné,Cecilia Gelfi,Kris Gevaert,Jeffrey M. Gimble,Florian Gnad,Renu Goel,Pavel Gromov,Samir M. Hanash,William S. Hancock,H. C. Harsha,Gerald W. Hart,Faith A. Hays,Fuchu He,Prashantha Hebbar,Kenny Helsens,Heiko Hermeking,Winston Hide,Karin Hjernø,Denis F. Hochstrasser,Oliver Hofmann,David M Horn,Ralph H. Hruban,Nieves Ibarrola,Peter James,Ole N. Jensen,Pia Hønnerup Jensen,Peter Jung,Kumaran Kandasamy,Kumaran Kandasamy,Indu Kheterpal,Reiko F. Kikuno,Ulrike Korf,Roman Körner,Bernhard Kuster,Min-Seok Kwon,Hyoung Joo Lee,Young Jin Lee,Michael Lefevre,Minna Lehvaslaiho,Pierre Lescuyer,Fredrik Levander,Megan S. Lim,Christian Löbke,Joseph A. Loo,Matthias Mann,Matthias Mann,Lennart Martens,Juan Martínez-Heredia,Mark E. McComb,James P. McRedmond,Alexander Mehrle,Rajasree Menon,Christine A. Miller,Harald Mischak,Subburaman Mohan,Riaz Mohmood,Henrik Molina,Michael Moran,James D. Morgan,Robert Moritz,Martine Morzel,David C. Muddiman,Anuradha Nalli,J. Daniel Navarro,Thomas A. Neubert,Osamu Ohara,Rafael Oliva,Gilbert S. Omenn,Masaaki Oyama,Young Ki Paik,Kyla Pennington,Rainer Pepperkok,Balamurugan Periaswamy,Balamurugan Periaswamy,Emanuel F. Petricoin,Guy G. Poirier,T. S. Keshava Prasad,Samuel O. Purvine,B. Abdul Rahiman,Prasanna Ramachandran,Y. L. Ramachandra,Robert H. Rice,Jens Rick,Ragna Rönnholm,Johanna Salonen,Jean-Charles Sanchez,Thierry Sayd,Beerelli Seshi,Kripa Shankari,Shi Jun Sheng,Vivekananda Shetty,K. Shivakumar,Richard J. Simpson,Ravi Sirdeshmukh,K. W. Michael Siu,Jeffrey C. Smith,Richard D. Smith,David J. States,Sumio Sugano,Matthew J. Sullivan,Giulio Superti-Furga,Maarit Takatalo,Visith Thongboonkerd,Jonathan C. Trinidad,Mathias Uhlén,Joël Vandekerckhove,Julian Vasilescu,Timothy D. Veenstra,Jose-Manuel Vidal-Taboada,Mauno Vihinen,Robin Wait,Xiaoyue Wang,Stefan Wiemann,Billy Wu,Tao Xu,John R. Yates,Jun Zhong,Ming Zhou,Yunping Zhu,Petra Zürbig,Akhilesh Pandey +163 more
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TLDR
MMCD is a practical tool for expediting the time-consuming steps of identifying and researching small molecules and is compatible with both NMR and MS data and facilitates high-throughput metabolomics investigations.Abstract:
Proteomic technologies, such as yeast two-hybrid, mass spectrometry (MS), protein/peptide arrays and fluorescence microscopy, yield multi-dimensional data sets, which are often quite large and either not published or published as supplementary information that is not easily searchable. Without a system in place for standardizing and sharing data, it is not fruitful for the biomedical community to contribute these types of data to centralized repositories.read more
Citations
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Journal ArticleDOI
Human Protein Reference Database—2009 update
T. S. Keshava Prasad,Renu Goel,Kumaran Kandasamy,Kumaran Kandasamy,Shivakumar Keerthikumar,Sameer Kumar,Suresh Mathivanan,Deepthi Telikicherla,Rajesh Raju,Beema Shafreen,Abhilash K. Venugopal,Lavanya Balakrishnan,Arivusudar Marimuthu,Sutopa Banerjee,Devi S. Somanathan,Aimy Sebastian,Sandhya G. Rani,Somak Ray,C. J. Harrys Kishore,Sashi Kanth,Mukhtar Ahmed,Manoj Kumar Kashyap,Manoj Kumar Kashyap,Riaz Mohmood,Y. L. Ramachandra,Venkatarangaiah Krishna,B. Abdul Rahiman,Subburaman Mohan,Prathibha Ranganathan,Subhashri Ramabadran,Raghothama Chaerkady,Akhilesh Pandey +31 more
TL;DR: A number of new features in HPRD are added, including PhosphoMotif Finder, which allows users to find the presence of over 320 experimentally verified phosphorylation motifs in proteins of interest, and a protein distributed annotation system—Human Proteinpedia.
Journal ArticleDOI
Towards a knowledge-based Human Protein Atlas
Mathias Uhlén,Per Oksvold,Linn Fagerberg,Emma Lundberg,Kalle Jonasson,Mattias Forsberg,Martin Zwahlen,Caroline Kampf,Kenneth Wester,Sophia Hober,Henrik Wernérus,Lisa Björling,Fredrik Pontén +12 more
TL;DR: The analysis here suggests that state stem cell funding programs are sufficiently large and established that simply ending the programs, at least in the absence of substantial investment in the field by other funding sources, could have deleterious effects.
Journal ArticleDOI
Selected reaction monitoring for quantitative proteomics: a tutorial
TL;DR: This tutorial explains the application of SRM for quantitative proteomics, including the selection of proteotypic peptides and the optimization and validation of transitions, and normalization and various factors affecting sensitivity and accuracy are discussed.
Journal ArticleDOI
Vesiclepedia: a compendium for extracellular vesicles with continuous community annotation
Hina Kalra,Richard J. Simpson,Hong Ji,Elena Aikawa,Peter Altevogt,Philip W. Askenase,Vincent C. Bond,Francesc E. Borràs,Xandra O. Breakefield,Vivian Budnik,Edit I. Buzás,Giovanni Camussi,Aled Clayton,Emanuele Cocucci,Juan M. Falcón-Pérez,Susanne Gabrielsson,Yong Song Gho,Dwijendra K. Gupta,H. C. Harsha,An Hendrix,Andrew F. Hill,Jameel M. Inal,Guido Jenster,Eva-Maria Krämer-Albers,Sai Kiang Lim,Alicia Llorente,Jan Lötvall,Antonio Marcilla,Lucia Mincheva-Nilsson,Irina Nazarenko,Rienk Nieuwland,Esther N. M. Nolte-‘t Hoen,Akhilesh Pandey,Tushar Patel,Melissa G. Piper,Stefano Pluchino,T. S. Keshava Prasad,Lawrence Rajendran,Graça Raposo,Michel Record,Gavin E. Reid,Francisco Sánchez-Madrid,Raymond M. Schiffelers,Pia Siljander,Allan Stensballe,Willem Stoorvogel,Douglas D. Taylor,Clotilde Théry,Hadi Valadi,Bas W.M. van Balkom,Jesús Vázquez,Michel Vidal,Marca H. M. Wauben,María Yáñez-Mó,Margot Zoeller,Suresh Mathivanan +55 more
TL;DR: Vesiclepedia is a community-annotated compendium of molecular data on extracellular vesicles that aims to provide a single authoritative source for information on vesicle structure and function.
Journal ArticleDOI
Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics
TL;DR: This work proposes a new targeted proteomics paradigm centered on the use of next generation, quadrupole-equipped high resolution and accurate mass instruments: parallel reaction monitoring (PRM), and suggests that PRM will be a promising new addition to the quantitative proteomics toolbox.
References
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Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
TL;DR: The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
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A Human Protein Atlas for Normal and Cancer Tissues Based on Antibody Proteomics
Mathias Uhlén,Erik Björling,Charlotta Agaton,Cristina Al-Khalili Szigyarto,Bahram Amini,Elisabet Andersen,Ann-Catrin Andersson,Pia Angelidou,Anna Asplund,Caroline Asplund,Lisa Berglund,Kristina Bergström,Harry Brumer,Dijana Cerjan,Marica Ekström,Adila El-Obeid,Cecilia Eriksson,Linn Fagerberg,Ronny Falk,Jenny Fall,Mattias Forsberg,Marcus Gry Björklund,Kristoffer Gumbel,Asif Halimi,Inga Hallin,Carl Hamsten,Marianne Hansson,My Hedhammar,Görel Hercules,Caroline Kampf,Karin Larsson,Mats Lindskog,Wald Lodewyckx,Jan Lund,Joakim Lundeberg,Kristina Magnusson,Erik Malm,Peter Nilsson,Jenny Ödling,Per Oksvold,IngMarie Olsson,Emma Öster,Jenny Ottosson,Linda Paavilainen,Anja Persson,Rebecca Rimini,Johan Rockberg,Marcus Runeson,Åsa Sivertsson,Anna Sköllermo,Johanna Steen,Maria Stenvall,Fredrik Sterky,Sara Strömberg,Mårten Sundberg,Hanna Tegel,Samuel Tourle,Eva Wahlund,Annelie Waldén,Jinghong Wan,Henrik Wernérus,Joakim Westberg,Kenneth Wester,Ulla Wrethagen,Lan Lan Xu,Sophia Hober,Fredrik Pontén +66 more
TL;DR: A new publicly available database containing, in the first version, ∼400,000 high resolution images corresponding to more than 700 antibodies toward human proteins, providing a knowledge base for functional studies and to allow queries about protein profiles in normal and disease tissues.
Journal ArticleDOI
Development of Human Protein Reference Database as an Initial Platform for Approaching Systems Biology in Humans
Suraj Peri,Suraj Peri,J. Daniel Navarro,J. Daniel Navarro,Ramars Amanchy,Troels Z. Kristiansen,Troels Z. Kristiansen,Chandra Kiran Jonnalagadda,Vineeth Surendranath,Vidya Niranjan,Babylakshmi Muthusamy,Tejal K. Gandhi,Mads Grønborg,Mads Grønborg,Nieves Ibarrola,Nandan P. Deshpande,K. Shanker,H N Shivashankar,B. P. Rashmi,M A Ramya,Zhixing Zhao,K N Chandrika,N. Padma,H. C. Harsha,A.J. Yatish,M.P. Kavitha,Minal Menezes,Dipanwita Roy Choudhury,Shubha Suresh,Neelanjana Ghosh,R. Saravana,Sreenath Chandran,Subhalakshmi Krishna,Mary Joy,Sanjeev K. Anand,V. Madavan,Ansamma Joseph,Guang W. Wong,William P. Schiemann,Stefan N. Constantinescu,Lily Jun Shen Huang,Roya Khosravi-Far,Hanno Steen,Muneesh Tewari,Saghi Ghaffari,Gerard C. Blobe,Chi V. Dang,Joe G.N. Garcia,Jonathan Pevsner,Ole N. Jensen,Peter Roepstorff,Krishna S. Deshpande,Arul M. Chinnaiyan,Ada Hamosh,Aravinda Chakravarti,Akhilesh Pandey +55 more
TL;DR: The Human Protein Reference Database (HPRD) as mentioned in this paper is an object database that integrates a wealth of information relevant to the function of human proteins in health and disease, including protein-protein interactions, posttranslational modifications, enzyme/substrate relationships, disease associations, tissue expression, and subcellular localization.
Related Papers (5)
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
Human Protein Reference Database—2009 update
T. S. Keshava Prasad,Renu Goel,Kumaran Kandasamy,Kumaran Kandasamy,Shivakumar Keerthikumar,Sameer Kumar,Suresh Mathivanan,Deepthi Telikicherla,Rajesh Raju,Beema Shafreen,Abhilash K. Venugopal,Lavanya Balakrishnan,Arivusudar Marimuthu,Sutopa Banerjee,Devi S. Somanathan,Aimy Sebastian,Sandhya G. Rani,Somak Ray,C. J. Harrys Kishore,Sashi Kanth,Mukhtar Ahmed,Manoj Kumar Kashyap,Manoj Kumar Kashyap,Riaz Mohmood,Y. L. Ramachandra,Venkatarangaiah Krishna,B. Abdul Rahiman,Subburaman Mohan,Prathibha Ranganathan,Subhashri Ramabadran,Raghothama Chaerkady,Akhilesh Pandey +31 more