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CORUM: the comprehensive resource of mammalian protein complexes—2009

Andreas Ruepp, Brigitte Waegele, Martin Lechner, Barbara Brauner, Irmtraud Dunger-Kaltenbach, Gisela Fobo, Goar Frishman, Corinna Montrone, H.-Werner Mewes
2009 Nucleic Acids Research  
The new CORUM 2.0 release encompasses 2837 protein complexes offering the largest and most comprehensive publicly available dataset of mammalian protein complexes.  ...  CORUM is a database that provides a manually curated repository of experimentally characterized protein complexes from mammalian organisms, mainly human (64%), mouse (16%) and rat (12%).  ...  ACKNOWLEDGEMENTS The authors thank Thomas Rattei for providing data from SIMAP. FUNDING  ... 
doi:10.1093/nar/gkp914 pmid:19884131 pmcid:PMC2808912 fatcat:d4tg33cdbzevdgzzafsvlia2nu

CORUM: the comprehensive resource of mammalian protein complexes—2019

Madalina Giurgiu, Julian Reinhard, Barbara Brauner, Irmtraud Dunger-Kaltenbach, Gisela Fobo, Goar Frishman, Corinna Montrone, Andreas Ruepp
2018 Nucleic Acids Research  
The new CORUM 3.0 release encompasses 4274 protein complexes offering the largest and most comprehensive publicly available dataset of mammalian protein complexes.  ...  CORUM is a database that provides a manually curated repository of experimentally characterized protein complexes from mammalian organisms, mainly human (67%), mouse (15%) and rat (10%).  ...  In order to provide a high-quality resource of information on mammalian protein complexes, we generated the comprehensive resource of mammalian protein complexes (CO-RUM) with 1750 complexes in the first  ... 
doi:10.1093/nar/gky973 pmid:30357367 pmcid:PMC6323970 fatcat:l6sjbhejtbebdcjlsagorffj4a

Accounting for Redundancy when Integrating Gene Interaction Databases

Antigoni Elefsinioti, Marit Ackermann, Andreas Beyer, Raya Khanin
2009 PLoS ONE  
Knowledge of the interaction partners of an unknown protein allows scientists to understand the complex relationships between genetic products, helps to reveal unknown biological functions and pathways  ...  , and get a more detailed picture of an organism's complexity.  ...  The first one consists of human interactions from the MIPS CORUM database (Comprehensive Resource of Mammalian protein complexes) [16] .  ... 
doi:10.1371/journal.pone.0007492 pmid:19847299 pmcid:PMC2760779 fatcat:ordwpzbb6nh63iyj47a3jobt44

SWATH-MS co-expression profiles reveal paralogue interference in protein complex evolution [article]

Luzia Stalder, Amir Banaei-Esfahani, Rodolfo Ciuffa, Joshua L. Payne, Ruedi Aebersold
2020 bioRxiv   pre-print
trajectories of protein complexes.  ...  Understanding the conservation and evolution of protein complexes is of critical value to decode their function in physiological and pathological processes.  ...  CORUM: The comprehensive resource of mammalian protein 370 complexes-2009. Nucleic Acids Res. 38, 497-501 (2009).371 16. Murali, T. et al.  ... 
doi:10.1101/2020.09.08.287334 fatcat:ytmtfsw5s5fkpcgh6cdedn5msq

Recent advances in large-scale protein interactome mapping

Virja Mehta, Laura Trinkle-Mulcahy
2016 F1000Research  
Ruepp A, Waegele B, Lechner M, et al.: CORUM: the comprehensive resource of mammalian protein complexes--2009. Nucleic Acids Res. 2010; 38(Database issue): D497-501.  ...  The comprehensive mapping of these complex networks of stable and transient associations thus remains a key goal, both for systems biology-based initiatives (where it can be combined with other 'omics'  ...  Importantly, both studies demonstrated significant overlap with the CORUM (Comprehensive Resource of Mammalian protein complexes) database, a manually curated repository of more than 2,800 mammalian protein  ... 
doi:10.12688/f1000research.7629.1 pmid:27158474 pmcid:PMC4856108 fatcat:cp7y4ena3bb7vesllsgazucrcm

A Census of Human Soluble Protein Complexes

Pierre C. Havugimana, G. Traver Hart, Tamás Nepusz, Haixuan Yang, Andrei L. Turinsky, Zhihua Li, Peggy I. Wang, Daniel R. Boutz, Vincent Fong, Sadhna Phanse, Mohan Babu, Stephanie A. Craig (+12 others)
2012 Cell  
in mammalian cells.  ...  protein complexes reported in CORUM.  ... 
doi:10.1016/j.cell.2012.08.011 pmid:22939629 pmcid:PMC3477804 fatcat:krqmk3jy5be2nhlthybyxuxxxq

Interrogation of Mammalian Protein Complex Structure, Function, and Membership Using Genome-Scale Fitness Screens

Joshua Pan, Robin M. Meyers, Brittany C. Michel, Nazar Mashtalir, Ann E. Sizemore, Jonathan N. Wells, Seth H. Cassel, Francisca Vazquez, Barbara A. Weir, William C. Hahn, Joseph A. Marsh, Aviad Tsherniak (+1 others)
2018 Cell Systems  
This study, to the best of our knowledge, represents the largest and most comprehensive analysis of protein complexes using fitness screening in human cells to date.  ...  Fraction of CORUM complex recall is defined as the fraction of CORUM protein complexes (n = 1,331) that exhibit correlations at or above that rank threshold.  ...  CONTACT FOR REAGENT AND RESOURCE SHARING Further information and requests for resources and reagents should be directed to and will be fulfilled by the Lead Contact, Cigall Kadoch  ... 
doi:10.1016/j.cels.2018.04.011 pmid:29778836 pmcid:PMC6152908 fatcat:4pvqocxi7ndlxasxur5i6dntum

Towards a systematic characterization of protein complex function: a natural language processing and machine-learning framework [article]

Varun S Sharma, Andrea Fossati, Rodolfo Ciuffa, Marija Buljan, Evan G Williams, Zhen Chen, Wenguang Shao, Patrick G.A. Pedrioli, Anthony W Purcell, Maria Rodriguez Martinez, Jiangning Song, Matteo Manica (+2 others)
2021 bioRxiv   pre-print
a protein complex query vector, and (2) a supervised approach using Random Forest (RF) models trained specifically for recovering the GO terms of protein complex queries described in the CORUM protein  ...  the potential functions of putative protein complexes.  ...  employed the CORUM database (Giurgiu et al., 2019) as the main resource for the 459 ground-truth annotation of protein complexes with GO terms, as CORUM is a compendium of manually 460 curated and experimentally  ... 
doi:10.1101/2021.02.24.432789 fatcat:qgoj3ntf4nhplhexwkix63kvgm

On the Planarity of Validated Complexes of Model Organisms in Protein-Protein Interaction Networks [chapter]

Kathryn Cooper, Nathan Cornelius, William Gasper, Sanjukta Bhowmick, Hesham Ali
2020 Lecture Notes in Computer Science  
When testing the planarity of known complex subgraphs in S. cerevisiae and selected mammalian PPIs, we find that a majority of validated complexes possess this planar property.  ...  Here, we investigate the planarity property in network models of protein complexes.  ...  and YHTP2008 (n = 400), and other mammalian complexes from the Comprehensive Resource of Mammalian Protein Compleses (CORUM) dataset (See Methods for more detailed information).  ... 
doi:10.1007/978-3-030-50371-0_48 fatcat:oh4mgvcbrfc2xkz23rx5cc5w5u

A comparison of three weighted human gene functional association networks

Jing Zhao, Chun-Lin Wang, Ting-Hong Yang, Bo Li, Xing Chen, Xiaona Shen, Ling Fang
2012 2012 IEEE 6th International Conference on Systems Biology (ISB)  
Gene-gene association or protein-protein interaction databases have been important resource for the study of cellular functions and human diseases.  ...  These years some meta-databases have been built by integrating various resources of gene functional associations and weighing the evidence of each association by some score systems.  ...  ACKNOWLEDGMENT This research was supported by the National Natural Science Foundation of China (10971227).  ... 
doi:10.1109/isb.2012.6314108 dblp:conf/isb/ZhaoWYLCSF12 fatcat:irviplxvkzektjfymohjblfvy4

Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx

Eli Meyer, Galina V Aglyamova, Shi Wang, Jade Buchanan-Carter, David Abrego, John K Colbourne, Bette L Willis, Mikhail V Matz
2009 BMC Genomics  
Our data provide the most comprehensive sequence resource currently available for reef-building corals, and include an extensive collection of potential genetic markers for association and population connectivity  ...  Based on sequence similarity with known proteins, these analyses identified ~11,000 different genes expressed in a range of conditions including thermal stress and settlement induction.  ...  This research was supported in part by the Indiana METACyt Initiative of Indiana University, funded in part through a major grant from the Lilly Endowment, Inc., by the University Information Technology  ... 
doi:10.1186/1471-2164-10-219 pmid:19435504 pmcid:PMC2689275 fatcat:qw3htpuht5hhlaug5zyavex36u

The BioPlex Network: A Systematic Exploration of the Human Interactome

Edward L. Huttlin, Lily Ting, Raphael J. Bruckner, Fana Gebreab, Melanie P. Gygi, John Szpyt, Stanley Tam, Gabriela Zarraga, Greg Colby, Kurt Baltier, Rui Dong, Virginia Guarani (+17 others)
2015 Cell  
BioPlex accurately depicts known complexes, attaining 80%-100% coverage for most CORUM complexes.  ...  The network readily subdivides into communities that correspond to complexes or clusters of functionally related proteins.  ...  This work was supported by the NIH (U41 HG006673 to S.P.  ... 
doi:10.1016/j.cell.2015.06.043 pmid:26186194 pmcid:PMC4617211 fatcat:w467auzm35ebtarqpqr6pbxmry

MoNetFamily: a web server to infer homologous modules and module–module interaction networks in vertebrates

Chun-Yu Lin, Yi-Wei Lin, Shang-Wen Yu, Yu-Shu Lo, Jinn-Moon Yang
2012 Nucleic Acids Research  
MoNetFamily then infers the homologous modules of the selected module candidate using protein-protein interaction (PPI) families.  ...  Finally, MoNetFamily shows the conserved proteins, PPI profiles and functional annotations of the module family.  ...  A total of 1785 protein complexes (three or more proteins) were selected from comprehensive resource of mammalian protein complexes database (CORUM; released on 02 September 2009) (9) and 1252 structure  ... 
doi:10.1093/nar/gks541 pmid:22689643 pmcid:PMC3394321 fatcat:5dqos6mnhvfrflqof6sawmloui

BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain

Reza Pourhaghighi, Peter E.A. Ash, Sadhna Phanse, Florian Goebels, Lucas Z.M. Hu, Siwei Chen, Yingying Zhang, Shayne D. Wierbowski, Samantha Boudeau, Mohamed T. Moutaoufik, Ramy H. Malty, Edyta Malolepsza (+23 others)
2020 Cell Systems  
Connectivity webs mediate the unique biology of the mammalian brain. Yet, while cell circuit maps are increasingly available, knowledge of their underlying molecular networks remains limited.  ...  This brain interaction map (BraInMap) resource facilitates mechanistic exploration of the unique molecular machinery driving core cellular processes of the central nervous system.  ...  This work was supported in part by funds from the ALS Society of Canada, Canadian Institutes of Health Research (FDN-154318) , and the U.S.  ... 
doi:10.1016/j.cels.2020.03.003 pmid:32325033 pmcid:PMC7938770 fatcat:3h373uoidncwvalx6qb65pbarm

iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence

B. Turner, S. Razick, A. L. Turinsky, J. Vlasblom, E. K. Crowdy, E. Cho, K. Morrison, I. M. Donaldson, S. J. Wodak
2010 Database: The Journal of Biological Databases and Curation  
Acknowledgements The authors wish to thank Sandra Orchard for helpful suggestions regarding several iRefWeb features. Conflict of interest statement. None declared. Author Contribution  ...  In CORUM, which specializes in the annotation of mammalian complexes, unique annotations comprise as much as 67% of its records, but for a much smaller pool of records (1749 unique annotations out of 2607  ...  Some focus entirely on interactions in human (HPRD), in mammalian organisms (CORUM, MPPI) or yeast (MPact).  ... 
doi:10.1093/database/baq023 pmid:20940177 pmcid:PMC2963317 fatcat:2o7m36ql4vdbbbix7venxl3i6m
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