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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

Quantitative proteomic analysis of prostate tissue specimens identifies deregulated protein complexes in primary prostate cancer

Bo Zhou, Yiwu Yan, Yang Wang, Sungyong You, Michael R. Freeman, Wei Yang
2019 Clinical Proteomics  
To identify specific protein complexes that are deregulated in PCa, quantified proteins were mapped to protein complexes in CORUM (v3.0), a high-quality collection of 4274 experimentally verified mammalian  ...  It may serve as a useful resource for better understanding the deregulation of protein complexes in primary PCa.  ...  Acknowledgements We thank the Cedars-Sinai Biobank and Translational Pathology core for providing the OCT-embedded prostate tissue specimens, the associated clinical information, and the histological analysis  ... 
doi:10.1186/s12014-019-9236-2 pmid:31011308 pmcid:PMC6461817 fatcat:oojr25o5kfgvddagl3envjm2sq

Conservation and divergence of protein pathways in the vertebrate heart

Joel D. Federspiel, Panna Tandon, Caralynn M. Wilczewski, Lauren Wasson, Laura E. Herring, Samvida S. Venkatesh, Ileana M. Cristea, Frank L. Conlon, Maggie Lam
2019 PLoS Biology  
To further investigate functional units within cardiac proteomes, we develop a computational approach to profile the abundance of protein complexes across species.  ...  We uncover mammalian- and amphibian-specific, as well as species-specific, enriched proteins and protein pathways.  ...  Acknowledgments The authors would like to thank the UNC Proteomics Core Facility for mass spectrometry data acquisition.  ... 
doi:10.1371/journal.pbio.3000437 pmid:31490923 pmcid:PMC6750614 fatcat:n4aowmitvvcfhc7vg4eg74id5q

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 368 complexes -2019. Nucleic Acids Res. 47, D559-D563 (2019). 369 15 . 15 Ruepp, A. et al.  ... 
doi:10.1101/2020.09.08.287334 fatcat:ytmtfsw5s5fkpcgh6cdedn5msq

Deep Hyperedges: a Framework for Transductive and Inductive Learning on Hypergraphs [article]

Josh Payne
2019 arXiv   pre-print
From social networks to protein complexes to disease genomes to visual data, hypergraphs are everywhere.  ...  jointly in the hypergraph context, despite a large body of prior work that has shown the utility of deep learning over graphs and sets.  ...  Ruepp, "Corum: the comprehensive resource of mammalian protein complexes-2019," Nucleic acids research, vol. 47, no. D1, pp. D559-D563, 2018. [43] K. Tu, P. Cui, X. Wang, F. Wang, and W.  ... 
arXiv:1910.02633v1 fatcat:hjxcbyjwgzczdftqh4dqvr4ebu

A novel alternative splicing-based prediction model for uteri corpus endometrial carcinoma

Li Gao, Zu-cheng Xie, Jin-shu Pang, Tian-tian Li, Gang Chen
2019 Aging  
Alternative splicing (AS) is crucial a mechanism by which the complexity of mammalian and viral proteom increased overwhelmingly.  ...  There lacks systematic and comprehensive analysis of the prognostic significance of AS profiling landscape for uteri corpus endometrial carcinoma (UCEC).  ...  ACKNOWLEDGEMENTS The authors would like to thank the TCGA Spliceseq and TCGA databases for the availability of the data. CONFLICTS OF INTEREST The authors have no conflicts of interests to declare.  ... 
doi:10.18632/aging.101753 pmid:30640723 pmcid:PMC6339785 fatcat:xsj65cr6bna2jnxkglr5szdl6y

Quantitative Phosphoproteomics Reveals System-Wide Phosphorylation Network Altered by Spry in Mouse Mammary Stromal Fibroblasts

Tiezhu Shi, Linli Yao, Ying Han, Piliang Hao, Pengfei Lu
2019 International Journal of Molecular Sciences  
By applying the quantitative phosphoproteomic analysis of Sprouty proteins (SPRYs), generic modulators of RTK signaling and deleted mouse mammary fibroblasts, we quantified a total of 11,215 unique phosphorylation  ...  Of these, 554 phosphosites, 362 sites on 277 proteins, were significantly increased, whereas 192 sites on 167 proteins were decreased.  ...  Acknowledgments: We thank the Mouse Core Facility at the National Institute for Protein Science Center at Shanghai, and the Molecular & Cell Biology Core Facility, School of Life Science and Technology  ... 
doi:10.3390/ijms20215400 pmid:31671542 pmcid:PMC6862705 fatcat:kffuvgimknh7jornvlbeb7ahpq

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

Multi-omics characterization of interaction-mediated control of human protein abundance levels

Abel Sousa, Emanuel Gonçalves, Bogdan Mirauta, David Ochoa, Oliver Stegle, Pedro Beltrao
2019 Molecular & Cellular Proteomics  
Proteogenomic studies of cancer samples have shown that copy-number variation can be attenuated at the protein level for a large fraction of the proteome, likely due to the degradation of unassembled protein  ...  complex subunits.  ...  Targets in Cancer; CORUM, comprehensive resource of mammalian protein complexes; eQTL, expression Quantatitive Trait Loci; NHGRI, National Human Genome Research Institute; EBI, European Bioinformatics  ... 
doi:10.1074/mcp.ra118.001280 pmid:31239291 pmcid:PMC6692786 fatcat:cbhub4zwzvesnk4dgq7q5bsdgi

Landscape of the Plasmodium Interactome Reveals Both Conserved and Species-Specific Functionality

Charles Hillier, Mercedes Pardo, Lu Yu, Ellen Bushell, Theo Sanderson, Tom Metcalf, Colin Herd, Burcu Anar, Julian C. Rayner, Oliver Billker, Jyoti S. Choudhary
2019 Cell Reports  
This search is hampered by more than one-third of the genes of malaria-causing Plasmodium parasites being uncharacterized.  ...  Our interactome represents a high-confidence map of the native organization of core cellular processes in Plasmodium parasites.  ...  To assess the validity of derived clusters, a cluster was considered to have captured an annotated protein complex from STRING or CORUM if at least half of its proteins had interactions with proteins from  ... 
doi:10.1016/j.celrep.2019.07.019 pmid:31390575 pmcid:PMC6693557 fatcat:pncp4i3e55bpdniknungxj7fo4

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.  ...  We also included the Comprehensive Resource of Mammalian Protein Complexes (CORUM) non-redundant complex dataset downloaded on June 27, 2019 from their website https://mips.helmholtz-muenchen.de/corum/  ... 
doi:10.1007/978-3-030-50371-0_48 fatcat:oh4mgvcbrfc2xkz23rx5cc5w5u

Complex+: Aided Decision-Making for the Study of Protein Complexes [article]

Mehrnoosh Oghbaie, Petr Sulc, David Fenyo, Michael Pennock, John LaCava
2019 bioRxiv   pre-print
Many experimental methods are capable of producing data of use for detecting and inferring the existence of physiological protein complexes.  ...  Knowing the constituents of protein complexes is therefore important for investigating their molecular biology.  ...  curated database of experimental data from mammalian protein complexes.  ... 
doi:10.1101/744656 fatcat:fdnhi5bc4zcz3lu6wezjpkhe3i

A seed-extended algorithm for detecting protein complexes based on density and modularity with topological structure and GO annotations

Rongquan Wang, Caixia Wang, Liyan Sun, Guixia Liu
2019 BMC Genomics  
SE-DMTG to improve the accuracy of protein complex detection.  ...  The detection of protein complexes is of great significance for researching mechanisms underlying complex diseases and developing new drugs.  ...  Acknowledgements The authors would like to thank Wu Min, Tamás  ... 
doi:10.1186/s12864-019-5956-y pmid:31390979 pmcid:PMC6686515 fatcat:r3nltztiibfrrpwu63jibycpve

Protein Interaction Screen on Peptide Matrix (PRISMA) reveals interaction footprints and PTM-dependent interactome of intrinsically disordered C/EBPβ

Gunnar Dittmar, Daniel Perez Hernandez, Elisabeth Kowenz-Leutz, Marieluise Kirchner, Günther Kahlert, Radoslaw Wesolowski, Katharina Baum, Maria Knoblich, Maria Hofstätter, Arnaud Muller, Jana Wolf, Ulf Reimer (+1 others)
2019 iScience  
The results suggest that C/EBPβ acts as a multi-tasking molecular switchboard, integrating signal-dependent modifications and structural plasticity to orchestrate interactions with numerous protein complexes  ...  proteomic analysis of protein interactions.  ...  Altogether, 816 proteins of the PRISMA-derived dataset and 490 proteins of the IP SU-DHL1 dataset were included in any of the 1,432 CORUM complexes.  ... 
doi:10.1016/j.isci.2019.02.026 pmid:30884312 pmcid:PMC6424098 fatcat:zrlhzheaqbb2felj54e6f2mxl4

Rewiring of the Human Mitochondrial Interactome During Neuronal Reprogramming Reveals Regulators of the Respirasome and Neurogenesis

Mohamed Taha Moutaoufik, Ramy Malty, Shahreen Amin, Qingzhou Zhang, Sadhna Phanse, Alla Gagarinova, Mara Zilocchi, Larissa Hoell, Zoran Minic, Maria Gagarinova, Hiroyuki Aoki, Jocelyn Stockwell (+16 others)
2019 iScience  
Mitochondrial protein (MP) assemblies undergo alterations during neurogenesis, a complex process vital in brain homeostasis and disease.  ...  By leveraging the networks, we show the orphan C20orf24 as a respirasome assembly factor whose disruption markedly reduces respiratory chain activity in patients deficient in complex IV.  ...  CORUM: the comprehensive resource of mammalian protein complexes-2009. Nucleic Acids Res. 38, D497-D501.  ... 
doi:10.1016/j.isci.2019.08.057 pmid:31536960 pmcid:PMC6831851 fatcat:owmhktmmjzc4tkxztgymu2on2a
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