CORUM: the comprehensive resource of mammalian protein complexes—2009

Ruepp, Andreas; Waegele, Brigitte; Lechner, Martin; Brauner, Barbara; Dunger-Kaltenbach, Irmtraud; Fobo, Gisela; Frishman, Goar; Montrone, Corinna; Mewes, Hans‐Werner

doi:10.1093/nar/gkp914

Cited by 948 publications

(714 citation statements)

References 29 publications

(38 reference statements)

Supporting

Mentioning

684

Contrasting

Unclassified

Order By: Relevance

“…We used 1,843 protein complexes in H. sapiens from the CORUM database (17) and 409 protein complexes in S. cerevisiae from the CYC2008 database (18). Both databases collect information about experimentally determined protein complexes from the literature.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Controllability in protein interaction networks

Wuchty

2014

Proc. Natl. Acad. Sci. U.S.A.

202

218

View full text Add to dashboard Cite

Recently, the focus of network research shifted to network controllability, prompting us to determine proteins that are important for the control of the underlying interaction webs. In particular, we determined minimum dominating sets of proteins (MDSets) in human and yeast protein interaction networks. Such groups of proteins were defined as optimized subsets where each non-MDSet protein can be reached by an interaction from an MDSet protein.Notably, we found that MDSet proteins were enriched with essential, cancer-related, and virus-targeted genes. Their central position allowed MDSet proteins to connect protein complexes and to have a higher impact on network resilience than hub proteins. As for their involvement in regulatory functions, MDSet proteins were enriched with transcription factors and protein kinases and were significantly involved in bottleneck interactions, regulatory links, phosphorylation events, and genetic interactions.

show abstract

Section: Methodsmentioning

confidence: 99%

“…Using data from the CORUM (Comprehensive Resource of Mammalian protein complexes) database, we collected 1,843 protein complexes in H. sapiens (17) and 409 protein complexes in S. cerevisiae from the CYC2008 database (18). Fig.…”

Section: Significancementioning

confidence: 99%

Controllability in protein interaction networks

Wuchty

2014

Proc. Natl. Acad. Sci. U.S.A.

202

218

View full text Add to dashboard Cite

show abstract

“…We also mapped candidate Cdk1 substrates onto the CORUM protein complex database to determine through which protein complexes and signaling pathways Cdk1 regulates these biological processes (72). The CORUM database is a collection of experimentally characterized protein complexes that are important for the function and regulation of cellular processes.…”

Section: Quantitative Analysis Of the Phosphoproteome Of Flavopiridolmentioning

confidence: 99%

Identification of Candidate Cyclin-dependent kinase 1 (Cdk1) Substrates in Mitosis by Quantitative Phosphoproteomics

Petrone

Adamo

Cheng

et al. 2016

Molecular & Cellular Proteomics

View full text Add to dashboard Cite

An important objective of a cell is to accurately replicate its genetic material and evenly divide along with its subcellular components into two identical daughter cells. To do so, a cell reduces or halts growth, transcription, cap-dependent translation, and undergoes dramatic changes in cellular structure and organization. These changes include chromosome condensation, nuclear envelope breakdown, disassembly of the endoplasmic reticulum and Golgi apparatus, reorganization of the actin cortex, and the formation of the mitotic spindle. Deregulation and errors in these processes can produce nonidentical daughter cells with aberrant chromosome numbers, a state known as aneuploidy and a hallmark of human cancer and the origin of many birth defects (1-5). Therefore, it is imperative that mitosis proceeds in a highly accurate and controlled manner. This is achieved by a sophisticated network of proteins that engage in a multitude of protein-protein interactions regulated by post-translational modifications, including dynamic protein phosphorylation by protein kinases and phosphatases (summarized in (6 -8)).One of the master regulators of mitosis that is conserved from yeast to human is the cyclin-dependent kinase 1 (Cdk1) 1 (9). Cdk1 expression is constant across the cell cycle and the regulation of its activity relies on its association with cyclin A and B, as well as on post-translational modifications including phosphorylation. Specifically, mRNA and protein abundance of cyclin A and B oscillate during the cell cycle due to temporally regulated transcription, translation, and degradation cycles that restrict Cdk1 activity from S-phase to mitosis

show abstract

“…3B). To gain further insight into the functions and interactions of the differentially expressed proteins in P17 KO synaptic fractions, we mapped the genes representing these proteins to the CORUM database (29), which contains curated data on 453 mouse protein complexes. Within this data set, 111 proteins from 183 complexes corresponded to proteins changed at P17.…”

Section: Differentially Expressed Proteins In Fmr1 Ko Mice Show Gene mentioning

confidence: 99%

Fmr1 deficiency promotes age-dependent alterations in the cortical synaptic proteome

Tang

Wang

Wan

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Fragile X syndrome (FXS) is an X-linked neurodevelopmental disorder characterized by severe intellectual disability and other symptoms including autism. Although caused by the silencing of a single gene, Fmr1 (fragile X mental retardation 1), the complexity of FXS pathogenesis is amplified because the encoded protein, FMRP, regulates the activity-dependent translation of numerous mRNAs. Although the mRNAs that associate with FMRP have been extensively studied, little is known regarding the proteins whose expression levels are altered, directly or indirectly, by loss of FMRP during brain development. Here we systematically measured protein expression in neocortical synaptic fractions from Fmr1 knockout (KO) and wild-type (WT) mice at both adolescent and adult stages. Although hundreds of proteins are up-regulated in the absence of FMRP in young mice, this up-regulation is largely diminished in adulthood. Up-regulated proteins included previously unidentified as well as known targets involved in synapse formation and function and brain development and others linked to intellectual disability and autism. Comparison with putative FMRP target mRNAs and autism susceptibility genes revealed substantial overlap, consistent with the idea that the autism endophenotype of FXS is due to a "multiple hit" effect of FMRP loss, particularly within the PSD95 interactome. Through studies of de novo protein synthesis in primary cortical neurons from KO and WT mice, we found that neurons lacking FMRP produce nascent proteins at higher rates, many of which are synaptic proteins and encoded by FMRP target mRNAs. Our results provide a greatly expanded view of protein changes in FXS and identify age-dependent effects of FMRP in shaping the neuronal proteome.fragile X | quantitative mass spectrometry | synaptic protein synthesis | autism | stable isotope labeling F ragile X syndrome (FXS) is an X-linked monogenic disorder that leads to highly debilitating changes in neurodevelopment. Affected individuals exhibit mental retardation, attention deficit and hyperactivity, anxiety, autism spectrum behaviors, and other symptoms that compound overall impairment (1). In the vast majority of cases, FXS is caused by an mRNA-dependent epigenetic silencing of the Fmr1 (fragile X mental retardation 1) gene (2), which occurs secondarily to a CGG repeat expansion in the 5′ UTR region of Fmr1 (3) and results in absence of the encoded protein FMRP. FMRP is an RNA-binding protein that regulates several aspects of mRNA translation (1), transport (4), and stability (5) in neurons. Substantial evidence indicates that FMRP is particularly critical as a suppressor of activity-dependent mRNA translation at glutamatergic synapses (6, 7) and that loss of this function results in abnormalities in dendritic spine shape and several forms of long-term synaptic plasticity (8, 9). In addition, significant changes have been described regarding the structure and/or function of other synaptic systems, including GABAergic and endocannabinoid synapses (10, 11). Loss of FMR...

show abstract

CORUM: the comprehensive resource of mammalian protein complexes—2009

Cited by 948 publications

References 29 publications

Controllability in protein interaction networks

Controllability in protein interaction networks

Identification of Candidate Cyclin-dependent kinase 1 (Cdk1) Substrates in Mitosis by Quantitative Phosphoproteomics

Fmr1 deficiency promotes age-dependent alterations in the cortical synaptic proteome

Contact Info

Product

Resources

About