R3NK8K last accessed: 2022-11-04

corum
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:36.114175

Other names: The Comprehensive Resource of Mammalian protein complexes, corum

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%). Each protein complex is described by a protein complex name, subunit composition, function as well as the literature reference that characterizes the respective protein complex.

Webpage:

http://mips.helmholtz-muenchen.de/corum/

Licence:

Name: Copyrights
URL: https://mips.helmholtz-muenchen.de/corum/

Publications:

Publications
More detailed information about this field from each metasource.

CORUM: the comprehensive resource of mammalian protein complexes--2009
PMID: 19884131
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:36.114175

CORUM: the comprehensive resource of mammalian protein complexes-2019
PMID: 30357367
metasource: Fairsharing.org
version: FAIRsharing.org: CORUM; CORUM; DOI: https://doi.org/10.25504/FAIRsharing.ohbpNw; Last edited: Dec. 19, 2019, 11:06 a.m.; Last accessed: Jan 03 2022 7:09 p.m.

CORUM: the comprehensive resource of mammalian protein complexes--2009 PubMed citations: 377.

377 articles citing: CORUM: the comprehensive resource of mammalian protein complexes--2009

N(6)-methyladenosine methylation-regulated polo-like kinase 1 cell cycle homeostasis as a potential target of radiotherapy in pancreatic adenocarcinoma. PMID:35773310
An atlas of posttranslational modifications on RNA binding proteins. PMID:35438783
A functional map of HIV-host interactions in primary human T cells. PMID:35365639
Functional buffering via cell-specific gene expression promotes tissue homeostasis and cancer robustness. PMID:35194081
Amyloid-like aggregating proteins cause lysosomal defects in neurons via gain-of-function toxicity. PMID:34933920
A Maximum Flow-Based Approach to Prioritize Drugs for Drug Repurposing of Chronic Diseases. PMID:34832991
Locally Adjust Networks Based on Connectivity and Semantic Similarities for Disease Module Detection. PMID:34759955
Gene Network Analysis of Alzheimer's Disease Based on Network and Statistical Methods. PMID:34682089
Entropy-Based Graph Clustering of PPI Networks for Predicting Overlapping Functional Modules of Proteins. PMID:34681995
Computational repurposing of therapeutic small molecules from cancer to pulmonary hypertension. PMID:34669463
Getting to know each other: PPIMem, a novel approach for predicting transmembrane protein-protein complexes. PMID:34630938
Reassembling protein complexes after controlled disassembly by top-down mass spectrometry in native mode. PMID:34539228
Proteogenomic characterization of pancreatic ductal adenocarcinoma. PMID:34534465
Identifying the dynamic gene regulatory network during latent HIV-1 reactivation using high-dimensional ordinary differential equations. PMID:34531927
Identifying digenic disease genes via machine learning in the Undiagnosed Diseases Network. PMID:34529933
Full-length isoform transcriptome of the developing human brain provides further insights into autism. PMID:34469739
Identification of covalent modifications regulating immune signaling complex composition and phenotype. PMID:34318608
A co-fractionation mass spectrometry-based prediction of protein complex assemblies in the developing rice aleurone-subaleurone. PMID:34270775
Systematic profiling of protein complex dynamics reveals DNA-PK phosphorylation of IFI16 en route to herpesvirus immunity. PMID:34144993
Somatic mutation subtypes of lung adenocarcinoma in East Asian reveal divergent biological characteristics and therapeutic vulnerabilities. PMID:34142036
Proteomic Analysis of Non-human Primate Peripheral Blood Mononuclear Cells During Burkholderia mallei Infection Reveals a Role of Ezrin in Glanders Pathogenesis. PMID:33967974
Peptide array-based interactomics. PMID:33942139
Discovery-Versus Hypothesis-Driven Detection of Protein-Protein Interactions and Complexes. PMID:33923221
Multimerization variants as potential drivers of neofunctionalization. PMID:33771868
Integrated cross-study datasets of genetic dependencies in cancer. PMID:33712601
A Molecular Interaction Map of Klebsiella pneumoniae and Its Human Host Reveals Potential Mechanisms of Host Cell Subversion. PMID:33679637
The regulatory enzymes and protein substrates for the lysine β-hydroxybutyrylation pathway. PMID:33627428
Proteogenomic and metabolomic characterization of human glioblastoma. PMID:33577785
Pan-cancer detection of driver genes at the single-patient resolution. PMID:33517897
MVP predicts the pathogenicity of missense variants by deep learning. PMID:33479230
The cytoprotective protein MANF promotes neuronal survival independently from its role as a GRP78 cofactor. PMID:33460650
Identification of significantly mutated subnetworks in the breast cancer genome. PMID:33436820
Classifying Breast Cancer Molecular Subtypes by Using Deep Clustering Approach. PMID:33324444
Golgi-Dependent Copper Homeostasis Sustains Synaptic Development and Mitochondrial Content. PMID:33208468
Avoid Oversimplifications in Machine Learning: Going beyond the Class-Prediction Accuracy. PMID:33205097
TREM2 Alzheimer's variant R47H causes similar transcriptional dysregulation to knockout, yet only subtle functional phenotypes in human iPSC-derived macrophages. PMID:33198789
Shared Mechanisms Govern HIV Transcriptional Suppression in Circulating CD103+ and Gut CD4+ T Cells. PMID:33115867
Evolution of Sequence-based Bioinformatics Tools for Protein-protein Interaction Prediction. PMID:33093807
Structure-based validation can drastically underestimate error rate in proteome-wide cross-linking mass spectrometry studies. PMID:32994567
NAUTICA: classifying transcription factor interactions by positional and protein-protein interaction information. PMID:32938476
Analytical Guidelines for co-fractionation Mass Spectrometry Obtained through Global Profiling of Gold Standard Saccharomyces cerevisiae Protein Complexes. PMID:32817346
Population-scale proteome variation in human induced pluripotent stem cells. PMID:32773033
Network-based modeling of drug effects on disease module in systemic sclerosis. PMID:32770109
Kinase Interaction Network Expands Functional and Disease Roles of Human Kinases. PMID:32707033
Complex-centric proteome profiling by SEC-SWATH-MS for the parallel detection of hundreds of protein complexes. PMID:32690956
Network-principled deep generative models for designing drug combinations as graph sets. PMID:32657357
mRNA display with library of even-distribution reveals cellular interactors of influenza virus NS1. PMID:32415096
Integration of multiple biological contexts reveals principles of synthetic lethality that affect reproducibility. PMID:32398776
BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain. PMID:32325033
Proteomic and interactomic insights into the molecular basis of cell functional diversity. PMID:32235894
Identification, quantification and bioinformatic analysis of RNA-dependent proteins by RNase treatment and density gradient ultracentrifugation using R-DeeP. PMID:32094787
A Global Screen for Assembly State Changes of the Mitotic Proteome by SEC-SWATH-MS. PMID:32027860
Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D. PMID:31980649
LePrimAlign: local entropy-based alignment of PPI networks to predict conserved modules. PMID:31874635
MaXLinker: Proteome-wide Cross-link Identifications with High Specificity and Sensitivity. PMID:31839598
Molecular determinants of nephron vascular specialization in the kidney. PMID:31836710
Allele-specific single-cell RNA sequencing reveals different architectures of intrinsic and extrinsic gene expression noises. PMID:31799601
Identifying Cancer genes by combining two-rounds RWR based on multiple biological data. PMID:31760937
The Architecture of the Human RNA-Binding Protein Regulatory Network. PMID:31733516
A Computational Framework for Predicting Direct Contacts and Substructures within Protein Complexes. PMID:31717703
Integrative proteomic and phosphoproteomic profiling of prostate cell lines. PMID:31675377
Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes. PMID:31665645
Ancestral reconstruction of protein interaction networks. PMID:31658251
A comprehensive expression landscape of RNA-binding proteins (RBPs) across 16 human cancer types. PMID:31607220
The MTH1 inhibitor TH588 is a microtubule-modulating agent that eliminates cancer cells by activating the mitotic surveillance pathway. PMID:31604991
Quantitative interactomics in primary T cells unveils TCR signal diversification extent and dynamics. PMID:31591574
Rewiring of the Human Mitochondrial Interactome during Neuronal Reprogramming Reveals Regulators of the Respirasome and Neurogenesis. PMID:31536960
Enabling Web-scale data integration in biomedicine through Linked Open Data. PMID:31531395
Chromosome-wide co-fluctuation of stochastic gene expression in mammalian cells. PMID:31525198
Identifying protein complexes based on an edge weight algorithm and core-attachment structure. PMID:31521132
CSF1R inhibitor JNJ-40346527 attenuates microglial proliferation and neurodegeneration in P301S mice. PMID:31504240
A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases. PMID:31494632
Conservation and divergence of protein pathways in the vertebrate heart. PMID:31490923
ComplexBrowser: A Tool for Identification and Quantification of Protein Complexes in Large-scale Proteomics Datasets. PMID:31447428
A seed-extended algorithm for detecting protein complexes based on density and modularity with topological structure and GO annotations. PMID:31390979
A Genome-wide Functional Signature Ontology Map and Applications to Natural Product Mechanism of Action Discovery. PMID:31378711
RITAN: rapid integration of term annotation and network resources. PMID:31355053
PS-MCL: parallel shotgun coarsened Markov clustering of protein interaction networks. PMID:31337329
EPIC: software toolkit for elution profile-based inference of protein complexes. PMID:31308550
A systematic approach to orient the human protein-protein interaction network. PMID:31289271
CTDP1 regulates breast cancer survival and DNA repair through BRCT-specific interactions with FANCI. PMID:31240132
Differential analysis of combinatorial protein complexes with CompleXChange. PMID:31159772
Optimized Cross-Linking Mass Spectrometry for in Situ Interaction Proteomics. PMID:31083951
R-DeeP: Proteome-wide and Quantitative Identification of RNA-Dependent Proteins by Density Gradient Ultracentrifugation. PMID:31076284
Integrating data and knowledge to identify functional modules of genes: a multilayer approach. PMID:31046665
Inferring cancer dependencies on metabolic genes from large-scale genetic screens. PMID:31039782
Quantitative proteomic analysis of prostate tissue specimens identifies deregulated protein complexes in primary prostate cancer. PMID:31011308
Understanding Human-Virus Protein-Protein Interactions Using a Human Protein Complex-Based Analysis Framework. PMID:30984872
A network of human functional gene interactions from knockout fitness screens in cancer cells. PMID:30979825
Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia. PMID:30944321
Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. PMID:30944313
A Network Module for the Perseus Software for Computational Proteomics Facilitates Proteome Interaction Graph Analysis. PMID:30931570
PRISMA: Protein Interaction Screen on Peptide Matrix Reveals Interaction Footprints and Modifications- Dependent Interactome of Intrinsically Disordered C/EBPβ. PMID:30884312
Post-transcriptional regulatory patterns revealed by protein-RNA interactions. PMID:30867517
Functional geometry of protein interactomes. PMID:30821317
An integrative systems genetic analysis of mammalian lipid metabolism. PMID:30814737
Quantification and discovery of sequence determinants of protein-per-mRNA amount in 29 human tissues. PMID:30777893
COmplexome Profiling ALignment (COPAL) reveals remodeling of mitochondrial protein complexes in Barth syndrome. PMID:30649188
A common neighbor based technique to detect protein complexes in PPI networks. PMID:30647726
Complex-centric proteome profiling by SEC-SWATH-MS. PMID:30642884
CoExpresso: assess the quantitative behavior of protein complexes in human cells. PMID:30626316
The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens. PMID:30606230
TICA: Transcriptional Interaction and Coregulation Analyzer. PMID:30578913
High-resolution mapping of cancer cell networks using co-functional interactions. PMID:30573688
iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data. PMID:30567491
Protein Interaction Mapping Identifies RBBP6 as a Negative Regulator of Ebola Virus Replication. PMID:30550789
Automatic gene annotation using GO terms from cellular component domain. PMID:30526566
funcExplorer: a tool for fast data-driven functional characterisation of high-throughput expression data. PMID:30428831
Higher-order molecular organization as a source of biological function. PMID:30423061
Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration. PMID:30389920
Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes. PMID:30357405
CORUM: the comprehensive resource of mammalian protein complexes-2019. PMID:30357367
Revealing the cellular degradome by mass spectrometry analysis of proteasome-cleaved peptides. PMID:30346940
Context-specific interactions in literature-curated protein interaction databases. PMID:30340458
Genomic data integration systematically biases interactome mapping. PMID:30332399
Context-enriched interactome powered by proteomics helps the identification of novel regulators of macrophage activation. PMID:30303482
Context-dependent prediction of protein complexes by SiComPre. PMID:30245847
Comprehensive evaluation of coding region point mutations in microsatellite-unstable colorectal cancer. PMID:30108113
Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery. PMID:30082644
Factors Associated with Heritable Pulmonary Arterial Hypertension Exert Convergent Actions on the miR-130/301-Vascular Matrix Feedback Loop. PMID:30081553
Estrogen receptor-1 is a key regulator of HIV-1 latency that imparts gender-specific restrictions on the latent reservoir. PMID:30061382
Protein-protein interactions of human viruses. PMID:30031213
Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei. PMID:30021884
Classification of Single Particles from Human Cell Extract Reveals Distinct Structures. PMID:29972786
Network-based association analysis to infer new disease-gene relationships using large-scale protein interactions. PMID:29949603
Local and global influences on protein turnover in neurons and glia. PMID:29914620
A systems immunology approach identifies the collective impact of 5 miRs in Th2 inflammation. PMID:29875322
KIAA0100 Modulates Cancer Cell Aggression Behavior of MDA-MB-231 through Microtubule and Heat Shock Proteins. PMID:29867023
Network-Based Disease Module Discovery by a Novel Seed Connector Algorithm with Pathobiological Implications. PMID:29791871
The Eukaryotic Proteome Is Shaped by E3 Ubiquitin Ligases Targeting C-Terminal Degrons. PMID:29779948
Interrogation of Mammalian Protein Complex Structure, Function, and Membership Using Genome-Scale Fitness Screens. PMID:29778836
MLL-fusion-driven leukemia requires SETD2 to safeguard genomic integrity. PMID:29777171
Xpo7 is a broad-spectrum exportin and a nuclear import receptor. PMID:29748336
Measuring phenotype-phenotype similarity through the interactome. PMID:29671400
Analysis of Human Nuclear Protein Complexes by Quantitative Mass Spectrometry Profiling. PMID:29655301
MTGO: PPI Network Analysis Via Topological and Functional Module Identification. PMID:29615773
Functional Precision Medicine Identifies Novel Druggable Targets and Therapeutic Options in Head and Neck Cancer. PMID:29599409
Systematic characterization of pan-cancer mutation clusters. PMID:29572294
SMILE: a novel procedure for subcellular module identification with localisation expansion. PMID:29533218
Toward an integrated map of genetic interactions in cancer cells. PMID:29467179
Defining Pharmacological Targets by Analysis of Virus-Host Protein Interactions. PMID:29459033
Systematic analysis of protein turnover in primary cells. PMID:29449567
Peptide Level Turnover Measurements Enable the Study of Proteoform Dynamics. PMID:29414762
PhenoDis: a comprehensive database for phenotypic characterization of rare cardiac diseases. PMID:29370821
Interactome INSIDER: a structural interactome browser for genomic studies. PMID:29355848
Refine gene functional similarity network based on interaction networks. PMID:29297381
CUFID-query: accurate network querying through random walk based network flow estimation. PMID:29297279
RocSampler: regularizing overlapping protein complexes in protein-protein interaction networks. PMID:29244010
The interactome of intact mitochondria by cross-linking mass spectrometry provides evidence for coexisting respiratory supercomplexes. PMID:29222160
Landscape of the regulatory elements for lysine 2-hydroxyisobutyrylation pathway. PMID:29192674
Protein complex scaffolding predicted as a prevalent function of long non-coding RNAs. PMID:29165713
Top-down characterization of endogenous protein complexes with native proteomics. PMID:29131144
The UCSC Genome Browser database: 2018 update. PMID:29106570
Two missense mutations in KCNQ1 cause pituitary hormone deficiency and maternally inherited gingival fibromatosis. PMID:29097701
Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells. PMID:29089484
CeFra-seq reveals broad asymmetric mRNA and noncoding RNA distribution profiles in Drosophila and human cells. PMID:29079635
Regulatory remodeling in the allo-tetraploid frog Xenopus laevis. PMID:29065907
A rapid and accurate approach for prediction of interactomes from co-elution data (PrInCE). PMID:29061110
The online Tabloid Proteome: an annotated database of protein associations. PMID:29040688
MCM2-regulated functional networks in lung cancer by multi-dimensional proteomic approach. PMID:29038488
A High-Resolution Genome-Wide CRISPR/Cas9 Viability Screen Reveals Structural Features and Contextual Diversity of the Human Cell-Essential Proteome. PMID:29038160
Proteomics of Eosinophil Activation. PMID:29034237
Widespread Post-transcriptional Attenuation of Genomic Copy-Number Variation in Cancer. PMID:29032074
A Compendium of Co-regulated Protein Complexes in Breast Cancer Reveals Collateral Loss Events. PMID:29032073
Rapamycin-induced miR-21 promotes mitochondrial homeostasis and adaptation in mTORC1 activated cells. PMID:29029388
Learning causal networks with latent variables from multivariate information in genomic data. PMID:28968390
Protein complex prediction via dense subgraphs and false positive analysis. PMID:28937982
Detection of dysregulated protein-association networks by high-throughput proteomics predicts cancer vulnerabilities. PMID:28892078
Predicting multicellular function through multi-layer tissue networks. PMID:28881986
PrePhyloPro: phylogenetic profile-based prediction of whole proteome linkages. PMID:28875072
Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells. PMID:28854368
eDGAR: a database of Disease-Gene Associations with annotated Relationships among genes. PMID:28812536
A new computational strategy for identifying essential proteins based on network topological properties and biological information. PMID:28753682
Defining a Cancer Dependency Map. PMID:28753430
Agonist-specific Protein Interactomes of Glucocorticoid and Androgen Receptor as Revealed by Proximity Mapping. PMID:28611094
An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes. PMID:28601559
Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes. PMID:28596423
GLADIATOR: a global approach for elucidating disease modules. PMID:28549478
Systems-wide Studies Uncover Commander, a Multiprotein Complex Essential to Human Development. PMID:28544880
Architecture of the human interactome defines protein communities and disease networks. PMID:28514442
Unbiased Protein Association Study on the Public Human Proteome Reveals Biological Connections between Co-Occurring Protein Pairs. PMID:28480704
Systematic Analyses and Prediction of Human Drug Side Effect Associated Proteins from the Perspective of Protein Evolution. PMID:28391292
Rewiring of the inferred protein interactome during blood development studied with the tool PPICompare. PMID:28376810
Protein complex-based analysis is resistant to the obfuscating consequences of batch effects --- a case study in clinical proteomics. PMID:28361693
The interactome of the copper transporter ATP7A belongs to a network of neurodevelopmental and neurodegeneration factors. PMID:28355134
Proteome-Scale Human Interactomics. PMID:28284537
Protein Kinase CK2: Intricate Relationships within Regulatory Cellular Networks. PMID:28273877
A Comprehensive Gene Expression Meta-analysis Identifies Novel Immune Signatures in Rheumatoid Arthritis Patients. PMID:28210261
TrypsNetDB: An integrated framework for the functional characterization of trypanosomatid proteins. PMID:28158179
Investigation of coordination and order in transcription regulation of innate and adaptive immunity genes in type 1 diabetes. PMID:28143555
The integration of weighted human gene association networks based on link prediction. PMID:28137253
Identification of Entry Factors Involved in Hepatitis C Virus Infection Based on Host-Mimicking Short Linear Motifs. PMID:28129350
Epigenetic profiling of human brain differential DNA methylation networks in schizophrenia. PMID:28117656
Discrete cytosolic macromolecular BRAF complexes exhibit distinct activities and composition. PMID:28093501
Modeling gene-wise dependencies improves the identification of drug response biomarkers in cancer studies. PMID:28082455
Interactome disassembly during apoptosis occurs independent of caspase cleavage. PMID:28082348
Network-based analysis of differentially expressed genes in cerebrospinal fluid (CSF) and blood reveals new candidate genes for multiple sclerosis. PMID:28028462
Somatic Mutation Patterns in Hemizygous Genomic Regions Unveil Purifying Selection during Tumor Evolution. PMID:28027311
Predictability of Genetic Interactions from Functional Gene Modules. PMID:28007839
The mTOR Complex Controls HIV Latency. PMID:27978436
Interactomic analysis of REST/NRSF and implications of its functional links with the transcription suppressor TRIM28 during neuronal differentiation. PMID:27976729
The Search Engine for Multi-Proteoform Complexes: An Online Tool for the Identification and Stoichiometry Determination of Protein Complexes. PMID:27930806
The Proteome of BLOC-1 Genetic Defects Identifies the Arp2/3 Actin Polymerization Complex to Function Downstream of the Schizophrenia Susceptibility Factor Dysbindin at the Synapse. PMID:27927957
An atlas of human kinase regulation. PMID:27909043
Proteomics profiling of interactome dynamics by colocalisation analysis (COLA). PMID:27824369
Local Action with Global Impact: Highly Similar Infection Patterns of Human Viruses and Bacteriophages. PMID:27822522
Integrative omics connects N-glycoproteome-wide alterations with pathways and regulatory events in induced pluripotent stem cells. PMID:27808266
A computational interactome and functional annotation for the human proteome. PMID:27770567
A New Method for Identifying Essential Proteins Based on Network Topology Properties and Protein Complexes. PMID:27529423
Multi-OMICs and Genome Editing Perspectives on Liver Cancer Signaling Networks. PMID:27403431
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
An integer programming framework for inferring disease complexes from network data. PMID:27307626
Outlier analysis of functional genomic profiles enriches for oncology targets and enables precision medicine. PMID:27296290
Endophenotype Network Models: Common Core of Complex Diseases. PMID:27278246
Dysregulated signaling hubs of liver lipid metabolism reveal hepatocellular carcinoma pathogenesis. PMID:27216817
Frequent mutations in acetylation and ubiquitination sites suggest novel driver mechanisms of cancer. PMID:27175787
Recent advances in large-scale protein interactome mapping. PMID:27158474
Identification of Candidate Cyclin-dependent kinase 1 (Cdk1) Substrates in Mitosis by Quantitative Phosphoproteomics. PMID:27134283
Global Membrane Protein Interactome Analysis using In vivo Crosslinking and Mass Spectrometry-based Protein Correlation Profiling. PMID:27114452
Single-Cell Co-expression Analysis Reveals Distinct Functional Modules, Co-regulation Mechanisms and Clinical Outcomes. PMID:27100869
Quantitative Tagless Copurification: A Method to Validate and Identify Protein-Protein Interactions. PMID:27099342
g:Profiler-a web server for functional interpretation of gene lists (2016 update). PMID:27098042
Compensation of Dosage-Sensitive Genes on the Chicken Z Chromosome. PMID:27044516
Proteomics-Based Analysis of Protein Complexes in Pluripotent Stem Cells and Cancer Biology. PMID:27011181
Spatiotemporal variation of mammalian protein complex stoichiometries. PMID:26975353
The human DNA ends proteome uncovers an unexpected entanglement of functional pathways. PMID:26921407
Positional proteomics reveals differences in N-terminal proteoform stability. PMID:26893308
Using contrast patterns between true complexes and random subgraphs in PPI networks to predict unknown protein complexes. PMID:26868667
An informatic framework for decoding protein complexes by top-down mass spectrometry. PMID:26780093
Computational discovery of pathway-level genetic vulnerabilities in non-small-cell lung cancer. PMID:26755624
Identifying communities from multiplex biological networks. PMID:26713261
3CPET: finding co-factor complexes from ChIA-PET data using a hierarchical Dirichlet process. PMID:26694485
A deep proteomics perspective on CRM1-mediated nuclear export and nucleocytoplasmic partitioning. PMID:26673895
Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage. PMID:26658111
Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad. PMID:26581338
Sphingosine kinase 2 is a chikungunya virus host factor co-localized with the viral replication complex. PMID:26576339
MouseNet v2: a database of gene networks for studying the laboratory mouse and eight other model vertebrates. PMID:26527726
NCG 5.0: updates of a manually curated repository of cancer genes and associated properties from cancer mutational screenings. PMID:26516186
Qualitative and Quantitative Protein Complex Prediction Through Proteome-Wide Simulations. PMID:26492574
Identification of Novel Epigenetic Markers of Prostate Cancer by NotI-Microarray Analysis. PMID:26491211
Towards a Hierarchical Strategy to Explore Multi-Scale IP/MS Data for Protein Complexes. PMID:26448546
The Nuclear Proteome of a Vertebrate. PMID:26441354
ncRDeathDB: A comprehensive bioinformatics resource for deciphering network organization of the ncRNA-mediated cell death system. PMID:26431463
Drug-set enrichment analysis: a novel tool to investigate drug mode of action. PMID:26415724
Integrative analysis of human protein, function and disease networks. PMID:26399914
A fast and high performance multiple data integration algorithm for identifying human disease genes. PMID:26399620
Translational compensation of genomic instability in neuroblastoma. PMID:26399178
Panorama of ancient metazoan macromolecular complexes. PMID:26344197
SwissPalm: Protein Palmitoylation database. PMID:26339475
Meta-Analysis of Large-Scale Toxicogenomic Data Finds Neuronal Regeneration Related Protein and Cathepsin D to Be Novel Biomarkers of Drug-Induced Toxicity. PMID:26335687
In vivo hematopoietic Myc activation directs a transcriptional signature in endothelial cells within the bone marrow microenvironment. PMID:26308666
Fmr1 deficiency promotes age-dependent alterations in the cortical synaptic proteome. PMID:26307763
Prediction of problematic complexes from PPI networks: sparse, embedded, and small complexes. PMID:26231465
Comparative proteomics analysis provide novel insight into laminitis in Chinese Holstein cows. PMID:26202328
Prediction of Links and Weights in Networks by Reliable Routes. PMID:26198206
The BioPlex Network: A Systematic Exploration of the Human Interactome. PMID:26186194
Detecting conserved protein complexes using a dividing-and-matching algorithm and unequally lenient criteria for network comparison. PMID:26136815
Global Mapping of the Inc-Human Interactome Reveals that Retromer Restricts Chlamydia Infection. PMID:26118995
Inferring drug-disease associations based on known protein complexes. PMID:26044949
A novel method for identifying disease associated protein complexes based on functional similarity protein complex networks. PMID:25969691
ProtPhylo: identification of protein-phenotype and protein-protein functional associations via phylogenetic profiling. PMID:25956654
Dissecting the calcium-induced differentiation of human primary keratinocytes stem cells by integrative and structural network analyses. PMID:25946651
MIMP: predicting the impact of mutations on kinase-substrate phosphorylation. PMID:25938373
Essentiality and centrality in protein interaction networks revisited. PMID:25880655
A DIseAse MOdule Detection (DIAMOnD) algorithm derived from a systematic analysis of connectivity patterns of disease proteins in the human interactome. PMID:25853560
Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST. PMID:25754993
Characterization of protein complexes and subcomplexes in protein-protein interaction databases. PMID:25722891
An integrative approach for a network based meta-analysis of viral RNAi screens. PMID:25691914
A combined proteomics/genomics approach links hepatitis C virus infection with nonsense-mediated mRNA decay. PMID:25616068
Evolutionary constraint and disease associations of post-translational modification sites in human genomes. PMID:25611800
Reconstructing genome-wide protein-protein interaction networks using multiple strategies with homologous mapping. PMID:25602759
Discovery of small protein complexes from PPI networks with size-specific supervised weighting. PMID:25559663
Network-based association of hypoxia-responsive genes with cardiovascular diseases. PMID:25530704
Transcriptome alterations of mitochondrial and coagulation function in schizophrenia by cortical sequencing analysis. PMID:25522158
Complex-based analysis of dysregulated cellular processes in cancer. PMID:25521701
The EHEC-host interactome reveals novel targets for the translocated intimin receptor. PMID:25519916
Systems Medicine: from molecular features and models to the clinic in COPD. PMID:25471042
A proteome-scale map of the human interactome network. PMID:25416956
Identifying disease genes by integrating multiple data sources. PMID:25350511
Incorporating computational resources in a cancer research program. PMID:25324189
The complex portal--an encyclopaedia of macromolecular complexes. PMID:25313161
Linear motif-mediated interactions have contributed to the evolution of modularity in complex protein interaction networks. PMID:25299147
Elucidating the genotype-phenotype relationships and network perturbations of human shared and specific disease genes from an evolutionary perspective. PMID:25287147
Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions. PMID:25275790
Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis. PMID:25236784
Construction and analysis of the protein-protein interaction networks based on gene expression profiles of Parkinson's disease. PMID:25170921
Unbiased functional clustering of gene variants with a phenotypic-linkage network. PMID:25166029
Fractionation profiling: a fast and versatile approach for mapping vesicle proteomes and protein-protein interactions. PMID:25165137
Asymmetric mRNA localization contributes to fidelity and sensitivity of spatially localized systems. PMID:25150862
The human plasma membrane peripherome: visualization and analysis of interactions. PMID:25057483
Functional gene groups are concentrated within chromosomes, among chromosomes and in the nuclear space of the human genome. PMID:25056310
Building a hierarchical organization of protein complexes out of protein association data. PMID:24978199
Deep proteomics of the Xenopus laevis egg using an mRNA-derived reference database. PMID:24954049
Proteomics analysis of the non-muscle myosin heavy chain IIa-enriched actin-myosin complex reveals multiple functions within the podocyte. PMID:24949636
Increasing the precision of orthology-based complex prediction through network alignment. PMID:24918034
A loss of function analysis of host factors influencing Vaccinia virus replication by RNA interference. PMID:24901222
A draft map of the human proteome. PMID:24870542
Contemporary network proteomics and its requirements. PMID:24833333
An integrated map of HIV-human protein complexes that facilitate viral infection. PMID:24817247
Controllability in protein interaction networks. PMID:24778220
PPSampler2: predicting protein complexes more accurately and efficiently by sampling. PMID:24565288
Prioritizing protein complexes implicated in human diseases by network optimization. PMID:24565064
Prediction of protein interaction types based on sequence and network features. PMID:24564924
Analysis of schizophrenia and hepatocellular carcinoma genetic network with corresponding modularity and pathways: novel insights to the immune system. PMID:24564241
Systematic large-scale study of the inheritance mode of Mendelian disorders provides new insight into human diseasome. PMID:24448549
Dissecting the expression landscape of RNA-binding proteins in human cancers. PMID:24410894
Transcriptional profiling reveals molecular signatures associated with HIV permissiveness in Th1Th17 cells and identifies peroxisome proliferator-activated receptor gamma as an intrinsic negative regulator of viral replication. PMID:24359430
Global screening of CK2 kinase substrates by an integrated phosphoproteomics workflow. PMID:24322422
Integrating in silico resources to map a signaling network. PMID:24233784
Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements. PMID:24218641
FunCoup 3.0: database of genome-wide functional coupling networks. PMID:24185702
Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome. PMID:24183448
HoPaCI-DB: host-Pseudomonas and Coxiella interaction database. PMID:24137008
The mutational landscape of phosphorylation signaling in cancer. PMID:24089029
Characterization of native protein complexes and protein isoform variation using size-fractionation-based quantitative proteomics. PMID:24043423
HSC-explorer: a curated database for hematopoietic stem cells. PMID:23936191
Summarizing cellular responses as biological process networks. PMID:23895181
Genome-wide generation and systematic phenotyping of knockout mice reveals new roles for many genes. PMID:23870131
Genome evolution predicts genetic interactions in protein complexes and reveals cancer drug targets. PMID:23851603
Complementing the Eukaryotic Protein Interactome. PMID:23825550
Dissecting the Characteristics and Dynamics of Human Protein Complexes at Transcriptome Cascade Using RNA-Seq Data. PMID:23824284
Human monogenic disease genes have frequently functionally redundant paralogs. PMID:23696728
Biological basis of miRNA action when their targets are located in human protein coding region. PMID:23671676
All or nothing: protein complexes flip essentiality between distantly related eukaryotes. PMID:23661563
The network organization of cancer-associated protein complexes in human tissues. PMID:23567845
Improved method for protein complex detection using bottleneck proteins. PMID:23566214
Comparative network-based recovery analysis and proteomic profiling of neurological changes in valproic acid-treated mice. PMID:23557376
Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines. PMID:23511206
Novel semantic similarity measure improves an integrative approach to predicting gene functional associations. PMID:23497449
Protein complex-based analysis framework for high-throughput data sets. PMID:23443684
Predicting physical interactions between protein complexes. PMID:23438732
Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers. PMID:23340843
Predicting PDZ domain mediated protein interactions from structure. PMID:23336252
PCDq: human protein complex database with quality index which summarizes different levels of evidences of protein complexes predicted from h-invitational protein-protein interactions integrative dataset. PMID:23282181
Supervised maximum-likelihood weighting of composite protein networks for complex prediction. PMID:23281936
Identification of novel type 2 diabetes candidate genes involved in the crosstalk between the mitochondrial and the insulin signaling systems. PMID:23236286
Network rewiring is an important mechanism of gene essentiality change. PMID:23198090
Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions. PMID:23157382
Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target prediction. PMID:23146171
Novel genes and pathways modulated by syndecan-1: implications for the proliferation and cell-cycle regulation of malignant mesothelioma cells. PMID:23144729
Integrating many co-splicing networks to reconstruct splicing regulatory modules. PMID:23046974
Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease. PMID:23013645
Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells. PMID:22968442
A census of human soluble protein complexes. PMID:22939629
Dissecting the gene network of dietary restriction to identify evolutionarily conserved pathways and new functional genes. PMID:22912585
Minireview: progress and challenges in proteomics data management, sharing, and integration. PMID:22902541
A high-throughput approach for measuring temporal changes in the interactome. PMID:22863883
Computational framework for analysis of prey-prey associations in interaction proteomics identifies novel human protein-protein interactions and networks. PMID:22845868
Sets2Networks: network inference from repeated observations of sets. PMID:22824380
CIDeR: multifactorial interaction networks in human diseases. PMID:22809392
Detecting mutually exclusive interactions in protein-protein interaction maps. PMID:22715412
Algorithm to identify frequent coupled modules from two-layered network series: application to study transcription and splicing coupling. PMID:22697243
MoNetFamily: a web server to infer homologous modules and module-module interaction networks in vertebrates. PMID:22689643
Interactions of an Arabidopsis RanBPM homologue with LisH-CTLH domain proteins revealed high conservation of CTLH complexes in eukaryotes. PMID:22676313
NetAligner--a network alignment server to compare complexes, pathways and whole interactomes. PMID:22618871
Cis-acting polymorphisms affect complex traits through modifications of microRNA regulation pathways. PMID:22606281
Community of protein complexes impacts disease association. PMID:22549411
Mapping the protein interaction network of the human COP9 signalosome complex using a label-free QTAX strategy. PMID:22474085
Construction and analysis of the protein-protein interaction networks for schizophrenia, bipolar disorder, and major depression. PMID:22373040
A novel framework for the comparative analysis of biological networks. PMID:22363585
Rare coding SNP in DZIP1 gene associated with late-onset sporadic Parkinson's disease. PMID:22355768
Modularity in protein complex and drug interactions reveals new polypharmacological properties. PMID:22279562
Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins. PMID:22278370
Recovering protein-protein and domain-domain interactions from aggregation of IP-MS proteomics of coregulator complexes. PMID:22219718
Global landscape of HIV-human protein complexes. PMID:22190034
The role of miRNAs in complex formation and control. PMID:22180412
iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database. PMID:22115179
The BioLexicon: a large-scale terminological resource for biomedical text mining. PMID:21992002
Functional analysis beyond enrichment: non-redundant reciprocal linkage of genes and biological terms. PMID:21949701
ppiTrim: constructing non-redundant and up-to-date interactomes. PMID:21873645
Selection for translation efficiency on synonymous polymorphisms in recent human evolution. PMID:21803767
Integrative analysis of many weighted co-expression networks using tensor computation. PMID:21698123
Analysis of the human endogenous coregulator complexome. PMID:21620140
ConsensusPathDB: toward a more complete picture of cell biology. PMID:21071422
PROMISCUOUS: a database for network-based drug-repositioning. PMID:21071407
Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks. PMID:20532046
A lentiviral functional proteomics approach identifies chromatin remodeling complexes important for the induction of pluripotency. PMID:20305087
CORUM: the comprehensive resource of mammalian protein complexes-2019 PubMed citations: 185.

185 articles citing: CORUM: the comprehensive resource of mammalian protein complexes-2019

Biological interacting units identified in human protein networks reveal tissue-functional diversification and its impact on disease. PMID:35891788
Multi-Level Biological Network Analysis and Drug Repurposing Based on Leukocyte Transcriptomics in Severe COVID-19: In Silico Systems Biology to Precision Medicine. PMID:35887528
Shared mechanisms across the major psychiatric and neurodegenerative diseases. PMID:35882878
ZetaSuite: computational analysis of two-dimensional high-throughput data from multi-target screens and single-cell transcriptomics. PMID:35879727
A supervised protein complex prediction method with network representation learning and gene ontology knowledge. PMID:35879648
Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery. PMID:35831314
Resolving missing protein problems using functional class scoring. PMID:35790756
Zika Virus Strains and Dengue Virus Induce Distinct Proteomic Changes in Neural Stem Cells and Neurospheres. PMID:35732867
SubCellBarCode: integrated workflow for robust spatial proteomics by mass spectrometry. PMID:35732783
PCfun: a hybrid computational framework for systematic characterization of protein complex function. PMID:35724564
Single-cell analysis reveals X upregulation is not global in pre-gastrulation embryos. PMID:35707719
Computational identification of protein complexes from network interactions: Present state, challenges, and the way forward. PMID:35685359
Immune-Related Protein Interaction Network in Severe COVID-19 Patients toward the Identification of Key Proteins and Drug Repurposing. PMID:35625619
Regulation of protein complex partners as a compensatory mechanism in aneuploid tumors. PMID:35575458
Arginine Methyltransferase PRMT7 Deregulates Expression of RUNX1 Target Genes in T-Cell Acute Lymphoblastic Leukemia. PMID:35565298
IMEx Databases: Displaying Molecular Interactions into a Single, Standards-Compliant Dataset. PMID:35507258
Membranome 3.0: Database of single-pass membrane proteins with AlphaFold models. PMID:35481632
Biometal Dyshomeostasis in Olfactory Mucosa of Alzheimer's Disease Patients. PMID:35456941
Integrated In Silico Analyses Identify PUF60 and SF3A3 as New Spliceosome-Related Breast Cancer RNA-Binding Proteins. PMID:35453681
DUX4 is a multifunctional factor priming human embryonic genome activation. PMID:35402882
Physical and functional interactome atlas of human receptor tyrosine kinases. PMID:35384245
SPCS: a spatial and pattern combined smoothing method for spatial transcriptomic expression. PMID:35380614
Multi-omics protein-coding units as massively parallel Bayesian networks: Empirical validation of causality structure. PMID:35355520
Integrative multi-omics and drug response profiling of childhood acute lymphoblastic leukemia cell lines. PMID:35354797
Computational methods, databases and tools for synthetic lethality prediction. PMID:35352098
Network Crosstalk as a Basis for Drug Repurposing. PMID:35350247
AutoCoEv-A High-Throughput In Silico Pipeline for Predicting Inter-Protein Coevolution. PMID:35328772
Genome-wide transcript and protein analysis highlights the role of protein homeostasis in the aging mouse heart. PMID:35277432
OpenCell: Endogenous tagging for the cartography of human cellular organization. PMID:35271311
Human transcription factor protein interaction networks. PMID:35140242
Evolutionary rewiring of regulatory networks contributes to phenotypic differences between human and mouse orthologous genes. PMID:35137181
PSL-LCCL: a resource for subcellular protein localization in liver cancer cell line SK_HEP1. PMID:35134877
CTCFL regulates the PI3K-Akt pathway and it is a target for personalized ovarian cancer therapy. PMID:35132075
A knowledge graph to interpret clinical proteomics data. PMID:35102292
Protein signatures to distinguish aggressive from indolent prostate cancer. PMID:35098564
Complexome Profiling-Exploring Mitochondrial Protein Complexes in Health and Disease. PMID:35096826
Simple But Efficacious Enrichment of Integral Membrane Proteins and Their Interactions for In-Depth Membrane Proteomics. PMID:35085786
Comparative assessment of genes driving cancer and somatic evolution in non-cancer tissues: an update of the Network of Cancer Genes (NCG) resource. PMID:35078504
Betacoronavirus-specific alternate splicing. PMID:35074468
Label-free visual proteomics: Coupling MS- and EM-based approaches in structural biology. PMID:35063097
Identification of a glioma functional network from gene fitness data using machine learning. PMID:35044082
Multiomic analysis identifies CPT1A as a potential therapeutic target in platinum-refractory, high-grade serous ovarian cancer. PMID:35028612
Protein complexes detection based on node local properties and gene expression in PPI weighted networks. PMID:34991441
Super.Complex: A supervised machine learning pipeline for molecular complex detection in protein-interaction networks. PMID:34972161
An Improved Memetic Algorithm for Detecting Protein Complexes in Protein Interaction Networks. PMID:34970305
Dosage sensitivity and exon shuffling shape the landscape of polymorphic duplicates in Drosophila and humans. PMID:34969986
Characterization of In Vivo Protein Complexes via Chemical Cross-Linking and Mass Spectrometry. PMID:34962381
Gene Ontology Enrichment Analysis of Renal Agenesis: Improving Prenatal Molecular Diagnosis. PMID:34899145
Proteogenomics of non-small cell lung cancer reveals molecular subtypes associated with specific therapeutic targets and immune evasion mechanisms. PMID:34870237
GFI1 tethers the NuRD complex to open and transcriptionally active chromatin in myeloid progenitors. PMID:34857890
ConsensusPathDB 2022: molecular interactions update as a resource for network biology. PMID:34850110
Germline biallelic mutation affecting the transcription factor Helios causes pleiotropic defects of immunity. PMID:34826259
IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis. PMID:34755877
Co-evolution based machine-learning for predicting functional interactions between human genes. PMID:34753957
Tumor relevant protein functional interactions identified using bipartite graph analyses. PMID:34728699
Complex Portal 2022: new curation frontiers. PMID:34718729
Analysis of multiple gene co-expression networks to discover interactions favoring CFTR biogenesis and ΔF508-CFTR rescue. PMID:34717611
The spliceosome pathway activity correlates with reduced anti-tumor immunity and immunotherapy response, and unfavorable clinical outcomes in pan-cancer. PMID:34667536
Multiomic profiling of the liver across diets and age in a diverse mouse population. PMID:34666007
A global cancer data integrator reveals principles of synthetic lethality, sex disparity and immunotherapy. PMID:34663427
OnTheFly2.0: a text-mining web application for automated biomedical entity recognition, document annotation, network and functional enrichment analysis. PMID:34632381
Efficient and accurate identification of protein complexes from protein-protein interaction networks based on the clustering coefficient. PMID:34630943
Getting to know each other: PPIMem, a novel approach for predicting transmembrane protein-protein complexes. PMID:34630938
Proteome-wide mapping of short-lived proteins in human cells. PMID:34626566
Novel ACE2 protein interactions relevant to COVID-19 predicted by evolutionary rate correlations. PMID:34616619
A protein network map of head and neck cancer reveals PIK3CA mutant drug sensitivity. PMID:34591642
Interpretation of cancer mutations using a multiscale map of protein systems. PMID:34591613
Identifying Protein Complexes With Clear Module Structure Using Pairwise Constraints in Protein Interaction Networks. PMID:34512712
Enzymes in the Cholesterol Synthesis Pathway: Interactomics in the Cancer Context. PMID:34440098
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
CANVS: an easy-to-use application for the analysis and visualization of mass spectrometry-based protein-protein interaction/association data. PMID:34432510
Multi-layered proteogenomic analysis unravels cancer metastasis directed by MMP-2 and focal adhesion kinase signaling. PMID:34429501
Characterizing Endogenous Protein Complexes with Biological Mass Spectrometry. PMID:34406752
Patients with PWS and related syndromes display differentially methylated regions involved in neurodevelopmental and nutritional trajectory. PMID:34389046
The molecular basis, genetic control and pleiotropic effects of local gene co-expression. PMID:34376650
FLAME: A Web Tool for Functional and Literature Enrichment Analysis of Multiple Gene Lists. PMID:34356520
Revealing protein-protein interactions at the transcriptome scale by sequencing. PMID:34348091
Heterogeneous Expression of Nuclear Encoded Mitochondrial Genes Distinguishes Inhibitory and Excitatory Neurons. PMID:34312306
Transfer learning via multi-scale convolutional neural layers for human-virus protein-protein interaction prediction. PMID:34273146
Mitochondrial Proteostasis Requires Genes Encoded in a Neurodevelopmental Syndrome Locus. PMID:34261699
An Azo Coupling-Based Chemoproteomic Approach to Systematically Profile the Tyrosine Reactivity in the Human Proteome. PMID:34251175
Betacoronavirus-specific alternate splicing. PMID:34230929
Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients. PMID:34223192
Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. PMID:34214467
Linear functional organization of the omic embedding space. PMID:34213534
Meta-analysis defines principles for the design and analysis of co-fractionation mass spectrometry experiments. PMID:34211188
Reduced mGluR5 Activity Modulates Mitochondrial Function. PMID:34199502
Super.Complex: A supervised machine learning pipeline for molecular complex detection in protein-interaction networks. PMID:34189530
Prediction of Human-Plasmodium vivax Protein Associations From Heterogeneous Network Structures Based on Machine-Learning Approach. PMID:34188457
FINER: enhancing the prediction of tissue-specific functions of isoforms by refining isoform interaction networks. PMID:34169280
mPPI: a database extension to visualize structural interactome in a one-to-many manner. PMID:34156447
Phosphoproteomic identification of ULK substrates reveals VPS15-dependent ULK/VPS34 interplay in the regulation of autophagy. PMID:34121209
Mapping Proximity Associations of Core Spindle Assembly Checkpoint Proteins. PMID:34087075
Estimates of gene ensemble noise highlight critical pathways and predict disease severity in H1N1, COVID-19 and mortality in sepsis patients. PMID:34031464
Comprehensive analysis of the lysine acetylome and succinylome in the hippocampus of gut microbiota-dysbiosis mice. PMID:34026284
A method for benchmarking genetic screens reveals a predominant mitochondrial bias. PMID:34018332
Human Immunodeficiency Virus Type 1 Vpr Mediates Degradation of APC1, a Scaffolding Component of the Anaphase-Promoting Complex/Cyclosome. PMID:34011540
Characterization and comparison of gene-centered human interactomes. PMID:34010955
hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies. PMID:33973408
Proteo3Dnet: a web server for the integration of structural information with interactomics data. PMID:33963857
Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. PMID:33961781
A New Sequential Forward Feature Selection (SFFS) Algorithm for Mining Best Topological and Biological Features to Predict Protein Complexes from Protein-Protein Interaction Networks (PPINs). PMID:33959851
Peptide array-based interactomics. PMID:33942139
Detecting Protein Communities in Native Cell Extracts by Machine Learning: A Structural Biologist's Perspective. PMID:33937337
CladeOScope: functional interactions through the prism of clade-wise co-evolution. PMID:33928243
Discovery-Versus Hypothesis-Driven Detection of Protein-Protein Interactions and Complexes. PMID:33923221
A New Framework for Discovering Protein Complex and Disease Association via Mining Multiple Databases. PMID:33905111
G-Protein-coupled Estrogen Receptor 1 Agonist G-1 Perturbs Sunitinib Resistance-related Phosphoproteomic Signatures in Renal Cell Carcinoma. PMID:33893075
MultiVERSE: a multiplex and multiplex-heterogeneous network embedding approach. PMID:33888761
Arena3Dweb: interactive 3D visualization of multilayered networks. PMID:33885790
DUSP7 regulates the activity of ERK2 to promote proper chromosome alignment during cell division. PMID:33865857
PCprophet: a framework for protein complex prediction and differential analysis using proteomic data. PMID:33859439
Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication. PMID:33849620
Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV. PMID:33845483
Profiling PRMT methylome reveals roles of hnRNPA1 arginine methylation in RNA splicing and cell growth. PMID:33782401
Genetic disruption of WASHC4 drives endo-lysosomal dysfunction and cognitive-movement impairments in mice and humans. PMID:33749590
ZFTA Translocations Constitute Ependymoma Chromatin Remodeling and Transcription Factors. PMID:33741711
Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell. PMID:33688646
Analysing the yeast complexome-the Complex Portal rising to the challenge. PMID:33677561
Global variability analysis of mRNA and protein concentrations across and within human tissues. PMID:33575562
Transcriptome profiling of insulin sensitive tissues from GH deficient mice following GH treatment. PMID:33433889
ChIP-seq of plasma cell-free nucleosomes identifies gene expression programs of the cells of origin. PMID:33432199
PC2P: Parameter-free network-based prediction of protein complexes. PMID:33416831
Interactions between nascent proteins translated by adjacent ribosomes drive homomer assembly. PMID:33384371
SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles. PMID:33333029
FIREWORKS: a bottom-up approach to integrative coessentiality network analysis. PMID:33328249
Comprehensive gene expression profiling of human astrocytes treated with a hepatic encephalopathy-inducible factor, alpha 1-antichymotripsin. PMID:33299931
RBP2GO: a comprehensive pan-species database on RNA-binding proteins, their interactions and functions. PMID:33196814
Evolution of Sequence-based Bioinformatics Tools for Protein-protein Interaction Prediction. PMID:33093807
CEN-tools: an integrative platform to identify the contexts of essential genes. PMID:33073517
Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. PMID:33060197
A strategy to incorporate prior knowledge into correlation network cutoff selection. PMID:33056991
Surfaceome dynamics reveal proteostasis-independent reorganization of neuronal surface proteins during development and synaptic plasticity. PMID:33020478
Quantitative analysis of global protein stability rates in tissues. PMID:32994440
Functional genomic landscape of cancer-intrinsic evasion of killing by T cells. PMID:32968282
Affinity proteomic dissection of the human nuclear cap-binding complex interactome. PMID:32960270
Systematic analysis of bypass suppression of essential genes. PMID:32939983
Mutations of the Transcriptional Corepressor ZMYM2 Cause Syndromic Urinary Tract Malformations. PMID:32891193
Classification in biological networks with hypergraphlet kernels. PMID:32886115
Analytical Guidelines for co-fractionation Mass Spectrometry Obtained through Global Profiling of Gold Standard Saccharomyces cerevisiae Protein Complexes. PMID:32817346
Mitochondria and Peroxisome Remodeling across Cytomegalovirus Infection Time Viewed through the Lens of Inter-ViSTA. PMID:32726614
Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes. PMID:32697802
Complex-centric proteome profiling by SEC-SWATH-MS for the parallel detection of hundreds of protein complexes. PMID:32690956
HBA-DEALS: accurate and simultaneous identification of differential expression and splicing using hierarchical Bayesian analysis. PMID:32660516
Comprehensive nucleosome interactome screen establishes fundamental principles of nucleosome binding. PMID:32658293
Network-based characterization of disease-disease relationships in terms of drugs and therapeutic targets. PMID:32657408
A Genetic Map of the Response to DNA Damage in Human Cells. PMID:32649862
The Global Phosphorylation Landscape of SARS-CoV-2 Infection. PMID:32645325
Predicting Functions of Uncharacterized Human Proteins: From Canonical to Proteoforms. PMID:32575886
Dynamic rewiring of the human interactome by interferon signaling. PMID:32539747
A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing. PMID:32511329
A novel landscape of nuclear human CDK2 substrates revealed by in situ phosphorylation. PMID:32494624
Integration of Heterogeneous Experimental Data Improves Global Map of Human Protein Complexes. PMID:32457940
BpForms and BcForms: a toolkit for concretely describing non-canonical polymers and complexes to facilitate global biochemical networks. PMID:32423472
A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. PMID:32353859
Systematic analysis of lysine acetylome and succinylome reveals the correlation between modification of H2A.X complexes and DNA damage response in breast cancer. PMID:32236595
Proteomic and interactomic insights into the molecular basis of cell functional diversity. PMID:32235894
An atlas of human metabolism. PMID:32209698
A Pan-plant Protein Complex Map Reveals Deep Conservation and Novel Assemblies. PMID:32191846
Structural Biology in the Multi-Omics Era. PMID:32129623
Keeping the Proportions of Protein Complex Components in Check. PMID:32105631
Exploring Integrative Analysis Using the BioMedical Evidence Graph. PMID:32097025
Heterogeneous Network Model to Identify Potential Associations Between Plasmodium vivax and Human Proteins. PMID:32075230
Multi-Omic Analyses of Growth Cones at Different Developmental Stages Provides Insight into Pathways in Adult Neuroregeneration. PMID:32058951
Temporal dynamics of protein complex formation and dissociation during human cytomegalovirus infection. PMID:32041945
Human and mouse essentiality screens as a resource for disease gene discovery. PMID:32005800
Quantitative Proteomics of the Cancer Cell Line Encyclopedia. PMID:31978347
Lessons from equilibrium statistical physics regarding the assembly of protein complexes. PMID:31871201
Next-generation Interactomics: Considerations for the Use of Co-elution to Measure Protein Interaction Networks. PMID:31792070
PRMT1-mediated methylation of the microprocessor-associated proteins regulates microRNA biogenesis. PMID:31777917
The great hairball gambit. PMID:31770365
Systematic bromodomain protein screens identify homologous recombination and R-loop suppression pathways involved in genome integrity. PMID:31753913
Quantitative Phosphoproteomics Reveals System-Wide Phosphorylation Network Altered by Spry in Mouse Mammary Stromal Fibroblasts. PMID:31671542
Paralog buffering contributes to the variable essentiality of genes in cancer cell lines. PMID:31652272
MTGO-SC, A Tool to Explore Gene Modules in Single-Cell RNA Sequencing Data. PMID:31649730
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. PMID:31647099
Candidate Genes and MiRNAs Linked to the Inverse Relationship Between Cancer and Alzheimer's Disease: Insights From Data Mining and Enrichment Analysis. PMID:31608105
Mapping the protein-protein and genetic interactions of cancer to guide precision medicine. PMID:31288129
Multi-omics Characterization of Interaction-mediated Control of Human Protein Abundance levels. PMID:31239291
Identification of Crucial Candidate Genes and Pathways in Glioblastoma Multiform by Bioinformatics Analysis. PMID:31137733
WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs. PMID:31114916
g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update). PMID:31066453
Quantitative proteomic analysis of prostate tissue specimens identifies deregulated protein complexes in primary prostate cancer. PMID:31011308
Identification of antiviral roles for the exon-junction complex and nonsense-mediated decay in flaviviral infection. PMID:30833725
The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection. PMID:30626175

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More detailed information about this field from each metasource.

functional domain
metasource: Fairsharing.org
version: FAIRsharing.org: CORUM; CORUM; DOI: https://doi.org/10.25504/FAIRsharing.ohbpNw; Last edited: Dec. 19, 2019, 11:06 a.m.; Last accessed: Jan 03 2022 7:09 p.m.

molecular function
metasource: Fairsharing.org
version: FAIRsharing.org: CORUM; CORUM; DOI: https://doi.org/10.25504/FAIRsharing.ohbpNw; Last edited: Dec. 19, 2019, 11:06 a.m.; Last accessed: Jan 03 2022 7:09 p.m.

protein-containing complex
metasource: Fairsharing.org
version: FAIRsharing.org: CORUM; CORUM; DOI: https://doi.org/10.25504/FAIRsharing.ohbpNw; Last edited: Dec. 19, 2019, 11:06 a.m.; Last accessed: Jan 03 2022 7:09 p.m.

metabolic and signaling pathways
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

protein-protein interactions
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

bioinformatics
metasource: re3data.org
version: re3data.org: The Comprehensive Resource of Mammalian protein complexes; editing status 2021-04-30; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NK8K last accessed: 2022-11-04

genetics
metasource: re3data.org
version: re3data.org: The Comprehensive Resource of Mammalian protein complexes; editing status 2021-04-30; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NK8K last accessed: 2022-11-04

genomics
metasource: re3data.org
version: re3data.org: The Comprehensive Resource of Mammalian protein complexes; editing status 2021-04-30; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NK8K last accessed: 2022-11-04

proteomics
metasource: re3data.org
version: re3data.org: The Comprehensive Resource of Mammalian protein complexes; editing status 2021-04-30; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3NK8K last accessed: 2022-11-04

protein interactions
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:36.114175

protein targeting and localisation
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:36.114175

functional domain molecular function protein-containing complex metabolic and signaling pathways protein-protein interactions bioinformatics genetics genomics proteomics protein interaction protein targeting and localisation

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Negatome

Complex Portal

MAtDB2

MIPSPlantsDB

PROtein-protein compleX MutAtion ThErmodynamics Database

The Complex Portal

TRIP

Protein Protein Interaction Inhibition Database

SIMAP

MFunGD

Database of fuzzy protein complexes

InterEvol database : Diving into the structure and evolution of protein complex interfaces

Human Protein-Protein Interaction rEference

DNAproDB

HoPaCI-DB

Dockground

The Protein Database

InterDom

PRotein Ontology

Protein-protein interfaces