COMPARTMENTS
COMPARTMENTS is a weekly updated web resource that integrates evidence on protein subcellular localization from manually curated literature, high-throughput screens, automatic text mining, and sequence-based prediction methods. We map all evidence to common protein identifiers and Gene Ontology terms, and further unify it by assigning confidence scores that facilitate comparison of the different types and sources of evidence and visualize these scores on a schematic cell.
Description
More detailed information about this field from each metasource.
COMPARTMENTS is a weekly updated web resource that integrates evidence on protein subcellular localization from manually curated literature, high-throughput screens, automatic text mining, and sequence-based prediction methods. We map all evidence to common protein identifiers and Gene Ontology terms, and further unify it by assigning confidence scores that facilitate comparison of the different types and sources of evidence and visualize these scores on a schematic cell.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:07.403080
Webpage:
https://compartments.jensenlab.org/Webpage
More detailed information about this field from each metasource.
https://compartments.jensenlab.org/
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:07.403080
Licence:
Name: CC-BY-4.0Licence name
More detailed information about this field from each metasource.
Publications:
Publications
More detailed information about this field from each metasource.
COMPARTMENTS: unification and visualization of protein subcellular localization evidence
PMID: 24573882
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:07.403080
Publications
More detailed information about this field from each metasource.
COMPARTMENTS: unification and visualization of protein subcellular localization evidence
PMID: 24573882
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:07.403080
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COMPARTMENTS: unification and visualization of protein subcellular localization evidence
PubMed citations: 163.
163 articles citing: COMPARTMENTS: unification and visualization of protein subcellular localization evidence
PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types. PMID:35208748
Predicting Essential Proteins Based on Integration of Local Fuzzy Fractal Dimension and Subcellular Location Information. PMID:35205217
New immunological potential markers for triple negative breast cancer: IL18R1, CD53, TRIM, Jaw1, LTB, PTPRCAP. PMID:35201443
An Iterative Method for Predicting Essential Proteins Based on Multifeature Fusion and Linear Neighborhood Similarity. PMID:35140599
The Cancer Surfaceome Atlas integrates genomic, functional and drug response data to identify actionable targets. PMID:35121907
Proteomic landscape of SARS-CoV-2- and MERS-CoV-infected primary human renal epithelial cells. PMID:35110370
Subcellular proteomics of dopamine neurons in the mouse brain. PMID:35098924
Single-cell transcriptomic analysis reveals a novel cell state and switching genes during hepatic stellate cell activation in vitro. PMID:35093101
Proteomic screen reveals diverse protein transport between connected neurons in the visual system. PMID:35081342
Tissue differences in the exosomal/small extracellular vesicle proteome and their potential as indicators of altered tissue metabolism. PMID:35045290
Transcriptional Analysis of Nuclear-Encoded Mitochondrial Genes in Eight Neurodegenerative Disorders: The Analysis of Seven Diseases in Reference to Friedreich's Ataxia. PMID:34987545
Differentially Expressed Extracellular Vesicle, Exosome and Non-Exosome miRNA Profile in High and Low Tick-Resistant Beef Cattle. PMID:34976862
E3 ubiquitin ligase Nedd4-2 exerts neuroprotective effects during endoplasmic reticulum stress. PMID:34935153
An integrated multi-omic analysis of iPSC-derived motor neurons from C9ORF72 ALS patients. PMID:34746695
A Novel Collaborative Filtering Model-Based Method for Identifying Essential Proteins. PMID:34745230
Aberrant DNA Methylation-Mediated FOXF2 Dysregulation Is a Prognostic Risk Factor for Gastric Cancer. PMID:34568422
Subcellular proteomics. PMID:34549195
Podocyte-specific KLF4 is required to maintain parietal epithelial cell quiescence in the kidney. PMID:34516901
An iteration model for identifying essential proteins by combining comprehensive PPI network with biological information. PMID:34496745
Human genetic analyses of organelles highlight the nucleus in age-related trait heritability. PMID:34467851
A Novel Method for Identifying Essential Proteins Based on Non-negative Matrix Tri-Factorization. PMID:34422014
A Novel Model for Identifying Essential Proteins Based on Key Target Convergence Sets. PMID:34394201
Evaluation of Colon-Specific Plasma Nanovesicles as New Markers of Colorectal Cancer. PMID:34359806
Thioesterase induction by 2,3,7,8-tetrachlorodibenzo-p-dioxin results in a futile cycle that inhibits hepatic β-oxidation. PMID:34344994
Mapping Autoantibodies in Children With Acute Rheumatic Fever. PMID:34335616
Knock-Out of ACBD3 Leads to Dispersed Golgi Structure, but Unaffected Mitochondrial Functions in HEK293 and HeLa Cells. PMID:34298889
Multi-omics integration of methyltransferase-like protein family reveals clinical outcomes and functional signatures in human cancer. PMID:34285249
Method for Identifying Essential Proteins by Key Features of Proteins in a Novel Protein-Domain Network. PMID:34267785
High expression of DNA damage-inducible transcript 4 (DDIT4) is associated with advanced pathological features in the patients with colorectal cancer. PMID:34211002
Identification of SARS-CoV-2-induced pathways reveals drug repurposing strategies. PMID:34193418
Compartmentalized Proteomic Profiling Outlines the Crucial Role of the Classical Secretory Pathway during Recombinant Protein Production in Chinese Hamster Ovary Cells. PMID:34056395
Computational Biology and Machine Learning Approaches to Understand Mechanistic Microbiome-Host Interactions. PMID:34046017
SARS-CoV-2 infects human adult donor eyes and hESC-derived ocular epithelium. PMID:34022129
A subcellular map of the human kinome. PMID:33988507
Dbnl and β-catenin promote pro-N-cadherin processing to maintain apico-basal polarity. PMID:33939796
The Small GTPases in Fungal Signaling Conservation and Function. PMID:33924947
The Human 2-Cys Peroxiredoxins form Widespread, Cysteine-Dependent- and Isoform-Specific Protein-Protein Interactions. PMID:33923941
Chemotherapy-induced CDA expression renders resistant non-small cell lung cancer cells sensitive to 5'-deoxy-5-fluorocytidine (5'-DFCR). PMID:33874986
Method for Essential Protein Prediction Based on a Novel Weighted Protein-Domain Interaction Network. PMID:33815480
Interactome Mapping of eIF3A in a Colon Cancer and an Immortalized Embryonic Cell Line Using Proximity-Dependent Biotin Identification. PMID:33799492
The role of GDP-l-galactose phosphorylase in the control of ascorbate biosynthesis. PMID:33793952
CEGSO: Boosting Essential Proteins Prediction by Integrating Protein Complex, Gene Expression, Gene Ontology, Subcellular Localization and Orthology Information. PMID:33772722
Down-regulation of solute carrier family 10 member 1 is associated with early recurrence and poorer prognosis of hepatocellular carcinoma. PMID:33763615
Global Profiling of the Lysine Crotonylome in Different Pluripotent States. PMID:33746086
A ligand-receptor interactome platform for discovery of pain mechanisms and therapeutic targets. PMID:33727337
HIR V2: a human interactome resource for the biological interpretation of differentially expressed genes via gene set linkage analysis. PMID:33677507
From fuzziness to precision medicine: on the rapidly evolving proteomics with implications in mitochondrial connectivity to rare human disease. PMID:33521598
Proteome-wide profiling and mapping of post translational modifications in human hearts. PMID:33500497
The human O-GlcNAcome database and meta-analysis. PMID:33479245
Personalized Genome-Scale Metabolic Models Identify Targets of Redox Metabolism in Radiation-Resistant Tumors. PMID:33476554
Multi-responses of O-methyltransferase genes to salt stress and fiber development of Gossypium species. PMID:33430775
Function of Deptor and its roles in hematological malignancies. PMID:33412518
A blood transcriptome-based analysis of disease progression, immune regulation, and symptoms in coronavirus-infected patients. PMID:33293514
Multiple functions of TBCK protein in neurodevelopment disorders and tumors. PMID:33240423
IGF2R-initiated proton rechanneling dictates an anti-inflammatory property in macrophages. PMID:33239287
Predicted rat interactome database and gene set linkage analysis. PMID:33216897
Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy. PMID:33212010
MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations. PMID:33174596
Predicted functional interactome of Caenorhabditis elegans and a web tool for the functional interpretation of differentially expressed genes. PMID:33076954
SYTL4 downregulates microtubule stability and confers paclitaxel resistance in triple-negative breast cancer. PMID:33042263
Mitochondria under the spotlight: On the implications of mitochondrial dysfunction and its connectivity to neuropsychiatric disorders. PMID:33033576
Genomic Signatures of Coevolution between Nonmodel Mammals and Parasitic Roundworms. PMID:32960966
ANDDigest: a new web-based module of ANDSystem for the search of knowledge in the scientific literature. PMID:32921303
Discriminatory Power of Combinatorial Antigen Recognition in Cancer T Cell Therapies. PMID:32916097
Intratumoral generation of photothermal gold nanoparticles through a vectorized biomineralization of ionic gold. PMID:32913195
Oncogenes overexpressed in metastatic oral cancers from patients with pain: potential pain mediators released in exosomes. PMID:32895418
Combining Gene-Disease Associations with Single-Cell Gene Expression Data Provides Anatomy-Specific Subnetworks in Age-Related Macular Degeneration. PMID:32789304
Computational Identification of Tumor Suppressor Genes Based on Gene Expression Profiles in Normal and Cancerous Gastrointestinal Tissues. PMID:32774369
Large-scale informatic analysis to algorithmically identify blood biomarkers of neurological damage. PMID:32764143
Anti-vimentin, anti-TUFM, anti-NAP1L1 and anti-DPYSL2 nanobodies display cytotoxic effect and reduce glioblastoma cell migration. PMID:32426045
Humanization of yeast genes with multiple human orthologs reveals functional divergence between paralogs. PMID:32421706
Lower oxygen consumption and Complex I activity in mitochondria isolated from skeletal muscle of fetal sheep with intrauterine growth restriction. PMID:32396498
Plasma-Derived Extracellular Vesicles Convey Protein Signatures that Reflect Pathophysiology in Lung and Pancreatic Adenocarcinomas. PMID:32370304
A novel method to predict essential proteins based on tensor and HITS algorithm. PMID:32252824
CAMKV Is a Candidate Immunotherapeutic Target in MYCN Amplified Neuroblastoma. PMID:32211329
A Genome-wide ER-phagy Screen Highlights Key Roles of Mitochondrial Metabolism and ER-Resident UFMylation. PMID:32160526
Predicted Drosophila Interactome Resource and web tool for functional interpretation of differentially expressed genes. PMID:32103267
Nucleocytoplasmic Proteomic Analysis Uncovers eRF1 and Nonsense-Mediated Decay as Modifiers of ALS/FTD C9orf72 Toxicity. PMID:32059759
Multi-Omic Analyses of Growth Cones at Different Developmental Stages Provides Insight into Pathways in Adult Neuroregeneration. PMID:32058951
Transcriptomic profiles reveal differences between the right and left ventricle in normoxia and hypoxia. PMID:31960631
Pan-cancer analysis of RNA methyltransferases identifies FTSJ3 as a potential regulator of breast cancer progression. PMID:31957540
The Emerging Role of Cytidine Deaminase in Human Diseases: A New Opportunity for Therapy? PMID:31870623
GPCRs show widespread differential mRNA expression and frequent mutation and copy number variation in solid tumors. PMID:31765370
Comprehensive Transcriptome Profiling of Cryptic CBFA2T3-GLIS2 Fusion-Positive AML Defines Novel Therapeutic Options: A COG and TARGET Pediatric AML Study. PMID:31719049
Common Nodes of Virus-Host Interaction Revealed Through an Integrated Network Analysis. PMID:31636628
Genetic Risk of Arrhythmic Phenotypes in Patients With Dilated Cardiomyopathy. PMID:31514951
Chemical Derivatization of Affinity Matrices Provides Protection from Tryptic Proteolysis. PMID:31498634
Redox Systems Biology: Harnessing the Sentinels of the Cysteine Redoxome. PMID:31368359
Systematic identification of recognition motifs for the hub protein LC8. PMID:31266884
An iteration method for identifying yeast essential proteins from heterogeneous network. PMID:31234779
Gene Information eXtension (GIX): effortless retrieval of gene product information on any website. PMID:31217594
A random walk-based method to identify driver genes by integrating the subcellular localization and variation frequency into bipartite graph. PMID:31088372
The Promoter Regions of Intellectual Disability-Associated Genes Are Uniquely Enriched in LTR Sequences of the MER41 Primate-Specific Endogenous Retrovirus: An Evolutionary Connection Between Immunity and Cognition. PMID:31031802
Protein complex detection based on flower pollination mechanism in multi-relation reconstructed dynamic protein networks. PMID:30925866
Syndecan 1 is a critical mediator of macropinocytosis in pancreatic cancer. PMID:30918400
Design, implementation, and operation of a rapid, robust named entity recognition web service. PMID:30850898
Identification of Essential Proteins Based on Improved HITS Algorithm. PMID:30823614
Analysis of Predicted Host-Parasite Interactomes Reveals Commonalities and Specificities Related to Parasitic Lifestyle and Tissues Tropism. PMID:30815000
Untouchable genes in the human genome: Identifying ideal targets for cancer treatment. PMID:30803560
Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics. PMID:30659192
High-resolution antibody array analysis of proteins from primary human keratinocytes and leukocytes. PMID:30589857
PhytoTypeDB: a database of plant protein inter-cultivar variability and function. PMID:30576486
Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data. PMID:30450911
Regulation of Neuroregeneration by Long Noncoding RNAs. PMID:30401432
UniProt: a worldwide hub of protein knowledge. PMID:30395287
The in silico human surfaceome. PMID:30373828
Antigen discovery and specification of immunodominance hierarchies for MHCII-restricted epitopes. PMID:30349087
Mesenchymal glioblastoma constitutes a major ceRNA signature in the TGF-β pathway. PMID:30279734
Variation among intact tissue samples reveals the core transcriptional features of human CNS cell classes. PMID:30154505
PMLPR: A novel method for predicting subcellular localization based on recommender systems. PMID:30104743
Loss of tumor suppressor IGFBP4 drives epigenetic reprogramming in hepatic carcinogenesis. PMID:29992318
Feature Selection via Swarm Intelligence for Determining Protein Essentiality. PMID:29958434
CDKN1B/p27 is localized in mitochondria and improves respiration-dependent processes in the cardiovascular system-New mode of action for caffeine. PMID:29927970
MinOmics, an Integrative and Immersive Tool for Multi-Omics Analysis. PMID:29927748
Improved flower pollination algorithm for identifying essential proteins. PMID:29745838
Meta-Analysis and Experimental Validation Identified FREM2 and SPRY1 as New Glioblastoma Marker Candidates. PMID:29734672
TISSUES 2.0: an integrative web resource on mammalian tissue expression. PMID:29617745
A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts. PMID:29447159
SAM68 is required for regulation of Pumilio by the NORAD long noncoding RNA. PMID:29386330
LocText: relation extraction of protein localizations to assist database curation. PMID:29343218
HN1L Promotes Triple-Negative Breast Cancer Stem Cells through LEPR-STAT3 Pathway. PMID:29249663
In-Cardiome: integrated knowledgebase for coronary artery disease enabling translational research. PMID:29220465
Prediction of essential proteins based on subcellular localization and gene expression correlation. PMID:29219067
Early pridopidine treatment improves behavioral and transcriptional deficits in YAC128 Huntington disease mice. PMID:29212949
Plasmin reduces fibronectin deposition by mesangial cells in a protease-activated receptor-1 independent manner. PMID:29114573
MIER3 suppresses colorectal cancer progression by down-regulating Sp1, inhibiting epithelial-mesenchymal transition. PMID:28887525
Paired Expression Analysis of Tumor Cell Surface Antigens. PMID:28871274
Autoantibody Repertoire in APECED Patients Targets Two Distinct Subgroups of Proteins. PMID:28861084
Circadian and Feeding Rhythms Orchestrate the Diurnal Liver Acetylome. PMID:28813682
A new computational strategy for identifying essential proteins based on network topological properties and biological information. PMID:28753682
Quantitative Phosphoproteomics Reveals a Role for Collapsin Response Mediator Protein 2 in PDGF-Induced Cell Migration. PMID:28638064
Secretagogin is Expressed by Developing Neocortical GABAergic Neurons in Humans but not Mice and Increases Neurite Arbor Size and Complexity. PMID:28449024
A rapid method for quantifying cytoplasmic versus nuclear localization in endogenous peripheral blood leukocytes by conventional flow cytometry. PMID:28371169
ADH1B: From alcoholism, natural selection, and cancer to the human phenome. PMID:28349588
Thrombus leukocytes exhibit more endothelial cell-specific angiogenic markers than peripheral blood leukocytes do in acute coronary syndrome patients, suggesting a possibility of trans-differentiation: a comprehensive database mining study. PMID:28335793
A Proof of Concept to Bridge the Gap between Mass Spectrometry Imaging, Protein Identification and Relative Quantitation: MSI~LC-MS/MS-LF. PMID:28248242
Genome-Scale Reconstruction of the Human Astrocyte Metabolic Network. PMID:28243200
RNAi reveals proteins for metabolism and protein processing associated with Langat virus infection in Ixodes scapularis (black-legged tick) ISE6 cells. PMID:28086865
Differential HDAC1 and 2 Recruitment by Members of the MIER Family. PMID:28046085
The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. PMID:27924014
Accounting for Protein Subcellular Localization: A Compartmental Map of the Rat Liver Proteome. PMID:27923875
Novel extracellular and nuclear caspase-1 and inflammasomes propagate inflammation and regulate gene expression: a comprehensive database mining study. PMID:27842563
Nuclear Proteomics Uncovers Diurnal Regulatory Landscapes in Mouse Liver. PMID:27818260
Network analysis of mitonuclear GWAS reveals functional networks and tissue expression profiles of disease-associated genes. PMID:27704213
Stemness-related transcriptional factors and homing gene expression profiles in hepatic differentiation and cancer. PMID:27623812
Thyroid malignant neoplasm-associated biomarkers as targets for oncolytic virotherapy. PMID:27579295
Predicting diabetes mellitus genes via protein-protein interaction and protein subcellular localization information. PMID:27535125
Membranome: a database for proteome-wide analysis of single-pass membrane proteins. PMID:27510400
Nuclear import sequence identification in hOAS3 protein. PMID:27379722
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
Genomic similarity between gastroesophageal junction and esophageal Barrett's adenocarcinomas. PMID:27363029
Genic insights from integrated human proteomics in GeneCards. PMID:27048349
Mapping the O-Mannose Glycoproteome in Saccharomyces cerevisiae. PMID:26764011
Plasma Proteome Biomarkers of Inflammation in School Aged Children in Nepal. PMID:26636573
Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad. PMID:26581338
Unexpected features of the dark proteome. PMID:26578815
MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins. PMID:26450961
The nuclear localization pattern and interaction partners of GTF2IRD1 demonstrate a role in chromatin regulation. PMID:26275350
MetazSecKB: the human and animal secretome and subcellular proteome knowledgebase. PMID:26255309
Proteomic and Metabolic Analyses of S49 Lymphoma Cells Reveal Novel Regulation of Mitochondria by cAMP and Protein Kinase A. PMID:26203188
Comprehensive comparison of large-scale tissue expression datasets. PMID:26157623
Rechecking the Centrality-Lethality Rule in the Scope of Protein Subcellular Localization Interaction Networks. PMID:26115027
Computational and experimental approaches to reveal the effects of single nucleotide polymorphisms with respect to disease diagnostics. PMID:24886813
Tags:
Tags
More detailed information about this field from each metasource.
protein targeting and localisation
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:07.403080
natural language processing
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:07.403080
data visualisation
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:07.403080
Tags
More detailed information about this field from each metasource.
protein targeting and localisation
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:07.403080
natural language processing
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:07.403080
data visualisation
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:07.403080
protein targeting and localisation natural language processing data visualisation
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