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[PMID]:29309430
[Au] Autor:Lilly JL; Gottipati A; Cahall CF; Agoub M; Berron BJ
[Ad] Endereço:Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky, United States of America.
[Ti] Título:Comparison of eosin and fluorescein conjugates for the photoinitiation of cell-compatible polymer coatings.
[So] Source:PLoS One;13(1):e0190880, 2018.
[Is] ISSN:1932-6203
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Targeted photopolymerization is the basis for multiple diagnostic and cell encapsulation technologies. While eosin is used in conjunction with tertiary amines as a water-soluble photoinitiation system, eosin is not widely sold as a conjugate with antibodies and other targeting biomolecules. Here we evaluate the utility of fluorescein-labeled bioconjugates to photopolymerize targeted coatings on live cells. We show that although fluorescein conjugates absorb approximately 50% less light energy than eosin in matched photopolymerization experiments using a 530 nm LED lamp, appreciable polymer thicknesses can still be formed in cell compatible environments with fluorescein photosensitization. At low photoinitiator density, eosin allows more sensitive initiation of gelation. However at higher functionalization densities, the thickness of fluorescein polymer films begins to rival that of eosin. Commercial fluorescein-conjugated antibodies are also capable of generating conformal, protective coatings on mammalian cells with similar viability and encapsulation efficiency as eosin systems.
[Mh] Termos MeSH primário: Materiais Revestidos Biocompatíveis
Amarelo de Eosina-(YS)/química
Fluoresceína/química
Luz
Polímeros/química
[Mh] Termos MeSH secundário: Células A549
Seres Humanos
Análise Serial de Proteínas
Espectrofotometria Ultravioleta
[Pt] Tipo de publicação:COMPARATIVE STUDY; JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL
[Nm] Nome de substância:
0 (Coated Materials, Biocompatible); 0 (Polymers); TDQ283MPCW (Eosine Yellowish-(YS)); TPY09G7XIR (Fluorescein)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180309
[Lr] Data última revisão:
180309
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180109
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0190880


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[PMID]:28460084
[Au] Autor:van der Meulen PM; Barendregt AM; Cuadrado E; Magro-Checa C; Steup-Beekman GM; Schonenberg-Meinema D; Van den Berg JM; Li QZ; Baars PA; Wouters D; Voskuyl AE; Ten Berge IRJM; Huizinga TWJ; Kuijpers TW
[Ad] Endereço:Department of Pediatric Hematology, Immunology and Infectious Diseases, Emma Children's Hospital Academic Medical Center.
[Ti] Título:Protein array autoantibody profiles to determine diagnostic markers for neuropsychiatric systemic lupus erythematosus.
[So] Source:Rheumatology (Oxford);56(8):1407-1416, 2017 Aug 01.
[Is] ISSN:1462-0332
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Objective: The aim was to investigate the association between autoantibodies (autoAbs) and neuropsychiatric (NP) involvement in patients with SLE and to evaluate whether any autoAb or a combination of these autoAbs could indicate the underlying pathogenic process. Methods: Using a multiplexed protein array for 94 antigens, we compared the serum autoAb profiles of 69 NPSLE patients, 203 SLE patients without NP involvement (non-NPSLE) and 51 healthy controls. Furthermore, we compared the profiles of NPSLE patients with clinical inflammatory (n = 38) and ischaemic (n = 31) NP involvement. Results: In total, 75 IgG and 47 IgM autoAbs were associated with SLE patients in comparison with healthy controls. Comparing NPSLE with non-NPSLE and healthy control sera, 9 IgG (amyloid, cardiolipin, glycoprotein 2, glycoprotein 210, heparin, heparan sulphate, histone H2A, prothrombin protein and vimentin) and 12 IgM (amyloid, cardiolipin, centromere protein A, collagen II, histones H2A and H2B, heparan sulphate, heparin, mitochondrial 2, nuclear Mi-2, nucleoporin 62 and vimentin) autoAbs were present at significantly different levels in NPSLE. The combination of IgG autoAbs against heparan sulphate, histone H2B and vimentin could differentiate NPSLE from non-NPSLE (area under the curve 0.845, 99.97% CI: 0.756, 0.933; P < 0.0001). Compared with non-NPSLE, four IgG and seven IgM autoAbs were significantly associated with inflammatory NPSLE. In ischaemic NPSLE, three IgG and three IgM autoAbs were significantly different from non-NPSLE patients. Conclusion: In our cohort, the presence of high levels of anti-heparan sulphate and anti-histone H2B combined with low levels of anti-vimentin IgG autoAbs is highly suggestive of NPSLE. These results need to be validated in external cohorts.
[Mh] Termos MeSH primário: Autoanticorpos/sangue
Vasculite Associada ao Lúpus do Sistema Nervoso Central/diagnóstico
[Mh] Termos MeSH secundário: Adulto
Autoanticorpos/imunologia
Biomarcadores/sangue
Estudos de Casos e Controles
Feminino
Heparitina Sulfato/imunologia
Histonas/imunologia
Seres Humanos
Imunoglobulina G/imunologia
Vasculite Associada ao Lúpus do Sistema Nervoso Central/imunologia
Masculino
Meia-Idade
Análise Serial de Proteínas
Vimentina/imunologia
[Pt] Tipo de publicação:EVALUATION STUDIES; JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Autoantibodies); 0 (Biomarkers); 0 (Histones); 0 (Immunoglobulin G); 0 (Vimentin); 9050-30-0 (Heparitin Sulfate)
[Em] Mês de entrada:1709
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:AIM; IM
[Da] Data de entrada para processamento:170502
[St] Status:MEDLINE
[do] DOI:10.1093/rheumatology/kex073


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[PMID]:28453684
[Au] Autor:Gupta S; De Puysseleyr V; Van der Heyden J; Maddelein D; Lemmens I; Lievens S; Degroeve S; Tavernier J; Martens L
[Ad] Endereço:Medical Biotechnology Center, VIB, Ghent, Belgium.
[Ti] Título:MAPPI-DAT: data management and analysis for protein-protein interaction data from the high-throughput MAPPIT cell microarray platform.
[So] Source:Bioinformatics;33(9):1424-1425, 2017 May 01.
[Is] ISSN:1367-4811
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Summary: Protein-protein interaction (PPI) studies have dramatically expanded our knowledge about cellular behaviour and development in different conditions. A multitude of high-throughput PPI techniques have been developed to achieve proteome-scale coverage for PPI studies, including the microarray based Mammalian Protein-Protein Interaction Trap (MAPPIT) system. Because such high-throughput techniques typically report thousands of interactions, managing and analysing the large amounts of acquired data is a challenge. We have therefore built the MAPPIT cell microArray Protein Protein Interaction-Data management & Analysis Tool (MAPPI-DAT) as an automated data management and analysis tool for MAPPIT cell microarray experiments. MAPPI-DAT stores the experimental data and metadata in a systematic and structured way, automates data analysis and interpretation, and enables the meta-analysis of MAPPIT cell microarray data across all stored experiments. Availability and Implementation: MAPPI-DAT is developed in Python, using R for data analysis and MySQL as data management system. MAPPI-DAT is cross-platform and can be ran on Microsoft Windows, Linux and OS X/macOS. The source code and a Microsoft Windows executable are freely available under the permissive Apache2 open source license at https://github.com/compomics/MAPPI-DAT. Contact: jan.tavernier@vib-ugent.be or lennart.martens@vib-ugent.be. Supplementary information: Supplementary data are available at Bioinformatics online.
[Mh] Termos MeSH primário: Análise Serial de Proteínas/métodos
Mapeamento de Interação de Proteínas/métodos
Software
[Mh] Termos MeSH secundário: Animais
Ensaios de Triagem em Larga Escala/métodos
Seres Humanos
Mamíferos/metabolismo
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180308
[Lr] Data última revisão:
180308
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170429
[St] Status:MEDLINE
[do] DOI:10.1093/bioinformatics/btx014


  4 / 7279 MEDLINE  
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[PMID]:29343722
[Au] Autor:Purohit S; Li T; Guan W; Song X; Song J; Tian Y; Li L; Sharma A; Dun B; Mysona D; Ghamande S; Rungruang B; Cummings RD; Wang PG; She JX
[Ad] Endereço:Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA, 30912, USA.
[Ti] Título:Multiplex glycan bead array for high throughput and high content analyses of glycan binding proteins.
[So] Source:Nat Commun;9(1):258, 2018 01 17.
[Is] ISSN:2041-1723
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:Glycan-binding proteins (GBPs) play critical roles in diverse cellular functions such as cell adhesion, signal transduction and immune response. Studies of the interaction between GBPs and glycans have been hampered by the availability of high throughput and high-content technologies. Here we report multiplex glycan bead array (MGBA) that allows simultaneous analyses of 384 samples and up to 500 glycans in a single assay. The specificity, sensitivity and reproducibility of MGBA are evaluated using 39 plant lectins, 13 recombinant anti-glycan antibodies, and mammalian GBPs. We demonstrate the utility of this platform by the analyses of natural anti-glycan IgM and IgG antibodies in 961 human serum samples and the discovery of anti-glycan antibody biomarkers for ovarian cancer. Our data indicate that the MGBA platform is particularly suited for large population-based studies that require the analyses of large numbers of samples and glycans.
[Mh] Termos MeSH primário: Biomarcadores Tumorais/análise
Polissacarídeos/química
Análise Serial de Proteínas/métodos
[Mh] Termos MeSH secundário: Anticorpos
Biomarcadores Tumorais/química
Feminino
Seres Humanos
Neoplasias Ovarianas/metabolismo
Lectinas de Plantas/química
Lectinas de Plantas/metabolismo
Plantas/metabolismo
Polissacarídeos/imunologia
Polissacarídeos/metabolismo
Bibliotecas de Moléculas Pequenas
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL; VALIDATION STUDIES
[Nm] Nome de substância:
0 (Antibodies); 0 (Biomarkers, Tumor); 0 (Plant Lectins); 0 (Polysaccharides); 0 (Small Molecule Libraries)
[Em] Mês de entrada:1803
[Cu] Atualização por classe:180305
[Lr] Data última revisão:
180305
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180119
[St] Status:MEDLINE
[do] DOI:10.1038/s41467-017-02747-y


  5 / 7279 MEDLINE  
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[PMID]:27774815
[Au] Autor:Kassegne K; Abe EM; Chen JH; Zhou XN
[Ad] Endereço:a National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Key Laboratory of Parasite and Vector Biology of the Chinese Ministry of Health , Shanghai ,
[Ti] Título:Immunomic approaches for antigen discovery of human parasites.
[So] Source:Expert Rev Proteomics;13(12):1091-1101, 2016 12.
[Is] ISSN:1744-8387
[Cp] País de publicação:England
[La] Idioma:eng
[Ab] Resumo:INTRODUCTION: Genetics combined with proteomics allows for a better understanding of parasite-host interactions and host immune responses. Immunomics elucidates that antigens are targets of induced or naturally acquired immunity (NAI), a promising solution to the challenge of eradicating human infections. High-throughput protein microarrays enhance rapid antigen discovery for the development of serodiagnostic tests/vaccines. Areas covered: This review systematically analyzes the emergence of protein microarrays as a powerful technology for parasite antigen discovery and subsequently summarizes some of the attributes and disadvantages of these approaches. Major insights on novel/validated serological biomarkers or vaccine candidates against malaria and Neglected Tropical Diseases (NTDs) are highlighted. We conclude with a brief description of the processes involved in immunomic protein microarrays. Expert commentary: Interesting discoveries have been made using protein microarrays. However, there is a need to evaluate targets that elicit strong immunogenicity and correlates of protective efficacy to aid prioritization and guide further clinical development. The goal of parasitic disease elimination will be best achieved through an integrated strategy that will incorporate and implement the different control components.
[Mh] Termos MeSH primário: Antígenos de Helmintos
Parasitos/imunologia
Análise Serial de Proteínas/métodos
Proteômica/métodos
Vacinas
[Mh] Termos MeSH secundário: Animais
Ensaios de Triagem em Larga Escala/métodos
Seres Humanos
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW; RESEARCH SUPPORT, NON-U.S. GOV'T
[Nm] Nome de substância:
0 (Antigens, Helminth); 0 (Vaccines)
[Em] Mês de entrada:1710
[Cu] Atualização por classe:180228
[Lr] Data última revisão:
180228
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161108
[St] Status:MEDLINE


  6 / 7279 MEDLINE  
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[PMID]:29226663
[Au] Autor:Yamashita YI; Yoshizumi T; Ikegami T; Uchiyama H; Tsujita E; Itoh S; Harimoto N; Soejima Y; Taketomi A; Baba H; Maehara Y
[Ti] Título:Inquiries About Biomarkers of Acute Liver Failure in Patients Who Underwent Living Donor Liver Transplantation Using a Protein Chip Array.
[So] Source:Fukuoka Igaku Zasshi;107(7):131-5, 2016 07.
[Is] ISSN:0016-254X
[Cp] País de publicação:Japan
[La] Idioma:eng
[Ab] Resumo:The causative agent of hepatic encephalopathy (HE) has not been identified with certainty. The recovery of consciousness in patients with acute liver failure (ALF) who underwent liver transplantation (LT) is sometimes drastic ; therefore, we thought that the causative agents of HE would change markedly peri-operatively in these patients. We examined the biomarkers including new agents in the serum of patients using the ProteinChip® System 4000 (Ciphergen Biosystems, Yokohama, JAPAN). Sixteen samples were obtained from four patients with ALF who underwent living donor LT (LDLT) at four time points ; pre-operative, one post-operative day (1POD), 3POD, and 7POD. We used three chips made by the Biomek2000 robot. All duplicated samples were assayed and analyzed using the CiphergenExpressTM data manager. We divided the peri-operative changes in the intensity of identified peaks into seven patterns. The number of peaks whose intensity shows significant changes peri-operatively reached 755. Of course, it is difficult to determine each structure in all 755 peaks ; therefore, we should narrow down the candidates for causative agents of HE in further studies. Our own results suggest that many difficulties lie ahead in determining the causative agent of HE.
[Mh] Termos MeSH primário: Biomarcadores/sangue
Falência Hepática Aguda/diagnóstico
Análise Serial de Proteínas/métodos
[Mh] Termos MeSH secundário: Seres Humanos
Transplante de Fígado
Doadores Vivos
[Pt] Tipo de publicação:CASE REPORTS; JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Biomarkers)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180221
[Lr] Data última revisão:
180221
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:171212
[St] Status:MEDLINE


  7 / 7279 MEDLINE  
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[PMID]:29384851
[Au] Autor:Soe HJ; Yong YK; Al-Obaidi MMJ; Raju CS; Gudimella R; Manikam R; Sekaran SD
[Ad] Endereço:Department of Medical Microbiology.
[Ti] Título:Identifying protein biomarkers in predicting disease severity of dengue virus infection using immune-related protein microarray.
[So] Source:Medicine (Baltimore);97(5):e9713, 2018 Feb.
[Is] ISSN:1536-5964
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Dengue virus is one of the most widespread flaviviruses that re-emerged throughout recent decades. The progression from mild dengue to severe dengue (SD) with the complications such as vascular leakage and hemorrhage increases the fatality rate of dengue. The pathophysiology of SD is not entirely clear. To investigate potential biomarkers that are suggestive of pathogenesis of SD, a small panel of serum samples selected from 1 healthy individual, 2 dengue patients without warning signs (DWS-), 2 dengue patients with warning signs (DWS+), and 5 patients with SD were subjected to a pilot analysis using Sengenics Immunome protein array. The overall fold changes of protein expressions and clustering heat map revealed that PFKFB4, TPM1, PDCL3, and PTPN20A were elevated among patients with SD. Differential expression analysis identified that 29 proteins were differentially elevated greater than 2-fold in SD groups than DWS- and DWS+. From the 29 candidate proteins, pathways enrichment analysis also identified insulin signaling and cytoskeleton pathways were involved in SD, suggesting that the insulin pathway may play a pivotal role in the pathogenesis of SD.
[Mh] Termos MeSH primário: Biomarcadores/sangue
Dengue/sangue
Dengue/imunologia
[Mh] Termos MeSH secundário: Seres Humanos
Projetos Piloto
Análise Serial de Proteínas
Índice de Gravidade de Doença
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Biomarkers)
[Em] Mês de entrada:1802
[Cu] Atualização por classe:180221
[Lr] Data última revisão:
180221
[Sb] Subgrupo de revista:AIM; IM
[Da] Data de entrada para processamento:180201
[St] Status:MEDLINE
[do] DOI:10.1097/MD.0000000000009713


  8 / 7279 MEDLINE  
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[PMID]:28455558
[Au] Autor:O'Connor HF; Huibregtse JM
[Ad] Endereço:Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
[Ti] Título:Enzyme-substrate relationships in the ubiquitin system: approaches for identifying substrates of ubiquitin ligases.
[So] Source:Cell Mol Life Sci;74(18):3363-3375, 2017 09.
[Is] ISSN:1420-9071
[Cp] País de publicação:Switzerland
[La] Idioma:eng
[Ab] Resumo:Protein ubiquitylation is an important post-translational modification, regulating aspects of virtually every biochemical pathway in eukaryotic cells. Hundreds of enzymes participate in the conjugation and deconjugation of ubiquitin, as well as the recognition, signaling functions, and degradation of ubiquitylated proteins. Regulation of ubiquitylation is most commonly at the level of recognition of substrates by E3 ubiquitin ligases. Characterization of the network of E3-substrate relationships is a major goal and challenge in the field, as this expected to yield fundamental biological insights and opportunities for drug development. There has been remarkable success in identifying substrates for some E3 ligases, in many instances using the standard protein-protein interaction techniques (e.g., two-hybrid screens and co-immunoprecipitations paired with mass spectrometry). However, some E3s have remained refractory to characterization, while others have simply not yet been studied due to the sheer number and diversity of E3s. This review will discuss the range of tools and techniques that can be used for substrate profiling of E3 ligases.
[Mh] Termos MeSH primário: Ubiquitina-Proteína Ligases/metabolismo
Ubiquitina/metabolismo
[Mh] Termos MeSH secundário: Sistemas CRISPR-Cas/genética
Seres Humanos
Imunoprecipitação
Análise Serial de Proteínas
Especificidade por Substrato
Ubiquitinação
[Pt] Tipo de publicação:JOURNAL ARTICLE; REVIEW
[Nm] Nome de substância:
0 (Ubiquitin); EC 2.3.2.27 (Ubiquitin-Protein Ligases)
[Em] Mês de entrada:1708
[Cu] Atualização por classe:180131
[Lr] Data última revisão:
180131
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:170430
[St] Status:MEDLINE
[do] DOI:10.1007/s00018-017-2529-6


  9 / 7279 MEDLINE  
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[PMID]:27777341
[Au] Autor:Hu CJ; Pan JB; Song G; Wen XT; Wu ZY; Chen S; Mo WX; Zhang FC; Qian J; Zhu H; Li YZ
[Ad] Endereço:From the ‡Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing, China100730.
[Ti] Título:Identification of Novel Biomarkers for Behcet Disease Diagnosis Using Human Proteome Microarray Approach.
[So] Source:Mol Cell Proteomics;16(2):147-156, 2017 Feb.
[Is] ISSN:1535-9484
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Behcet disease (BD) is a chronic systemic vasculitis and considered as an autoimmune disease. Although rare, BD can be fatal due to ruptured vascular aneurysms or severe neurological complications. To date, no known biomarker has been reported for this disease, making it difficult to diagnosis in the clinics. To undertake this challenge, we employed the HuProt arrays, each comprised of ∼20,000 unique human proteins, to identify BD-specific autoantibodies using a Two-Phase strategy established previously. In Phase I, we profiled the autoimmunity on the HuProt arrays with 75 serum samples collected from 40 BD patients, 15 diagnosed autoimmune patients who suffer from Takayasu arteritis (TA; n = 5)), ANCA associated vasculitis (AAV; n = 5), and Sjogren's syndrome (SS; n = 5), and 20 healthy subjects, and identified 20 candidate autoantigens that were significantly associated with BD. To validate these candidates, in Phase II we constructed a focused array with these 20 candidate BD-associated antigens, and use it to profile a much larger cohort, comprised of serum samples collected from 130 BD patients, 103 autoimmune patients (i.e. 40TA, 40 AAV and 23 SS), and 110 healthy controls. This allowed us to validate CTDP1 (RNA polymerase II subunit A C-terminal domain phosphatase)as a BD-specific autoantigen. The association of anti-CTDP1 with BD patients was further validated using the traditional Western blotting analysis. In conclusion, anti-CTDP1 antibody serves a novel autoantibody for Behcet disease and is expected to help more accurate clinical diagnosis.
[Mh] Termos MeSH primário: Síndrome de Behçet/diagnóstico
Fosfoproteínas Fosfatases/metabolismo
Análise Serial de Proteínas/métodos
Proteômica/métodos
[Mh] Termos MeSH secundário: Adulto
Autoanticorpos/imunologia
Autoantígenos/metabolismo
Síndrome de Behçet/imunologia
Biomarcadores/metabolismo
Feminino
Seres Humanos
Masculino
Meia-Idade
[Pt] Tipo de publicação:JOURNAL ARTICLE
[Nm] Nome de substância:
0 (Autoantibodies); 0 (Autoantigens); 0 (Biomarkers); EC 3.1.3.16 (Phosphoprotein Phosphatases); EC 3.1.3.16 (carboxy-terminal domain phosphatase)
[Em] Mês de entrada:1706
[Cu] Atualização por classe:180201
[Lr] Data última revisão:
180201
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:161026
[St] Status:MEDLINE
[do] DOI:10.1074/mcp.M116.061002


  10 / 7279 MEDLINE  
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[PMID]:29293502
[Au] Autor:Koplev S; Lin K; Dohlman AB; Ma'ayan A
[Ad] Endereço:Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, United States of America.
[Ti] Título:Integration of pan-cancer transcriptomics with RPPA proteomics reveals mechanisms of epithelial-mesenchymal transition.
[So] Source:PLoS Comput Biol;14(1):e1005911, 2018 01.
[Is] ISSN:1553-7358
[Cp] País de publicação:United States
[La] Idioma:eng
[Ab] Resumo:Integrating data from multiple regulatory layers across cancer types could elucidate additional mechanisms of oncogenesis. Using antibody-based protein profiling of 736 cancer cell lines, along with matching transcriptomic data, we show that pan-cancer bimodality in the amounts of mRNA, protein, and protein phosphorylation reveals mechanisms related to the epithelial-mesenchymal transition (EMT). Based on the bimodal expression of E-cadherin, we define an EMT signature consisting of 239 genes, many of which were not previously associated with EMT. By querying gene expression signatures collected from cancer cell lines after small-molecule perturbations, we identify enrichment for histone deacetylase (HDAC) inhibitors as inducers of EMT, and kinase inhibitors as mesenchymal-to-epithelial transition (MET) promoters. Causal modeling of protein-based signaling identifies putative drivers of EMT. In conclusion, integrative analysis of pan-cancer proteomic and transcriptomic data reveals key regulatory mechanisms of oncogenic transformation.
[Mh] Termos MeSH primário: Transição Epitelial-Mesenquimal/genética
Neoplasias/genética
Neoplasias/metabolismo
[Mh] Termos MeSH secundário: Caderinas/genética
Caderinas/metabolismo
Carcinogênese
Linhagem Celular Tumoral
Biologia Computacional
Transição Epitelial-Mesenquimal/efeitos dos fármacos
Inibidores de Histona Desacetilases/farmacologia
Seres Humanos
Modelos Genéticos
Modelos Estatísticos
Neoplasias/patologia
Fosforilação
Análise Serial de Proteínas/estatística & dados numéricos
Inibidores de Proteínas Quinases/farmacologia
Proteômica
RNA Mensageiro/genética
RNA Mensageiro/metabolismo
RNA Neoplásico/genética
RNA Neoplásico/metabolismo
Transcriptoma
[Pt] Tipo de publicação:JOURNAL ARTICLE; RESEARCH SUPPORT, N.I.H., EXTRAMURAL
[Nm] Nome de substância:
0 (CDH1 protein, human); 0 (Cadherins); 0 (Histone Deacetylase Inhibitors); 0 (Protein Kinase Inhibitors); 0 (RNA, Messenger); 0 (RNA, Neoplasm)
[Em] Mês de entrada:1801
[Cu] Atualização por classe:180128
[Lr] Data última revisão:
180128
[Sb] Subgrupo de revista:IM
[Da] Data de entrada para processamento:180103
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pcbi.1005911



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BIREME/OPAS/OMS - Centro Latino-Americano e do Caribe de Informação em Ciências da Saúde