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Id: biblio-1011407
Autor: Yin, Hongtao; Yu, Yan.
Título: Identification of the targets of hematoporphyrin derivative in lung adenocarcinoma using integrated network analysis
Fonte: Biol. Res;52:4, 2019. tab, graf.
Idioma: en.
Resumo: BACKGROUND: Hematoporphyrin derivative (HPD) has a sensibilization effect in lung adenocarcinoma. This study was conducted to identify the target genes of HPD in lung adenocarcinoma. METHODS: RNA sequencing was performed using the lung adenocarcinoma cell line A549 after no treatment or treatment with X-ray or X-ray + HPD. The differentially expressed genes (DEGs) were screened using Mfuzz package by noise-robust soft clustering analysis. Enrichment analysis was carried out using "BioCloud" online tool. Protein-protein interaction (PPI) network and module analyses were performed using Cytoscape software. Using WebGestalt tool and integrated transcription factor platform (ITFP), microRNA target and transcription factor (TF) target pairs were separately predicted. An integrated regulatory network was visualized with Cytoscape software. RESULTS: A total of 815 DEGs in the gene set G1 (continuously dysregulated genes along with changes in processing conditions [untreated-treated with X-ray-X-ray + treated with HPD]) and 464 DEGs in the gene set G2 (significantly dysregulated between X-ray + HPD-treated group and untreated/X-ray-treated group) were screened. The significant module identified from the PPI network for gene set G1 showed that ribosomal protein L3 (RPL3) gene could interact with heat shock protein 90 kDa alpha, class A member 1 (HSP90AA1). TFs AAA domain containing 2 (ATAD2) and protein inhibitor of activated STAT 1 (PIAS1) were separately predicted for the genes in gene set G1 and G2, respectively. In the integrated network for gene set G2, ubiquitin-specific peptidase 25 (USP25) was targeted by miR-200b, miR-200c, and miR-429. CONCLUSION: RPL3, HSP90AA1, ATAD2, and PIAS1 as well as USP25, which is targeted by miR-200b, miR-200c, and miR-429, may be the potential targets of HPD in lung adenocarcinoma.
Descritores: Derivado da Hematoporfirina/farmacologia
Redes Reguladoras de Genes/genética
Adenocarcinoma de Pulmão/genética
Neoplasias Pulmonares/genética
-Proteínas Ribossômicas/efeitos dos fármacos
Proteínas Ribossômicas/genética
Fatores de Transcrição
Análise por Conglomerados
Regulação Neoplásica da Expressão Gênica
Análise de Sequência de RNA
Proteínas de Choque Térmico HSP90/efeitos dos fármacos
Proteínas de Choque Térmico HSP90/genética
Proteínas Modificadoras Pequenas Relacionadas à Ubiquitina/efeitos dos fármacos
Proteínas Modificadoras Pequenas Relacionadas à Ubiquitina/genética
MicroRNAs/metabolismo
Linhagem Celular Tumoral
Proteínas de Ligação a DNA/efeitos dos fármacos
Proteínas de Ligação a DNA/genética
Proteínas Inibidoras de STAT Ativados/efeitos dos fármacos
Proteínas Inibidoras de STAT Ativados/genética
Citometria de Fluxo
ATPases Associadas a Diversas Atividades Celulares/efeitos dos fármacos
ATPases Associadas a Diversas Atividades Celulares/genética
Adenocarcinoma de Pulmão/tratamento farmacológico
Adenocarcinoma de Pulmão/radioterapia
Neoplasias Pulmonares/tratamento farmacológico
Neoplasias Pulmonares/radioterapia
Limites: Humanos
Responsável: CL1.1 - Biblioteca Central


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Id: biblio-889318
Autor: Jiang, Xue; Feng, Lichun; Dai, Baoqiang; Li, Liping; Lu, Weiwei.
Título: Identification of key genes involved in nasopharyngeal carcinoma / Identificação dos principais genes envolvidos no carcinoma nasofaríngeo
Fonte: Braz. j. otorhinolaryngol. (Impr.);83(6):670-676, Nov.-Dec. 2017. tab, graf.
Idioma: en.
Resumo: Abstract Introduction: Nasopharyngeal carcinoma is the most common cancer originating from the nasopharynx. Objective: To study the mechanisms of nasopharyngeal carcinoma, we analyzed GSE12452 microarray data. Methods: GSE12452 was downloaded from the Gene Expression Omnibus database and included 31 nasopharyngeal carcinoma samples and 10 normal nasopharyngeal tissue samples. The differentially expressed genes were screened by ANOVA in the PGS package. Using the BiNGO plugin in Cytoscape and pathway enrichment analysis in the PGS package, functional and pathway enrichment analyses were performed separately to predict potential functions of the differentially expressed genes. Furthermore, Transcription factor-differentially expressed gene pairs were searched, and then the transcription factor-differentially expressed gene regulatory network was visualized using Cytoscape software. Results: A total of 487 genes were screened as differentially expressed genes between the nasopharyngeal carcinoma samples and the normal nasopharyngeal tissue samples. Enrichment analysis indicated that PTGS2 was involved in the regulation of biological process and small cell lung cancer. ZIC2 and OVOL1 may function in nasopharyngeal carcinoma through targeting significantly up-regulated genes (such as PTGS2, FN1, CXCL9 and CXCL10) in the Transcription factor-differentially expressed gene regulatory network (e.g., ZIC2→PTGS2 and OVOL1→CXCL10). Conclusion: PTGS2, FN1, CXCL9, CXCL10, ZIC2 and OVOL1 might play roles in nasopharyngeal carcinoma.

Resumo Introdução: O carcinoma nasofaríngeo é o câncer mais comum originário da nasofaringe. Objetivo: Estudar os mecanismos do câncer de nasofaringe; dados do microarray GSE12452 foram analisados. Método: GSE12452 foi obtido da base de dados Gene Expression Omnibus e inclui 31 amostras de carcinoma nasofaríngeo e 10 amostras de tecido nasofaríngeo normal. Os genes diferencialmente expressos foram analisados por ANOVA no kit PGS. Usando o plugin BiNGO no Cytoscape e análise de enriquecimento da via no kit PGS, análises de enriquecimento funcional e da via foram realizadas separadamente para prever as potenciais funções dos genes diferencialmente expressos. Além disso, os pares Fator de Transcrição - genes diferencialmente expressos foram pesquisados e em seguida a sua rede reguladora foi visualizada usando o programa Cytoscape. Resultados: Um total de 487 genes foram analisados como genes diferencialmente expressos entre as amostras de carcinoma nasofaríngeo e amostras de tecido nasofaríngeo normal. A análise de enriquecimento indicou que PTGS2 estava envolvido na regulação do processo biológico e câncer pulmonar de pequenas células. ZIC2 e OVOL1 podem funcionar no carcinoma nasofaríngeo almejando-se de maneira significativa os genes suprarregulados (como o PTGS2, FN1, CXCL9 e CXCL10) na rede reguladora de fator de transcrição - genes diferencialmente expressos (p.ex., ZIC2→PTGS2 e OVOL1→CXCL10). Conclusão: PTGS2, FN1, CXCL9, CXCL10, ZIC2 e OVOL1 podem desempenhar alguns papéis no carcinoma de nasofaringe.
Descritores: Carcinoma/genética
Expressão Gênica
Neoplasias Nasofaríngeas/genética
-Fatores de Transcrição/genética
Proteínas Nucleares/genética
Carcinoma/patologia
Análise por Conglomerados
Regulação para Baixo
Regulação para Cima
Neoplasias Nasofaríngeas/patologia
Análise de Variância
Perfilação da Expressão Gênica
Bases de Dados Genéticas
Análise em Microsséries
Redes Reguladoras de Genes
Quimiocina CXCL9/genética
Quimiocina CXCL10/genética
Carcinoma Nasofaríngeo
Limites: Humanos
Responsável: BR1.1 - BIREME


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Id: biblio-1087161
Autor: Yin, Ronghuan; Wang, Yanru; Wang, Zeying; Zhu, Yubo; Cong, Yuyan; Wang, Wei; Deng, Liang; Liu, Haiying; Guo, Dan; Bai, Wenlin.
Título: Discovery and molecular analysis of conserved circRNAs from cashmere goat reveal their integrated regulatory network and potential roles in secondary hair follicle
Fonte: Electron. j. biotechnol;41:37-47, sept. 2019. tab, graf, ilus.
Idioma: en.
Projeto: National Natural Science Foundation of China; . Key Project Foundation of Educational Department of Liaoning Province, China; . Innovative Talent Support Program Foundation of Universities and Colleges in Liaoning Province, China; . Science and Technology Innovation Talent Support Foundation for Young and Middle-aged People of Shenyang City, China.
Resumo: Background: Circular RNAs, a novel class in the eukaryotic transcriptome, are characterized by the 3' and 5' ends that are covalently joined in a covalently closed loop without free ends. Circular RNAs are considerably stable molecules and act as microRNA sponges with regulatory potential to the protein-coding genes. Results: Eight circular RNAs were found to be significantly upregulated at anagen skin tissue of cashmere goat compared with their counterparts at telogen. Rich and complex regulatory patterns were revealed among the eight upregulated circular RNAs at anagen and related miRNAs with their potential regulatory genes. The potential regulatory genes of eight upregulated circular RNAs at anagen were involved in several pathways related to the main physiological process of hair follicle, such as histone acetylation and axon. For chi_circ_1926, chi_circ_3541, chi_circ_0483, chi_circ_3196, and chi_circ_2092, overall, the relative expression in secondary hair follicle exhibited highly similar trends with their corresponding host genes during the different stages of the hair follicle cycle. However, the expression trends of chi_circ_0100, chi_circ_2829, and chi_circ_1967 were found to diverge from their corresponding host genes during the different stages of the hair follicle cycle. Conclusions: A total of eighteen circular RNAs were identified and characterized from skin tissue of cashmere goat. The eight upregulated circular RNAs at anagen might have significant roles in the secondary hair follicle of cashmere goat. Our results would provide a novel regulatory layer to elucidate the molecular mechanisms underlying the development of secondary hair follicle and the growth of cashmere fiber in cashmere goat.
Descritores: Cabras/genética
Folículo Piloso/crescimento & desenvolvimento
RNA Circular/genética
-Pele
Expressão Gênica
Biologia Computacional
MicroRNAs
Células Eucarióticas
Redes Reguladoras de Genes
Transcriptoma
RNA Circular/metabolismo
Limites: Animais
Responsável: CL1.1 - Biblioteca Central


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Id: biblio-1055347
Autor: Camilo, Caroline; Maschietto, Mariana; Vieira, Henrique C; Tahira, Ana C; Gouveia, Gisele R; Feio dos Santos, Ana C; Negrão, André B; Ribeiro, Marcelo; Laranjeira, Ronaldo; Vallada, Homero; Brentani, Helena.
Título: Genome-wide DNA methylation profile in the peripheral blood of cocaine and crack dependents
Fonte: Braz. J. Psychiatry (São Paulo, 1999, Impr.);41(6):485-493, Nov.-Dec. 2019. tab, graf.
Idioma: en.
Projeto: FAPESP; . CAPES; PROEX; . MM and ACT were supported by FAPESP.
Resumo: Objective: Cocaine use disorders (CUDs) represent a major public health problem in many countries. To better understand the interaction between the environmental modulations and phenotype, the aim of the present study was to investigate the DNA methylation pattern of CUD patients, who had concomitant cocaine and crack dependence, and healthy controls. Methods: We studied DNA methylation profiles in the peripheral blood of 23 CUD patients and 24 healthy control subjects using the Illumina Infinium HumanMethylation450 BeadChip arrays. Results: Comparison between CUD patients and controls revealed 186 differentially methylated positions (DMPs; adjusted p-value [adjP] < 10-5) related to 152 genes, with a subset of CpGs confirmed by pyrosequencing. DNA methylation patterns discriminated CUD patients and control groups. A gene network approach showed that the EHMT1, EHMT2, MAPK1, MAPK3, MAP2K1, and HDAC5 genes, which are involved in transcription and chromatin regulation cellular signaling pathways, were also associated with cocaine dependence. Conclusion: The investigation of DNA methylation patterns may contribute to a better understanding of the biological mechanisms involved in CUD.
Descritores: Cocaína Crack
Metilação de DNA
Transtornos Relacionados ao Uso de Cocaína/genética
Transtornos Relacionados ao Uso de Cocaína/sangue
Estudo de Associação Genômica Ampla/métodos
-Estudos de Casos e Controles
Modelos Lineares
Histona-Lisina N-Metiltransferase/genética
Estatísticas não Paramétricas
Proteína Quinase 1 Ativada por Mitógeno/genética
MAP Quinase Quinase 1/genética
Proteína Quinase 3 Ativada por Mitógeno/genética
Redes Reguladoras de Genes
Sequenciamento de Nucleotídeos em Larga Escala
Antígenos de Histocompatibilidade/genética
Histona Desacetilases/genética
Limites: Humanos
Masculino
Adulto
Adulto Jovem
Responsável: BR1.1 - BIREME


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Id: biblio-1001087
Autor: Tao, Qiu; Tianyu, Wang; Jiangqiao, Zhou; Zhongbao, Chen; Xiaoxiong, Ma; Long, Zhang; Jilin, Zou.
Título: Expression analysis of long non-coding RNAs in a renal ischemia-reperfusion injury model
Fonte: Acta cir. bras;34(4):e201900403, 2019. tab, graf.
Idioma: en.
Projeto: National Natural Science Foundation of China.
Resumo: Abstract Purpose: To investigate the long non-coding RNAs (lncRNAs) profile on renal ischemia reperfusion in a mouse model. Methods: Microarray analysis was used to study the expression of misregulated lncRNA in a mouse model of renal ischemia reperfusion(I/R) with long ischemia time. Quantitative real-time PCR (qPCR) was used to verify the expression of selected lncRNAs and mRNAs.The potential functions of the lncRNA was analyzed by bioinformatics tools and databases. Results: Kidney function was impaired in I/R group compared to the normal group. Analysis showed that a total of 2267 lncRNAs and 2341 messenger RNAs (mRNAs) were significantly expressed in I/R group (≥2.0-fold, p < 0.05).The qPCR result showed that lncRNAs and mRNAs expression were consistent with the microarray analysis. The co-expression network profile analysis based on five validated lncRNAs and 203 interacted mRNAs showed it existed a total of 208 nodes and 333 connections. The GO and KEEG pathway analysis results showed that multiple lncRNAs are involved the mechanism of I/R. Conclusion: Multiple lncRNAs are involved in the mechanism of I/R.These analysis results will help us to further understand the mechanism of I/R and promote the new methods targeted at lncRNA to improve I/R injury.
Descritores: RNA Mensageiro/análise
Traumatismo por Reperfusão/genética
RNA Longo não Codificante/análise
Rim/irrigação sanguínea
-Valores de Referência
Regulação para Baixo
Expressão Gênica
Regulação para Cima
Perfilação da Expressão Gênica
Análise Serial de Tecidos/métodos
Redes Reguladoras de Genes
Reação em Cadeia da Polimerase em Tempo Real
Camundongos Endogâmicos C57BL
Limites: Animais
Ratos
Responsável: BR1.1 - BIREME


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Id: biblio-1023378
Autor: Hirata, Thiago Dominguez Crespo.
Título: Analysis of the transcriptional regulatory mechanisms mediated by microRNAs in Metabolic Syndrome / Análise dos mecanismos regulatórios transcricionais mediados por microRNAs na Síndrome Metabólica.
Fonte: São Paulo; s.n; 2019. 110 p. graf, tab.
Idioma: en.
Tese: Apresentada a Universidade de São Paulo. Faculdade de Ciências Farmacêuticas para obtenção do grau de Doutor.
Resumo: Metabolic Syndrome (MetS) is a combination of diseases interrelated and associated with increased mortality and risk of cardiovascular events. Among the elucidated molecular mechanisms of MetS, there are several genes regulated by miRNAs - small non-coding RNAs. A large number of transcriptomic studies in public databases integrated with new analysis methods can generate new insights. Therefore, this study aimed to identify circulating miRNAs and their target genes in MetS using a Systems Biology approach. For this, we used GEO-NCBI to download and analyse 26 microarray transcriptome studies of MetS and obesity. After preprocessing, the data underwent differential expression (LIMMA method), gene co-expression (CEMiTool), and enrichment (GSEA, Reactome) analyses. We retrieved a gene expression signature for subcutaneous adipose tissue (SAT) for obese individuals that included 291 consistent differentially expressed genes (DEG). This signature had a positive normalized enrichment score (NES) for adaptive immune system activation responses, and negative NES for metabolic pathways. The consensus co-expression network of SAT revealed 3 communities (CM) of densely interconnected genes. These CMs had a high number of up regulated genes and a consistent positive NES among the studies. The co-expressed genes of these 3 CMs were related to neutrophil degranulation, infiltration of immune system cells, and inflammatory processes. Also, a small brazillian cohort (6 individuals with MetS and 6 controls) underwent a seric miRNA profiling using PCR array. From the 222 miRNAs detected in serum, the differential expression analysis identified 4 upregulated miRNAs (miR-30c-5p, miR-421, miR-542-5p and miR-574) in MetS patients (p<0.01). The integrative miRNAs-mRNAs analysis revealed that the circulating upregulated miRNAs had 12 targets in the SAT, 3 targets in the liver; and no targets in the muscle and blood. Many of these target genes are known modulators of proinflammatory pathways. In conclusion, the use of Systems Biology in the analysis of gene networks and circulating miRNAs identified some potential molecular and pathophysiological mechanisms of the Metabolic Syndrome. The circulating miRNAs identified in this study are potential biomarkers and/or therapeutic targets. However, further studies are needed to validate these miRNAs and their target mRNA

A Síndrome Metabólica (MetS) é um conjunto de doenças inter-relacionadas e associadas ao aumento de mortalidade e risco de eventos cardiovasculares. Entre os mecanismos moleculares elucidados da MetS, existem muitos genes regulados por miRNAs - RNAs pequenos não codificadores. O grande número de estudos transcriptômicos em banco dados públicos integrado a novos métodos de análise podem gerar novas descobertas. Deste modo, o objetivo deste estudo foi identificar miRNAs circulantes e genes alvos na MetS usando a abordagem de Biologia de Sistemas. Para isso, GEO-NCBI foi usado para obter e analisar 26 estudos de transcriptoma por microarray de MetS e obesidade. Após o pré-processamento, realizamos análises de expressão diferencial (método LIMMA), co-expressão gênica (CEMiTool), e enriquecimento (GSEA, Reactome). Identificamos uma assinatura de expressão gênica do tecido adiposo subcutâneo (SAT) de indivíduos obesos, composta por 291 genes consistentemente diferencialmente expressos (DEG). Essa assinatura teve um escore de enriquecimento normalizado (NES) positivo para ativação de respostas do sistema imune adaptativo, e NES negativo para vias de metabolismo. A rede consenso de co-expressão do SAT revelou 3 comunidades (CM) de genes densamente interconectadas. Essas CMs continham muitos genes regulados positivamente e com consistência de NES positivo entre os estudos. Os genes co-expressos dessas 3 comunidades pertenciam a vias de a degranulação de neutrófilos, infiltração de células do sistema imune e processos inflamatórios. Além disso, uma pequena coorte brasileira (6 indivíduos com MetS e 6 controles) foi submetida à dosagem sérica de miRNAs por PCR array. Dos 222 miRNAs detectados no soro, a análise de expressão diferencial identificou 4 miRNAs regulados positivamente (miR-30c-5p, miR-421, miR-542-5p e miR-574) nos pacientes com MetS (p<0.01). A análise integrativa miRNAs-mRNAs revelou que osmiRNAs circulantes superexpressos tinham 12 alvos no SAT, 3 alvos no fígado; e nenhum alvo no músculo e no sangue. Muitos desses alvos são moduladores de vias ró-inflamatórias. Em conclusão, a utilização da Biologia de Sistemas na análise de redes gênicas e miRNAs circulantes identificou alguns potenciais mecanismos moleculares e fisiopatológicos da Síndrome Metabólica. Os miRNAs circulantes identificados neste trabalho são potenciais biomarcadores e/ou alvos terapêuticos. Entretanto, mais estudos são necessários para validar esses miRNAs e seus mRNAs alvos
Descritores: Síndrome Metabólica/diagnóstico
MicroRNAs/análise
Biologia de Sistemas/instrumentação
-RNA Mensageiro/análise
Redes Reguladoras de Genes
Obesidade/classificação
Responsável: BR40.1 - DBD - Divisão de Biblioteca e Documentacão do Conjunto das Químicas
BR40.1; T574.88, H688a. 30100022638-F


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Id: biblio-889107
Autor: Wu, Wei; Huang, Bo; Yan, Yan; Zhong, Zhi-Qiang.
Título: Exploration of gene functions for esophageal squamous cell carcinoma using network-based guilt by association principle
Fonte: Braz. j. med. biol. res = Rev. bras. pesqui. méd. biol;51(6):e6801, 2018. tab, graf.
Idioma: en.
Resumo: Gene networks have been broadly used to predict gene functions based on guilt by association (GBA) principle. Thus, in order to better understand the molecular mechanisms of esophageal squamous cell carcinoma (ESCC), our study was designed to use a network-based GBA method to identify the optimal gene functions for ESCC. To identify genomic bio-signatures for ESCC, microarray data of GSE20347 were first downloaded from a public functional genomics data repository of Gene Expression Omnibus database. Then, differentially expressed genes (DEGs) between ESCC patients and controls were identified using the LIMMA method. Afterwards, construction of differential co-expression network (DCN) was performed relying on DEGs, followed by gene ontology (GO) enrichment analysis based on a known confirmed database and DEGs. Eventually, the optimal gene functions were predicted using GBA algorithm based on the area under the curve (AUC) for each GO term. Overall, 43 DEGs and 67 GO terms were gained for subsequent analysis. GBA predictions demonstrated that 13 GO functions with AUC>0.7 had a good classification ability. Significantly, 6 out of 13 GO terms yielded AUC>0.8, which were determined as the optimal gene functions. Interestingly, there were two GO categories with AUC>0.9, which included cell cycle checkpoint (AUC=0.91648), and mitotic sister chromatid segregation (AUC=0.91597). Our findings highlight the clinical implications of cell cycle checkpoint and mitotic sister chromatid segregation in ESCC progression and provide the molecular foundation for developing therapeutic targets.
Descritores: Carcinoma de Células Escamosas/genética
Biologia Computacional/métodos
Neoplasias Esofágicas/genética
Perfilação da Expressão Gênica/métodos
Regulação Neoplásica da Expressão Gênica/genética
Redes Reguladoras de Genes/genética
-Área Sob a Curva
Limites: Humanos
Responsável: BR1.1 - BIREME


  8 / 22 LILACS  
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Id: biblio-889056
Autor: Song, Zhonghua; Zhao, Wenhua; Cao, Danfeng; Zhang, Jinqing; Chen, Shouhua.
Título: Elementary screening of lymph node metastatic-related genes in gastric cancer based on the co-expression network of messenger RNA, microRNA and long non-coding RNA
Fonte: Braz. j. med. biol. res = Rev. bras. pesqui. méd. biol;51(4):e6685, 2018. tab, graf.
Idioma: en.
Resumo: Gastric cancer (GC) is the fifth most common cancer and the third leading cause of cancer-related deaths worldwide. The high mortality might be attributed to delay in detection and is closely related to lymph node metastasis. Therefore, it is of great importance to explore the mechanism of lymph node metastasis and find strategies to block GC metastasis. Messenger RNA (mRNA), microRNA (miRNA) and long non-coding RNA (lncRNA) expression data and clinical data were downloaded from The Cancer Genome Atlas (TCGA) database. A total of 908 differentially expressed factors with variance >0.5 including 542 genes, 42 miRNA, and 324 lncRNA were screened using significant analysis microarray algorithm, and interaction networks were constructed using these differentially expressed factors. Furthermore, we conducted functional modules analysis in the network, and found that yellow and turquoise modules could separate samples efficiently. The groups classified in the yellow and turquoise modules had a significant difference in survival time, which was verified in another independent GC mRNA dataset (GSE62254). The results suggested that differentially expressed factors in the yellow and turquoise modules may participate in lymph node metastasis of GC and could be applied as potential biomarkers or therapeutic targets for GC.
Descritores: Regulação Neoplásica da Expressão Gênica/genética
Redes Reguladoras de Genes/genética
MicroRNAs/genética
RNA Longo não Codificante/genética
RNA Mensageiro/genética
Neoplasias Gástricas/genética
-China/epidemiologia
Perfilação da Expressão Gênica
Linfonodos/metabolismo
Linfonodos/patologia
Metástase Linfática/genética
Prognóstico
RNA Mensageiro/metabolismo
Neoplasias Gástricas/mortalidade
Neoplasias Gástricas/secundário
Limites: Humanos
Responsável: BR1.1 - BIREME


  9 / 22 LILACS  
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Id: biblio-888994
Autor: Zhu, TG; Xiao, X; Wei, Q; Yue, M; Zhang, LX.
Título: Revealing potential long non-coding RNA biomarkers in lung adenocarcinoma using long non-coding RNA-mediated competitive endogenous RNA network
Fonte: Braz. j. med. biol. res = Rev. bras. pesqui. méd. biol;50(9):e6297, 2017. tab, graf.
Idioma: en.
Resumo: In our study, we aimed to reveal potential long non-coding RNAs (lncRNA) biomarkers in lung adenocarcinoma (LAD) using lncRNA-mediated competing endogenous RNAs (ceRNAs) network (LMCN). Competing lncRNA-mRNA interactions were identified using the hypergeometric test. Co-expression analysis for the competing lncRNA-mRNA interactions was implemented, and relying on the weight value >0.8, a highly competitive LMCN was further constructed. Degree distribution, betweenness and closeness for LMCN were carried out to analyze the network structure. Functional analyses of mRNAs in LMCN were carried out to further explore the biological functions of lncRNAs. Biclique algorithm was utilized to extract competing modules from the LMCN. Finally, we verified our findings in an independent sample set using qRT-PCR. Based on degrees >60, we identified 4 hubs, including DLEU2, SNHG12, HCP5, and LINC00472. Furthermore, 2 competing modules were identified, and LINC00472 in module 1 functioned as a hub in both LMCN and module. Functional implications of lncRNAs demonstrated that lncRNAs were related to histone modification, negative regulation of cell cycle, neuroactive ligand-receptor interaction, and regulation of actin cytoskeleton. qRT-PCR results demonstrated that lncRNAs LINC00472, and HCP5 were down-regulated in LAD tissues, while the expression level of SNHG12 was up-regulated in LAD tissues. Our study sheds novel light on the roles of lncRNA-related ceRNA network in LAD and facilitates the detection of potential lncRNA biomarkers for LAD diagnosis and treatment. Remarkably, in our study, LINC00472, HCP5, and SNHG12 might be potential biomarkers for LAD management.
Descritores: Adenocarcinoma/genética
Biomarcadores Tumorais/genética
Regulação Neoplásica da Expressão Gênica/genética
Redes Reguladoras de Genes/genética
Neoplasias Pulmonares/genética
RNA Longo não Codificante/genética
-Prognóstico
Limites: Humanos
Responsável: BR1.1 - BIREME


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Id: biblio-888976
Autor: Jiang, T; Jiang, CY; Shu, JH; Xu, YJ.
Título: Excavation of attractor modules for nasopharyngeal carcinoma via integrating systemic module inference with attract method
Fonte: Braz. j. med. biol. res = Rev. bras. pesqui. méd. biol;50(8):e6416, 2017. tab, graf.
Idioma: en.
Resumo: The molecular mechanism of nasopharyngeal carcinoma (NPC) is poorly understood and effective therapeutic approaches are needed. This research aimed to excavate the attractor modules involved in the progression of NPC and provide further understanding of the underlying mechanism of NPC. Based on the gene expression data of NPC, two specific protein-protein interaction networks for NPC and control conditions were re-weighted using Pearson correlation coefficient. Then, a systematic tracking of candidate modules was conducted on the re-weighted networks via cliques algorithm, and a total of 19 and 38 modules were separately identified from NPC and control networks, respectively. Among them, 8 pairs of modules with similar gene composition were selected, and 2 attractor modules were identified via the attract method. Functional analysis indicated that these two attractor modules participate in one common bioprocess of cell division. Based on the strategy of integrating systemic module inference with the attract method, we successfully identified 2 attractor modules. These attractor modules might play important roles in the molecular pathogenesis of NPC via affecting the bioprocess of cell division in a conjunct way. Further research is needed to explore the correlations between cell division and NPC.
Descritores: Carcinoma/genética
Regulação Neoplásica da Expressão Gênica/genética
Redes Reguladoras de Genes/genética
Neoplasias Nasofaríngeas/genética
-Perfilação da Expressão Gênica
Mapeamento de Interação de Proteínas
Limites: Humanos
Responsável: BR1.1 - BIREME



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