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Registros recuperados: 19
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Analysis of gene expression changes associated with human carcinoma-associated fibroblasts in non-small cell lung carcinoma Biol. Res.
Wu,Xiaofen; Ruan,Lei; Yang,Yi; Mei,Qi.
Abstract Background This study aimed to investigate the gene expression changes associated with carcinoma-associated fibroblasts (CAFs) involving in non-small cell lung carcinoma (NSCLC). Methods We downloaded the GEO series GSE22862, which contained matched gene expression values for 15 CAF and normal fibroblasts samples, and series GSE27289 containing SNP genotyping for four matched NSCLC samples. The differentially expressed genes in CAF samples were identified using the limma package in R. Then we performed gene ontology (GO) and pathway enrichment analysis and protein–protein interaction (PPI) network construction using the identified DEGs. Moreover, aberrant cell fraction, ploidy, allele-specific copy number, and loss of heterozygosity...
Tipo: Journal article Palavras-chave: Carcinoma-associated fibroblast; Non-small cell lung carcinoma; Differentially expressed genes; Allele-specific copy number; Functional analysis.
Ano: 2017 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602017000100204
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Analysis of gene expression profiles in response to Sporisorium reilianum f. sp. zeae in maize (Zea mays L.) Electron. J. Biotechnol.
Yu,Tao; Wang,Zhenhua; Jin,Xiaochun; Liu,Xianjun; Kan,Shuaishuai.
Background Head smut of maize, which is caused by Sporisorium reilianum f. sp. zeae (Kühn), is a serious disease in maize. In order to reveal the molecular mechanism of the resistance to head smut in maize, a microarray containing ~ 14,850 probes was used to monitor the gene expression profiles between a disease resistant near isogenic line (NIL) and a highly susceptible inbred line after S. reilianum was injected with an artificial inoculation method. Results Levels of expression for 3,532 genes accounting for 23.8% of the total probes changed after inoculation. Gene Ontology analysis revealed that the differentially expressed genes participated in physiological and biochemical pathways. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis...
Tipo: Journal article Palavras-chave: Differentially expressed genes; Head smut resistance gene; Maize; Microarray.
Ano: 2014 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582014000500007
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Analyzing gene expression profiles in dilated cardiomyopathy via bioinformatics methods BJMBR
Wang,Liming; Zhu,L.; Luan,R.; Wang,L.; Fu,J.; Wang,X.; Sui,L..
Dilated cardiomyopathy (DCM) is characterized by ventricular dilatation, and it is a common cause of heart failure and cardiac transplantation. This study aimed to explore potential DCM-related genes and their underlying regulatory mechanism using methods of bioinformatics. The gene expression profiles of GSE3586 were downloaded from Gene Expression Omnibus database, including 15 normal samples and 13 DCM samples. The differentially expressed genes (DEGs) were identified between normal and DCM samples using Limma package in R language. Pathway enrichment analysis of DEGs was then performed. Meanwhile, the potential transcription factors (TFs) and microRNAs (miRNAs) of these DEGs were predicted based on their binding sequences. In addition, DEGs were mapped...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Dilated cardiomyopathy; Differentially expressed genes; Pathway enrichment analysis; Transcription factors; MicroRNAs; Small molecules.
Ano: 2016 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2016001000706
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Association of skeletal muscle transcripts with fatty acid content in Nellore cattle. Repositório Alice
CESAR, A. S. M.; REGITANO, L. C. de A.; POLETI, M. D.; ANDRADE, S. C. da S.; TIZIOTO, P. C.; OLIVEIRA, P. S. N. de; LANNA, D. P. D.; TULLIO, R. R.; NASSU, R. T.; KOLTES, J. E.; WATERS, E. F.; REECY, J. M.; COUTINHO, L. L..
2016
Tipo: Artigo em anais de congresso (ALICE) Palavras-chave: Conjugated linoleic acid; Oleic acid; Differentially expressed genes.
Ano: 2016 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1060623
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Exploration of gene functions for esophageal squamous cell carcinoma using network-based guilt by association principle BJMBR
Wu,Wei; Huang,Bo; Yan,Yan; Zhong,Zhi-Qiang.
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...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Esophageal squamous cell carcinoma; Gene oncology; Guilt by association; Differentially expressed genes; Area under the curve.
Ano: 2018 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2018000600601
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Expressão diferencial de genes associados ao metabolismo muscular e de deposição de gordura intramuscular em grupos genéticos de suínos divergentes. Repositório Alice
MACEDO, M. I. S..
Resumo: Com este estudo, objetivou-se analisar a expressão diferencial de genes relacionados com desenvolvimento muscular (ATP6, SDHD, LDHA e LDHB) e deposição de gordura intramuscular (FABP4, PPAR? e fator de transcrição GATA-2) no músculo de suínos de genéticas divergentes. Para isso foram analisadas amostras de músculo Longissimus dorsi por meio do RNA extraído de 32 animais de dois grupos genéticos, sendo 16 suínos naturalizados Piau e 16 suínos da Linhagem Comercial em 4 idades pós-natal: ao nascer, 56, 112 e 156 dias. Foram selecionados dois genes que atuam na vias oxidativa (SDHD e ATP6), dois genes da via glicolítica (LDHA e LDHB) que atuam na função mitocondrial do músculo esquelético, dois genes (FABP4 e PPAR?) e um fator de transcrição (GATA-2)...
Tipo: Tese/dissertação (ALICE) Palavras-chave: Desenvolvimento muscular; RT-qPCR 3; Genes diferencialmente expresso; Função mitocondrial; Differentially expressed genes; Mitochondrial function; Pigs; Genetic processes; Suíno; Gene expression; Genetically modified organisms; Animal genetics; Genetic engineering.
Ano: 2017 URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1100637
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Expressão gênica diferencial envolvida com Condronecrose bacteriana com osteomielite em frangos de corte com 35 dias de idade. Repositório Alice
PEIXOTO, J. de O.; IBELLI, A. M. G.; CANTAO, M. E.; ZANELLA, R.; JAENISCH, F. R. F.; GIACHETTO, P. F.; SETTLES, M. L.; PANDOLFI, J. R. C.; COUTINHO, L. L.; LEDUR, M. C..
Resumo: A incidência de problemas ósseos é considerada uma das principais preocupações para a indústria avícola devido à perdas econômicas significativas e ao impacto negativo no bem-estar. As vias metabólicas e os genes envolvidos nas patologias ósseas permanecem desconhecidos. A condronecrose bacteriana com osteomielite (BCO) é uma das principais doenças ligadas a problemas locomotores em frangos. Na tentativa de esclarecer os mecanismos genéticos envolvidos na manifestação da BCO, objetivou-se identificar os genes diferencialmente expressos no fêmur de frangos de corte normais e afetados por esta desordem, por meio da tecnologia de RNA-Seq. Neste estudo foram utilizados frangos de corte comerciais machos aos 35 dias de idade sendo 4 normais e 4 com BCO...
Tipo: Artigo em anais de congresso (ALICE) Palavras-chave: BCO; Differentially expressed genes; RNA-Seq; Bacterial Chondronecrosis with Osteomyelitis; Patologia óssea; Genes; Ontologia gênica; Genes.
Ano: 2015 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1024034
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Gene expression profiling analysis of lung adenocarcinoma BJMBR
Xu,H.; Ma,J.; Wu,J.; Chen,L.; Sun,F.; Qu,C.; Zheng,D.; Xu,S..
The present study screened potential genes related to lung adenocarcinoma, with the aim of further understanding disease pathogenesis. The GSE2514 dataset including 20 lung adenocarcinoma and 19 adjacent normal tissue samples from 10 patients with lung adenocarcinoma aged 45-73 years was downloaded from Gene Expression Omnibus. Differentially expressed genes (DEGs) between the two groups were screened using the t-test. Potential gene functions were predicted using functional and pathway enrichment analysis, and protein-protein interaction (PPI) networks obtained from the STRING database were constructed with Cytoscape. Module analysis of PPI networks was performed through MCODE in Cytoscape. In total, 535 upregulated and 465 downregulated DEGs were...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Lung adenocarcinoma; Pathogenesis; Differentially expressed genes; Protein-protein interaction; Network module.
Ano: 2016 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2016000300601
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Identification of genes related to high royal jelly production in the honey bee (Apis mellifera) using microarray analysis Genet. Mol. Biol.
Nie,Hongyi; Liu,Xiaoyan; Pan,Jiao; Li,Wenfeng; Li,Zhiguo; Zhang,Shaowu; Chen,Shenglu; Miao,Xiaoqing; Zheng,Nenggan; Su,Songkun.
Abstract China is the largest royal jelly producer and exporter in the world, and high royal jelly-yielding strains have been bred in the country for approximately three decades. However, information on the molecular mechanism underlying high royal jelly production is scarce. Here, a cDNA microarray was used to screen and identify differentially expressed genes (DEGs) to obtain an overview on the changes in gene expression levels between high and low royal jelly producing bees. We developed a honey bee gene chip that covered 11,689 genes, and this chip was hybridised with cDNA generated from RNA isolated from heads of nursing bees. A total of 369 DEGs were identified between high and low royal jelly producing bees. Amongst these DEGs, 201 (54.47%) genes...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Honeybee; Royal jelly production; Gene chip; Molecular marker; Differentially expressed genes.
Ano: 2017 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572017000500781
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Identification of novel gene and pathway targets for human epilepsy treatment Biol. Res.
Jin,Ying; Zhao,Chunzhe; Chen,Lihui; Liu,Xiangyu; Pan,Shuxiao; Ju,Dongsheng; Ma,Jing; Li,Jinying; Wei,Bo.
BACKGROUND: The aim of this study was to explore epilepsy-related mechanism so as to figure out the possible targets for epilepsy treatment. METHODS: The gene expression profile dataset GES32534 was downloaded from Gene Expression Omnibus database. We identified the differentially expressed genes (DEGs) by Affy package. Then the DEGs were used to perform gene ontology (GO) and pathway enrichment analyses. Furthermore, a protein-protein interaction (PPI) network was constructed with the DEGs followed by co-expression modules construction and analysis. RESULTS: Total 420 DEGs were screened out, including 214 up-regulated and 206 down-regulated genes. Functional enrichment analysis revealed that down-regulated genes were mainly involved in the process of...
Tipo: Journal article Palavras-chave: Epilepsy; Differentially expressed genes; Functional annotation; Protein-protein interaction network; Co-expression module.
Ano: 2016 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602016000100003
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Identification of the molecular mechanisms associated with acute type A aortic dissection through bioinformatics methods BJMBR
Jiang,Tao; Si,Liangyi.
Aortic dissection is characterized by the redirection of blood flow, which flows through an intimal tear into the aortic media. The purpose of this study was to find potential acute type A aortic dissection (AAAD)-related genes and molecular mechanisms by bioinformatics. The gene expression profiles of GSE52093 were obtained from Gene Expression Omnibus (GEO) database, including 7 AAAD samples and 5 normal samples. The differentially expressed genes (DEGs) were detected between AAAD and normal samples. The functional annotation and pathway enrichment analysis were conducted through the Database for Annotation, Visualization and Integration Discovery (DAVID). A protein-protein interaction network was established by the Search Tool for the Retrieval of...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Aortic dissection; Differentially expressed genes; Functional enrichment analysis; Protein-protein interaction network; MicroRNAs; Small molecules.
Ano: 2019 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2019001100610
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Integrated analyses of copy number variations and gene differential expression in lung squamous-cell carcinoma Biol. Res.
Yang,Zhao; Zhuan,Bing; Yan,Ying; Jiang,Simin; Wang,Tao.
BACKGROUND: Although numerous efforts have been made, the pathogenesis underlying lung squamous-cell carcinoma (SCC) remains unclear. This study aimed to identify the CNV-driven genes by an integrated analysis of both the gene differential expression and copy number variation (CNV). RESULTS: A higher burden of the CNVs was found in 10-50 kb length. The 16 CNV-driven genes mainly located in chr 1 and chr 3 were enriched in immune response [e.g. complement factor H (CFH) and Fc fragment of IgG, low affinity Ilia, receptor (FCGR3A)], starch and sucrose metabolism [e.g. amylase alpha 2A (AMY2A)]. Furthermore, 38 TFs were screened for the 9 CNV-driven genes and then the regulatory network was constructed, in which the...
Tipo: Journal article Palavras-chave: Lung squamous-cell carcinoma; Differentially expressed genes; Copy number variation; Copy number variation-driven genes.
Ano: 2015 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0716-97602015000100047
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Isolation and analysis of differentially expressed genes from peanut in response to challenge with Ralstonia solanacearum Electron. J. Biotechnol.
Ding,Yu Fei; Wang,Chuan Tang; Tang,Yue Yi; Wang,Xiu Zhen; Wu,Qi; Hu,Dong Qing; Yu,Hong Tao; Zhang,Jian Cheng; Cui,Feng Gao; Song,Guo Sheng; Gao,Hua Yuan; Yu,Shan Lin.
Background: Bacterial wilt caused by Ralstonia solanacearum is the most devastating disease in peanut. Planting resistant peanut cultivars is deemed as the sole economically viable means for effective control of the disease. To understand the molecular mechanism underlying resistance and facilitate breeding process, differences in gene expression between seeds of Rihua 1 (a Virginia type peanut variety resistant to bacterial wilt) inoculated with the bacterial pathogen suspension (10(9) cfu ml-1) and seeds of the same cultivar treated with water (control), were studied using the GenefishingTM technology. Results: A total of 25 differentially expressed genes were isolated. Expression of genes encoding cyclophilin and ADP-ribosylation factor, respectively,...
Tipo: Journal article Palavras-chave: Arachis hypogaea; ARF; Cyclophilin; Differentially expressed genes; Genefishing; Ralstonia solanacearum.
Ano: 2012 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582012000500001
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Neuroprotective changes in degeneration-related gene expression in the substantia nigra following acupuncture in an MPTP mouse model of Parkinsonism: Microarray analysis Genet. Mol. Biol.
Yeo,Sujung; An,Keon Sang; Hong,Yeon-Mi; Choi,Yeong-Gon; Rosen,Bruce; Kim,Sung-Hoon; Lim,Sabina.
Parkinson’s disease (PD) is a neurodegenerative disorder characterized by the death of dopamine-generating cells in the substantia nigra (SN). Acupuncture stimulation results in an enhanced survival of dopaminergic neurons in the SN in Parkinsonism animal models. The present study investigated changes in gene expression profiles measured using whole transcript array in the SN region related to the inhibitory effects of acupuncture in a chronic 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) Parkinsonism model. In this model, acupuncture stimulation at GB34 and LR3 attenuated the decrease in tyrosine hydroxylase in the SN region; stimulation at non-acupoints did not suppress this decrease. Gene array analysis revealed that 22 (10 annotated genes: Cdh1,...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Parkinson’s disease; Gene array; Differentially expressed genes; Neurodegeneration; Acupoints.
Ano: 2015 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572015000100115
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Predicting pathway cross-talks in ankylosing spondylitis through investigating the interactions among pathways BJMBR
Gu,Xiang; Liu,Cong-Jian; Wei,Jian-Jie.
Given that the pathogenesis of ankylosing spondylitis (AS) remains unclear, the aim of this study was to detect the potentially functional pathway cross-talk in AS to further reveal the pathogenesis of this disease. Using microarray profile of AS and biological pathways as study objects, Monte Carlo cross-validation method was used to identify the significant pathway cross-talks. In the process of Monte Carlo cross-validation, all steps were iterated 50 times. For each run, detection of differentially expressed genes (DEGs) between two groups was conducted. The extraction of the potential disrupted pathways enriched by DEGs was then implemented. Subsequently, we established a discriminating score (DS) for each pathway pair according to the distribution of...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Ankylosing spondylitis; Monte Carlo cross-validation; Differentially expressed genes; Random forest classification; Pathway cross-talk.
Ano: 2018 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2018000100607
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Transcriptome analyses of Ditylenchus destructor in responses to cold and desiccation stress Genet. Mol. Biol.
Ma,Juan; Gao,Bo; Wang,Rongyan; Li,Xiuhua; Chen,Shulong.
Abstract The objective of this study was to identify molecular responses in Ditylenchus destructor to cold and desiccation by means of transcriptomes analyses. A total of 102,517 unigenes were obtained, with an average length of 1,076 bp, in which 58,453 (57%) had a functional annotation. A total of 1154 simple sequence repeats (SSRs) distributed over 1078 unigenes were detected. Gene expression profiles in response to cold and desiccation stress and the expression of specific stress-related genes were compared. Gene ontology analysis and pathway-based analysis were used to further investigate the functions of the differentially expressed genes. The reliability of the sequencing data was verified through quantitative real-time PCR analysis of 19...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Potato rot nematode; Transcriptome; Tolerance; Differentially expressed genes.
Ano: 2020 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572020000100202
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Transcriptome analysis in Coffea eugenioides, an Arabica coffee ancestor, reveals differentially expressed genes inleaves and fruits. Repositório Alice
YUYAMA, P. M.; REIS JUNIOR, O.; IVAMOTO, S. T.; DOMINGUES, D. S.; CARAZZOLLE, M. F.; PEREIRA, G. A. G.; CHARMETANT, P.; LEROY, T.; PEREIRA, L. F. P..
Studies in diploid parental species of polyploid plants are important to understand their contributions to the formation of plant and species evolution. Coffea eugenioides is a diploid species that is considered to be an ancestor of allopolyploid Coffea arabica together with Coffea canephora. Despite its importance in the evolutionary history of the main economic species of coffee, no study has focused on C. eugenioides molecular genetics. RNA-seq creates the possibility to generate reference transcriptomes and identify coding genes and potential candidates related to important agronomic traits. Therefore, the main objectives were to obtain a global overview of transcriptionally active genes in this species using next generation sequencing and to analyze...
Tipo: Artigo em anais de congresso (ALICE) Palavras-chave: Coffea; RNA-seq; Gene annotation; Differentially expressed genes; Homeologous.
Ano: 2016 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1040005
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Whole transcriptome analysis of pectoralis major muscle reveals differences in calcium signaling pathway between white striping affected and unaffected broilers. Repositório Alice
MARCHESI, J. A. P.; IBELLI, A. M. G.; CANTAO, M. E.; ZANELLA, R.; SETTLES, M. L.; PEIXOTO, J. de O.; COUTINHO, L. L.; LEDUR, M. C..
2015
Tipo: Resumo em anais de congresso (ALICE) Palavras-chave: RNA Seq; Muscle disorder; Myopathy; Differentially expressed genes; Gallus gallus.
Ano: 2015 URL: http://www.alice.cnptia.embrapa.br/handle/doc/1033769
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การวิเคราะห์ข้อมูลการถอดรหัส ที่ส่งผลต่อการแสดงออกของยีนที่แตกต่างกันในช่อดอกจากจีโนมข้าวลูกผสมและพันธุ์พ่อแม่ Thai Agricultural
Kulchana Ketsuwan.
Next Generation Sequencing (NGS): SOLiD System Sequencing Platform was applied to investigate the whole transcriptome of two hybrids (PTT06001H; H1 and PTT06008H: H2), two paternal lines (CK81; P1 and CK120; P2), and maternal line (IR79156; M). The data sets were aligned against the reference, precisely, the total numbers of the individual rice panicles sample aligned with Nipponbare ranking from the highest were as follows, P2 (9,747,077 reads), H1 (7,386,061 reads) , P1 (5,361,077 reads) , H2 (5,196,982 reads), and M (2,244,306 reads), respectively. The differentially expressed genes (DEGs) were identified and found that 2902, 1604, 3168, 3068, 1171, and 3031 genes were up-regulated (> 2 fold) between M vs. H1, P1 vs. H1, M vs.P1, M vs. H2, P2 vs. H2,...
Tipo: PhysicalObject Palavras-chave: Hybrid rice; Heterosis; Differentially expressed genes; DEGs; Genetic transformation; Gene expression; Transcription; Nucleotide analysis; Plant breeding; Rice productivity; ข้าว; พันธุ์ลูกผสม; ช่อดอก; การถ่ายทอดทางพันธุกรรม; การแสดงออกของยีน; การถอดรหัสพันธุกรรม; การวิเคราะห์นิวคลีโอไทด์; การปรับปรุงพันธุ์; ศักยภาพความดีเด่นเหนือพ่อแม่; การเพิ่มผลผลิต.
Ano: 2014 URL: http://anchan.lib.ku.ac.th/agnet/handle/001/5659
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