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‣ Searching for molecular markers in head and neck squamous cell carcinomas (HNSCC) by statistical and bioinformatic analysis of larynx-derived SAGE libraries

SILVEIRA, Nelson J. F.; VARUZZA, Leonardo; MACHADO-LIMA, Ariane; LAURETTO, Marcelo S.; PINHEIRO, Daniel G.; RODRIGUES, Rodrigo V.; SEVERINO, Patricia; NOBREGA, Francisco G.; SILVA JR., Wilson A.; PEREIRA, Carlos A. de B.; TAJARA, Eloiza H.
Fonte: BIOMED CENTRAL LTD Publicador: BIOMED CENTRAL LTD
Tipo: Artigo de Revista Científica
Português
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Background: Head and neck squamous cell carcinoma (HNSCC) is one of the most common malignancies in humans. The average 5-year survival rate is one of the lowest among aggressive cancers, showing no significant improvement in recent years. When detected early, HNSCC has a good prognosis, but most patients present metastatic disease at the time of diagnosis, which significantly reduces survival rate. Despite extensive research, no molecular markers are currently available for diagnostic or prognostic purposes. Methods: Aiming to identify differentially-expressed genes involved in laryngeal squamous cell carcinoma (LSCC) development and progression, we generated individual Serial Analysis of Gene Expression (SAGE) libraries from a metastatic and non-metastatic larynx carcinoma, as well as from a normal larynx mucosa sample. Approximately 54,000 unique tags were sequenced in three libraries. Results: Statistical data analysis identified a subset of 1,216 differentially expressed tags between tumor and normal libraries, and 894 differentially expressed tags between metastatic and non-metastatic carcinomas. Three genes displaying differential regulation, one down-regulated (KRT31) and two up-regulated (BST2, MFAP2), as well as one with a non-significant differential expression pattern (GNA15) in our SAGE data were selected for real-time polymerase chain reaction (PCR) in a set of HNSCC samples. Consistent with our statistical analysis...

‣ Identificação de genes diferencialmente expressos em árvores de Eucalyptus grandis susceptíveis e resistentes à Puccinia psidii; Identification of differentially expressed genes in susceptivel and resistant Eucalyptus grandis trees exposed to Puccinia psidii

Salvatierra, Guillermo Rafael
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 29/05/2006 Português
Relevância na Pesquisa
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A atividade florestal apresenta-se como um vetor de desenvolvimento social, ambiental e econômico no Brasil. Em 2004 as exportações ligadas ao setor renderam US$ 7 bilhões e contribuíram com US$ 5,5 bilhões em impostos. No mesmo ano, no Brasil, dos 6 milhões de hectares de reflorestamento comercial, mais de 50% dos hectares são ocupados por eucalipto. Esta cultura pode ser utilizada para diversas funções, desde à produção de papel e celulose, até a produção de carvão vegetal. Mas a produtividade desta cultura atualmente tem uma série de fatores limitantes. Destes fatores, um dos mais severos é uma doença denominada ferrugem, causada pelo fungo Puccinia psiddii Winter. Este patógeno entre tanto, não é conhecido nos centros de origem do gênero Eucalyptus, mas, utiliza como hospedeiros vários gêneros das Mirtáceas, infectando folhas, flores e frutos em desenvolvimento. O controle da doença é normalmente realizado mediante o uso de fungicidas. Porém, a utilização de plantas resistentes é o método mais aconselhável por diversos motivos, como o baixo custo, a praticidade e o menor impacto ambiental. Neste trabalho a metodologia do SAGE - Serial Analysis of Gene Expression foi utilizada, para a análise da expressão gênica uma vez que permite detectar e quantificar...

‣ Identificação de genes de maracujá azedo diferencialmente expressos durante a interação com Xanthomonas axonopodis; Identification of differentially expressed genes during the yellow passion fruit- Xanthomonas axonopodis interaction

Munhoz, Carla de Freitas
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 04/10/2013 Português
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803.7067%
O Brasil é o maior produtor mundial de maracujá azedo (Passiflora edulis f. flavicarpa) sendo esta a espécie de maior expressão comercial dentre as passifloras cultivadas. A bacteriose do maracujazeiro, causada por Xanthomonas axonopodis pv. passiflorae (Xap), é uma das doenças mais severas da cultura, acarretando grandes prejuízos aos produtores. Atualmente, é incipiente o conhecimento sobre a interação maracujá azedo-Xap. Diante disso, a identificação e a caracterização dos genes envolvidos no processo de defesa são passos importantes para dar suporte ao desenvolvimento de variedades resistentes. Assim, o objetivo deste trabalho foi identificar e caracterizar genes de maracujá azedo diferencialmente expressos durante a resposta de defesa à Xap, bem como mensurar a sua expressão. Para isso, foram construídas duas bibliotecas subtrativas de cDNA (forward e reverse) usando o método SSH a partir de transcritos de folhas, que foram inoculadas com o patógeno ou solução salina (controle). Após o sequenciamento dos clones, o processamento e a montagem das sequências, as unisequências foram anotadas através da Plataforma PLAZA e do programa computacional Blast2GO. Genes envolvidos em diversos processos biológicos foram selecionados para a validação das bibliotecas por PCR quantitativo. Usando a Plataforma PLAZA...

‣ Construction of a hepatic stellate cells subtracted cDNA library of differentially expressed genes in normal mice and mice with Schistosomiasis japonica*

Zheng, Min; Wu, Yi-jun; Cai, Wei-min; Weng, Hong-lei; Liu, Rong-hua
Fonte: Zhejiang University Press Publicador: Zhejiang University Press
Tipo: Artigo de Revista Científica
Português
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To construct a hepatic stellate cells (HSCs) subtracted cDNA library to find differentially expressed genes in normal mice and mice infected with Schistosoma japonicum (S. japonicum). Suppression subtractive hybridization (SSH) was used. The cDNA fragments of normal mouse were compared to those of schistosoma-infected mice to find differentially expressed genes. Then differentially expressed cDNA fragments were directly inserted into T/A cloning vector to set up the subtractive library. Amplification of the library was carried out with transformation of DH5α. The amplified library contained more than 400 positive bacterial clones, which were then hybridized with forward and backward subtracted probes for differential screening. One hundred positive bacterial clones were randomly selected for sequencing and BLAST analysis. Finally, virtual Northern Blot confirmed such differential expression. The subtracted cDNA library of differentially expressed genes of HSCs was constructed successfully, the library is efficient and lays foundation for screening and cloning new and specific genes of schistosomiasis.

‣ Identification of differentially expressed genes in HPV-positive and HPV-negative oropharyngeal squamous cell carcinomas

Martinez, Ivan; Wang, Jun; Hobson, Kenosha F.; Ferris, Robert L.; Khan, Saleem A.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Português
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Human papillomaviruses (HPVs) have been implicated in the pathogenesis of a subset of squamous cell carcinoma of the head and neck (SCCHN). The goal of this study was to compare the cellular gene expression profiles of HPV-positive and HPV-negative oropharyngeal carcinomas with those of the normal oral epithelium. Using Affymetrix Human U133A GeneChip, our results showed that 397 genes were differentially expressed in HPV-positive SCCHN compared to the normal oral epithelium. The up-regulated genes included those involved in cell cycle regulation (CDKN2A), cell differentiation (SFRP4) and DNA repair (RAD51AP1), while the down-regulated genes included those involved in proteolysis (PRSS3). We also found 162 differentially expressed genes in HPV-negative SCCHN compared to the normal oral mucosa. The up-regulated genes included those involved in cell proliferation (AKR1C3) and transcription regulation (SNAPC1), while down-regulated genes included those involved in apoptosis (CLU) and RNA processing (RBM3). Our studies also identified a subgroup of 59 differentially expressed genes in HPV-positive SCCHN as compared to both HPV-negative SCCHN and normal oral tissues. Such up-regulated genes included those involved in nuclear structure and meiosis (SYCP2)...

‣ Biological Validation of Differentially Expressed Genes in Chronic Lymphocytic Leukemia Identified by Applying Multiple Statistical Methods to Oligonucleotide Microarrays

Abruzzo, Lynne V.; Wang, Jing; Kapoor, Mini; Medeiros, L. Jeffrey; Keating, Michael J.; Highsmith, W. Edward; Barron, Lynn L.; Cromwell, Candy C.; Coombes, Kevin R.
Fonte: American Society for Investigative Pathology Publicador: American Society for Investigative Pathology
Tipo: Artigo de Revista Científica
Publicado em /08/2005 Português
Relevância na Pesquisa
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Oligonucleotide microarrays are a powerful tool for profiling the expression levels of thousands of genes. Different statistical methods for identifying differentially expressed genes can yield different results. To our knowledge, no experimental test has been performed to decide which method best identifies genes that are truly differentially expressed. We applied three statistical methods (dChip, t-test on log-transformed data, and Wilcoxon test) to identify differentially expressed genes in previously untreated patients with chronic lymphocytic leukemia (CLL). We used a training set of Affymetrix Hu133A microarray data from 11 patients with unmutated immunoglobulin (Ig) heavy chain variable region (VH) genes and 8 patients with mutated Ig VH genes. Differential expression was validated using semiquantitative real-time polymerase chain reaction assays and by validating models to predict the somatic mutation status of an independent test set of nine CLL samples. The methods identified 144 genes that were differentially expressed between cases of CLL with unmutated compared with mutated Ig VH genes. Eighty genes were identified by Wilcoxon test, 60 by t-test, and 65 by dChip, but only 11 were identified by all three methods. Greater agreement was found between the t-test and the Wilcoxon test. Differential expression was validated by semiquantitative real-time polymerase chain reaction assays for 83% of individual genes...

‣ Finding Differentially Expressed Genes in Two-Channel DNA Microarray Datasets: How to Increase Reliability of Data Preprocessing

Rotter, Ana; Hren, Matjaž; Baebler, Špela; Blejec, Andrej; Gruden, Kristina
Fonte: Mary Ann Liebert, Inc. Publicador: Mary Ann Liebert, Inc.
Tipo: Artigo de Revista Científica
Publicado em /09/2008 Português
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Due to the great variety of preprocessing tools in two-channel expression microarray data analysis it is difficult to choose the most appropriate one for a given experimental setup. In our study, two independent two-channel inhouse microarray experiments as well as a publicly available dataset were used to investigate the influence of the selection of preprocessing methods (background correction, normalization, and duplicate spots correlation calculation) on the discovery of differentially expressed genes. Here we are showing that both the list of differentially expressed genes and the expression values of selected genes depend significantly on the preprocessing approach applied. The choice of normalization method to be used had the highest impact on the results. We propose a simple but efficient approach to increase the reliability of obtained results, where two normalization methods which are theoretically distinct from one another are used on the same dataset. Then the intersection of results, that is, the lists of differentially expressed genes, is used in order to get a more accurate estimation of the genes that were de facto differentially expressed.

‣ Comparison of methods for identifying differentially expressed genes across multiple conditions from microarray data

Tan, Yuande; Liu, Yin
Fonte: Biomedical Informatics Publicador: Biomedical Informatics
Tipo: Artigo de Revista Científica
Publicado em 21/12/2011 Português
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Identification of genes differentially expressed across multiple conditions has become an important statistical problem in analyzing large-scale microarray data. Many statistical methods have been developed to address the challenging problem. Therefore, an extensive comparison among these statistical methods is extremely important for experimental scientists to choose a valid method for their data analysis. In this study, we conducted simulation studies to compare six statistical methods: the Bonferroni (B-) procedure, the Benjamini and Hochberg (BH-) procedure, the Local false discovery rate (Localfdr) method, the Optimal Discovery Procedure (ODP), the Ranking Analysis of F-statistics (RAF), and the Significant Analysis of Microarray data (SAM) in identifying differentially expressed genes. We demonstrated that the strength of treatment effect, the sample size, proportion of differentially expressed genes and variance of gene expression will significantly affect the performance of different methods. The simulated results show that ODP exhibits an extremely high power in indentifying differentially expressed genes, but significantly underestimates the False Discovery Rate (FDR) in all different data scenarios. The SAM has poor performance when the sample size is small...

‣ Data Mining in Networks of Differentially Expressed Genes during Sow Pregnancy

Wang, Ligang; Zhang, Longchao; Li, Yong; Li, Wen; Luo, Weizhen; Cheng, Duxue; Yan, Hua; Ma, Xiaojun; Liu, Xin; Song, Xin; Liang, Jing; Zhao, Kebin; Wang, Lixian
Fonte: Ivyspring International Publisher Publicador: Ivyspring International Publisher
Tipo: Artigo de Revista Científica
Publicado em 16/04/2012 Português
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Small to moderate gains in Pig fertility can mean large returns in overall efficiency, and developing methods to improve it is highly desirable. High fertility rates depend on completion of successful pregnancies. To understand the molecular signals associated with pregnancy in sows, expression profiling experiments were conducted to identify differentially expressed genes in ovary and myometrium at different pregnancy periods using the Affymetrix Porcine GeneChipTM. A total of 974, 1800, 335 and 710 differentially expressed transcripts were identified in the myometrium during early pregnancy (EP) and late pregnancy (LP), and in the ovary during EP and LP, respectively. Self-Organizing Map (SOM) clusters indicated the differentially expressed genes belonged to 7 different functional groups. Based on BLASTX searches and Gene Ontology (GO) classifications, 129 unique genes closely related to pregnancy showed differential expression patterns. GO analysis also indicated that there were 21 different molecular function categories, 20 different biological process categories, and 8 different cellular component categories of genes differentially expressed during sow pregnancy. Gene regulatory network reconstruction provided us with an interaction model of known genes such as insulin-like growth factor 2 (IGF2) gene...

‣ CEDER: Accurate detection of differentially expressed genes by combining significance of exons using RNA-Seq

Wan, Lin; Sun, Fengzhu
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em //2012 Português
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RNA-Seq is widely used in transcriptome studies, and the detection of differentially expressed genes (DEGs) between two classes of individuals, e.g. cases vs controls, using RNA-Seq is of fundamental importance. Many statistical methods for DEG detection based on RNA-Seq data have been developed and most of them are based on the read counts mapped to individual genes. On the other hand, genes are composed of exons and the distribution of reads for the different exons can be heterogeneous. We hypothesize that the detection accuracy of differentially expressed genes can be increased by analyzing individual exons within a gene and then combining the results of the exons. We therefore developed a novel program, termed CEDER, to accurately detect DGEs by combining the significance of the exons. CEDER first tests for differentially expressed exons yielding a p-value for each, and then gives a score indicating the potential for a gene to be differentially expressed by integrating the p-values of the exons in the gene. We showed that CEDER can significantly increase the accuracy of existing methods for detecting DEGs on two benchmark RNA-Seq datasets and simulated datasets.

‣ Robust PCA based method for discovering differentially expressed genes

Liu, Jin-Xing; Wang, Yu-Tian; Zheng, Chun-Hou; Sha, Wen; Mi, Jian-Xun; Xu, Yong
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
Publicado em 09/05/2013 Português
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How to identify a set of genes that are relevant to a key biological process is an important issue in current molecular biology. In this paper, we propose a novel method to discover differentially expressed genes based on robust principal component analysis (RPCA). In our method, we treat the differentially and non-differentially expressed genes as perturbation signals S and low-rank matrix A, respectively. Perturbation signals S can be recovered from the gene expression data by using RPCA. To discover the differentially expressed genes associated with special biological progresses or functions, the scheme is given as follows. Firstly, the matrix D of expression data is decomposed into two adding matrices A and S by using RPCA. Secondly, the differentially expressed genes are identified based on matrix S. Finally, the differentially expressed genes are evaluated by the tools based on Gene Ontology. A larger number of experiments on hypothetical and real gene expression data are also provided and the experimental results show that our method is efficient and effective.

‣ Screening of differentially expressed genes associated with non-union skeletal fractures and analysis with a DNA microarray

XU, JIAMING; ZHANG, CHANGQING; SONG, WENQI
Fonte: D.A. Spandidos Publicador: D.A. Spandidos
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
714.1961%
The purpose of this study was to identify the feature genes that are associated with non-union skeletal fractures using samples of normal union and non-union skeletal fracture microarray data. The gene expression profile GSE494 was downloaded from the Gene Expression Omnibus database and included 12 samples based on three different platforms (GPL92, GPL93 and GPL8300). Each of the platforms had four sets of expression data, two from normal union skeletal fracture samples and two from non-union skeletal fracture samples. The differentially expressed genes within the three platforms of expression data were identified using packages in R language and the differentially expressed genes common to the three platforms were selected. The selected common differentially expressed genes were further analyzed using bioinformatic methods. The software HitPredict was used to search interactions of the common differentially expressed genes and then FuncAssociate was used to conduct a functional analysis of the genes in the interaction network. Further, the associated pathways were identified using the software WebGestalt. Under the three different platforms, GPL92, GPL93 and GPL8300, the numbers of differentially expressed genes identified were 531...

‣ Developing discriminate model and comparative analysis of differentially expressed genes and pathways for bloodstream samples of diabetes mellitus type 2

Liu, Chang; Lu, Lili; Kong, Quan; Li, Yan; Wu, Haihua; Yang, William; Xu, Shandan; Yang, Xinyu; Song, Xiaolei; Yang, Jack Y; Yang, Mary Qu; Deng, Youping
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
Português
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Background: Diabetes mellitus of type 2 (T2D), also known as noninsulin-dependent diabetes mellitus (NIDDM) or adult-onset diabetes, is a common disease. It is estimated that more than 300 million people worldwide suffer from T2D. In this study, we investigated the T2D, pre-diabetic and healthy human (no diabetes) bloodstream samples using genomic, genealogical, and phonemic information. We identified differentially expressed genes and pathways. The study has provided deeper insights into the development of T2D, and provided useful information for further effective prevention and treatment of the disease. Results: A total of 142 bloodstream samples were collected, including 47 healthy humans, 22 pre-diabetic and 73 T2D patients. Whole genome scale gene expression profiles were obtained using the Agilent Oligo chips that contain over 20,000 human genes. We identified 79 significantly differentially expressed genes that have fold change ≥ 2. We mapped those genes and pinpointed locations of those genes on human chromosomes. Amongst them, 3 genes were not mapped well on the human genome, but the rest of 76 differentially expressed genes were well mapped on the human genome. We found that most abundant differentially expressed genes are on chromosome one...

‣ Evaluation of Some Statistical Methods for the Identification of Differentially Expressed Genes

Haddon, Andrew L
Fonte: FIU Digital Commons Publicador: FIU Digital Commons
Tipo: Artigo de Revista Científica Formato: application/pdf
Português
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Microarray platforms have been around for many years and while there is a rise of new technologies in laboratories, microarrays are still prevalent. When it comes to the analysis of microarray data to identify differentially expressed (DE) genes, many methods have been proposed and modified for improvement. However, the most popular methods such as Significance Analysis of Microarrays (SAM), samroc, fold change, and rank product are far from perfect. When it comes down to choosing which method is most powerful, it comes down to the characteristics of the sample and distribution of the gene expressions. The most practiced method is usually SAM or samroc but when the data tends to be skewed, the power of these methods decrease. With the concept that the median becomes a better measure of central tendency than the mean when the data is skewed, the tests statistics of the SAM and fold change methods are modified in this thesis. This study shows that the median modified fold change method improves the power for many cases when identifying DE genes if the data follows a lognormal distribution.

‣ Identifikation von differentiell exprimierten Genen beim metastasierenden Melanom im Vergleich zum Primärtumor; Identification of differentially expressed genes in metastatic melanoma compared to primary melanoma

Fonseca da Cruz Lopes, Olga Isabel
Fonte: Universidade de Tubinga Publicador: Universidade de Tubinga
Tipo: Dissertação
Português
Relevância na Pesquisa
711.5567%
Da die Gendefekte, die zur Metastasierung des malignen Melanoms führen, weiterhin unbekannt sind, und geeignete Zielstrukturen für eine Therapie des Melanoms identifiziert werden müssen, erwächst die Notwendigkeit, weitere Gene zu identifizieren, die im Melanom bzw. in der Metastase spezifische exprimiert bzw. reprimiert werden. Dazu wurden die Methoden der Laser Capture Microdissection, SMART-Kit und die PCR-amplifizierte subtraktive Hybridisierung verwendet. In dieser Arbeit gelang unter Verwendung der Laser Capture Microdissections Methode die Isolierung reiner Melanomzellen aus Primärtumor- bzw. Lymphknotenmetastasen Gewebe für die anschliessende Identifizierung differentiell exprimierter Gene. Durch das Poolen von isolierter RNA aus je vier Primärmelanom bzw. aus je vier Lymphknotenmetastasen können individuelle Expressionsschwankungen ausgeglichen bzw. kompensiert werden. So können Gene identifiziert werden, die bei einer Mehrzahl der Patienten differentiell exprimiert sind. Eine ausreichende cDNA Quantität wurde mit Hilfe des SMART-Kit erreicht, hierbei wird die suffiziente cDNA Menge durch eine long distance PCR gewonnen. Die PCR amplifizierte subtraktive Hybridisierung wurde in zwei verschiedenen Richtungen durchgeführt...

‣ Identification of genes and pathways involved in kidney renal clear cell carcinoma

Yang, William; Yoshigoe, Kenji; Qin, Xiang; Liu, Jun S; Yang, Jack Y; Niemierko, Andrzej; Deng, Youping; Liu, Yunlong; Dunker, A Keith; Chen, Zhongxue; Wang, Liangjiang; Xu, Dong; Arabnia, Hamid R; Tong, Weida; Yang, Mary Qu
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
822.1806%
Background: Kidney Renal Clear Cell Carcinoma (KIRC) is one of fatal genitourinary diseases and accounts for most malignant kidney tumours. KIRC has been shown resistance to radiotherapy and chemotherapy. Like many types of cancers, there is no curative treatment for metastatic KIRC. Using advanced sequencing technologies, The Cancer Genome Atlas (TCGA) project of NIH/NCI-NHGRI has produced large-scale sequencing data, which provide unprecedented opportunities to reveal new molecular mechanisms of cancer. We combined differentially expressed genes, pathways and network analyses to gain new insights into the underlying molecular mechanisms of the disease development. Results: Followed by the experimental design for obtaining significant genes and pathways, comprehensive analysis of 537 KIRC patients' sequencing data provided by TCGA was performed. Differentially expressed genes were obtained from the RNA-Seq data. Pathway and network analyses were performed. We identified 186 differentially expressed genes with significant p-value and large fold changes (P < 0.01, |log(FC)| > 5). The study not only confirmed a number of identified differentially expressed genes in literature reports, but also provided new findings. We performed hierarchical clustering analysis utilizing the whole genome-wide gene expressions and differentially expressed genes that were identified in this study. We revealed distinct groups of differentially expressed genes that can aid to the identification of subtypes of the cancer. The hierarchical clustering analysis based on gene expression profile and differentially expressed genes suggested four subtypes of the cancer. We found enriched distinct Gene Ontology (GO) terms associated with these groups of genes. Based on these findings...

‣ Detecting Differentially Expressed Genes with RNA-seq Data Using Backward Selection to Account for the Effects of Relevant Covariates

Nguyen, Yet; Nettleton, Dan; Liu, Haibo; Tuggle, Christopher K.
Fonte: Springer US Publicador: Springer US
Tipo: Artigo de Revista Científica
Português
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710.1353%
A common challenge in analysis of transcriptomic data is to identify differentially expressed genes, i.e., genes whose mean transcript abundance levels differ across the levels of a factor of scientific interest. Transcript abundance levels can be measured simultaneously for thousands of genes in multiple biological samples using RNA sequencing (RNA-seq) technology. Part of the variation in RNA-seq measures of transcript abundance may be associated with variation in continuous and/or categorical covariates measured for each experimental unit or RNA sample. Ignoring relevant covariates or modeling the effects of irrelevant covariates can be detrimental to identifying differentially expressed genes. We propose a backward selection strategy for selecting a set of covariates whose effects are accounted for when searching for differentially expressed genes. We illustrate our approach through the analysis of an RNA-seq study intended to identify genes differentially expressed between two lines of pigs divergently selected for residual feed intake. We use simulation to show the advantages of our backward selection procedure over alternative strategies that either ignore or adjust for all measured covariates.

‣ Transcriptional Profiling Identifies Location-Specific and Breed-Specific Differentially Expressed Genes in Embryonic Myogenesis in Anas Platyrhynchos

Zhang, Rong-Ping; Liu, He-He; Liu, Jun-Ying; Hu, Ji-Wei; Yan, Xi-Ping; Wang, Ding-Min-Cheng; Li, Liang; Wang, Ji-Wen
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Publicado em 02/12/2015 Português
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Skeletal muscle growth and development are highly orchestrated processes involving significant changes in gene expressions. Differences in the location-specific and breed-specific genes and pathways involved have important implications for meat productions and meat quality. Here, RNA-Seq was performed to identify differences in the muscle deposition between two muscle locations and two duck breeds for functional genomics studies. To achieve those goals, skeletal muscle samples were collected from the leg muscle (LM) and the pectoral muscle (PM) of two genetically different duck breeds, Heiwu duck (H) and Peking duck (P), at embryonic 15 days. Functional genomics studies were performed in two experiments: Experiment 1 directly compared the location-specific genes between PM and LM, and Experiment 2 compared the two breeds (H and P) at the same developmental stage (embryonic 15 days). Almost 13 million clean reads were generated using Illumina technology (Novogene, Beijing, China) on each library, and more than 70% of the reads mapped to the Peking duck (Anas platyrhynchos) genome. A total of 168 genes were differentially expressed between the two locations analyzed in Experiment 1, whereas only 8 genes were differentially expressed when comparing the same location between two breeds in Experiment 2. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes pathways (KEGG) were used to functionally annotate DEGs (differentially expression genes). The DEGs identified in Experiment 1 were mainly involved in focal adhesion...

‣ Characterization of differentially expressed genes using high-dimensional co-expression networks

de Abreu, Gabriel C. G.; Labouriau, Rodrigo
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 15/11/2010 Português
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We present a technique to characterize differentially expressed genes in terms of their position in a high-dimensional co-expression network. The set-up of Gaussian graphical models is used to construct representations of the co-expression network in such a way that redundancy and the propagation of spurious information along the network are avoided. The proposed inference procedure is based on the minimization of the Bayesian Information Criterion (BIC) in the class of decomposable graphical models. This class of models can be used to represent complex relationships and has suitable properties that allow to make effective inference in problems with high degree of complexity (e.g. several thousands of genes) and small number of observations (e.g. 10-100) as typically occurs in high throughput gene expression studies. Taking advantage of the internal structure of decomposable graphical models, we construct a compact representation of the co-expression network that allows to identify the regions with high concentration of differentially expressed genes. It is argued that differentially expressed genes located in highly interconnected regions of the co-expression network are less informative than differentially expressed genes located in less interconnected regions. Based on that idea...

‣ Characteristic Direction Approach to Identify Differentially Expressed Genes

Clark, Neil R.; Hu, Kevin; Chen, Edward Y.; Duan, Qioanan; Ma`ayan, Avi
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 31/07/2013 Português
Relevância na Pesquisa
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Genome-wide gene expression profiles, as measured with microarrays or RNA-Seq experiments, have revolutionized biological and biomedical research by providing a quantitative measure of the entire mRNA transcriptome. Typically, researchers set up experiments where control samples are compared to a treatment condition, and using the t-test they identify differentially expressed genes upon which further analysis and ultimately biological discovery from such experiments is based. Here we describe an alternative geometrical approach to identify differentially expressed genes. We show that this alternative method, called the Characteristic Direction, is capable of identifying more relevant genes. We evaluate our approach in three case studies. In the first two, we match transcription factor targets determined by ChIP-seq profiling with differentially expressed genes after the same transcription factor knockdown or over-expression in mammalian cells. In the third case study, we evaluate the quality of enriched terms when comparing normal epithelial cells with cancer stem cells. In conclusion, we demonstrate that the Characteristic Direction approach is much better in calling the significantly differentially expressed genes and should replace the widely currently in used t-test method for this purpose. Implementations of the method in MATLAB...