Gene-set variation analysis
Analysis of strain and regional variation in gene expression in mouse brain
... each gene is considered, where fold change is defined as the ratio of gene expression in a test condition to that in a control ...Microarray Analysis Suite (Affymetrix), one also has the option of ...
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Genetic Analysis of Variation in Gene Expression in Arabidopsis thaliana
... whole set of sig- nificant differential ...additive gene expression between Col and Cvi, Ler and Cvi, and Col and Ler, respectively (Table 1), ranging from ...respective gene lists are provided at ...
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Variation in the RAD51 gene and familial breast cancer
... An analysis of 93 early-onset breast cancer cases, 9% of which had a strong family history, revealed no coding region variation ...(SSCP) analysis and detected one relatively rare variant, an ...
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A longitudinal feature selection method identifies relevant genes to distinguish complicated injury and uncomplicated injury over time
... investigating gene expression patterns across time, in an effort to capture dynamical changes that are biologically meaningful to the ...in gene expression patterns over time ...the gene expression ...
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Variation In Greedy Approach To Set Covering Problem
... The exact procedure (Ex) is intended to achieve the optimal solution for the SCP. This category includes dynamic programming, branch and bound techniques. Heuristic (He) aims to achieve near-optimal solution also known ...
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Gene set analysis methods applied to chicken microarray expression data
... Gene set analysis was performed using software packages developed in Bioconductor [8] and R ...the gene set ...testing gene sets and the corresponding p-values were computed ...
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Estimating the Empirical Null Distribution of Maxmean Statistics in Gene Set Analysis
... A gene pathway commonly refers to a set of genes that share a particular prop- erty, carry out a biological function or lead to a certain product in ...(DE) analysis on such gene sets ...
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Gene set analysis controlling for length bias in RNA-seq experiments
... the gene level by modeling the number of reads or test statistics by gene length or GC ...of gene length is a simple solution, but it does not completely remove the length ...length gene ...
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A Homologue of the Recombination-Dependent Growth Gene, rdgC, Is Involved in Gonococcal Pilin Antigenic Variation
... antigenic variation (Wainwright et al. 1994), is the Molecular methods: Unless otherwise noted, all enzymes target for multiple site-specific binding proteins (Wain- used in this study were supplied and used under ...
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MOLECULAR ANALYSIS OF THE PROMOTER REGION OF THE SMN2 GENE IN PATIENTS OF SPINAL MUSCULAR ATROPHY TOWARDS SCRUTINIZING THE CLINICAL SEVERITY OF SPINAL MUSCULAR ATROPHY
... www.wjpr.net Vol 3, Issue 8, 2014. 140 As previously reported [14] , the CRE-II element was analyzed for the molecular variation in normal healthy individuals and SMA patients from different clinical types. The ...
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Ten hub genes associated with progression and prognosis of pancreatic carcinoma identified by co-expression analysis
... regression analysis by using GSE62452 and TCGA dataset, we identified 10 real hub genes (CCNA2, CCNB1, CENPF, DLGAP5, KIF14, KIF23, NEK2, RACGAP1, TPX2 and UBE2C) tightly related to progression of ...hub ...
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Transcriptomics and methylomics in chronic periodontitis with tobacco use: a pilot study
... Methylation analysis indicated that smoking affected both DNA methylation and gene expression, which showed negative correlation ...affect gene expression were localized to positions near ...
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Pathprinting: An integrative approach to understand the functional basis of disease
... in gene membership is intro- duced when combining multiple pathway ...Overlapping gene membership can be due to redundancy in the pathway sets, for example different views of the Wnt pathway in the ...
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The genetic overlap of attention deficit hyperactivity disorder and autistic spectrum disorder
... Second, pragmatic decisions have been made regard- ing the representation of linkage studies. Unfortunately, no consensus exists about the precise distance around the linkage peak that should be considered important. ...
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A cross-study gene set enrichment analysis identifies critical pathways in endometriosis
... tests to distinguish minimal/mild and moderate/severe disease, by sampling the endometrium, should be focused on the early secretory phase of the menstrual cycle [50]. We hypothesize that all cell types in the ...
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Integrative Analysis of Multi-Platform Genomic Data.
... Different gene and probe sequences will affect its binding affinity and the detection ...the gene specific bias from different GC content (Wu, et ...to gene specific bias (Dohm, et ...the gene ...
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ADH genes were examined. ADH mRNA expression level was markedly reduced in HBV-related HCC tumor tissue. ADH1C and ADH5 overexpres-
... A total of 218 HBV-related HCC patients with complete follow-up profiles were recruited for the study; the clinical characteristics are sum- marized in Table 1. At the time of analysis, 84/218 patients (38.5%) had ...
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EPHB2 carried on small extracellular vesicles induces tumor angiogenesis via activation of ephrin reverse signaling
... 6B). Analysis of the total tube length and numbers of junctions of HUVECs treated with EVs from DICER-KD cells did not show significant changes compared with that of HUVECs treated with control EVs (Supplemental ...
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Gene Set Enrichment Analysis using Linear Models and Diagnostics
... As stated previously, the residuals methods has not been as thoroughly optimized, and offering a competitor to Hertzberg et al. (2007) was not our goal here. However, the similarity in performance is encouraging, given ...
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Antisense oligonucleotide–mediated ataxin-1 reduction prolongs survival in SCA1 mice and reveals disease-associated transcriptome profiles
... Statistics. qPCR, RNA-seq, and motor performance data are expressed as mean ± SEM. Statis- tical analyses were performed using GraphPad Prism software (version 7.03) and R (version 3.3.3). Significant differences were ...
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