fixed paraffin embedded sections for gene expression analysis

... the expression of gene in the KO strain Gene names and the p-values are shown for all genes There is a considerable change in the expression of SIC1 genes between WT and KO strain 58 4.14 Expression ... th generation d Distance metric used for clustering i Dk Direction of change of information for ith cluster i gk Change of information for ith cluster Gk Generation k Gmax Maximum number of generations ... time-course gene expression data analysis 1.4 Challenges in Gene Expression Data-mining Though gene expression data provides the state of a cell by measuring the expres- sion levels of almost all its genes,...

Ngày tải lên: 11/09/2015, 09:01

... µm formula of hybridization solution was described previously [3] For detection of hybridization, sections were incubated with anti-digoxigenin conjugated with alkaline phosphatase (Roche) for ... assay for the detection of CHV These results suggest that ISH assay using digoxigenin-labeled probe, which was optimized in this study, may be recommended for diagnosis of CHV in formalin -fixed ... biological diagnostic methods for the detection of intracellular viral DNAs in paraffin sections J Vet Med Sci 2003, 64, 231-235 73 Kim O, Chae C In situ hybridization for the detection and localization...

Ngày tải lên: 07/08/2014, 17:22

... , ω2 ]; 2: Perform power spectral analysis on gene expression data; 3: Perform statistical tests so that the periodically expressed genes are recognized and stored in set C; 4: for each xi ∈ ... Cerevisiae genes Gene expression levels are indicated by the heatmap This cluster contains 130 genes The gene expressions in the cdc15 experiment oscillate between low and high levels Most of these genes ... the 104 genes The false positive control removed genes and left 722 genes marked as potential cell cycle involved genes The identified genes are provided in the additional files in MS Excel format...

Ngày tải lên: 22/06/2014, 00:20

... the level of gene expression The two main sources of heterogeneity in gene expression variations — additive and multiplicative components — are excluded in our analysis by eliminating expression ... log-transformation of the data Expression deviations η are determined for each sample as a deviation of the gene expression ordinates from regression line calculated against the averaged profile for gene ... Differential gene expression analysis of active disease Statistical analysis of the difference of gene expression in samples from patients and 12 healthy controls gave the following results 1716 genes...

Ngày tải lên: 09/08/2014, 01:23

... immune -gene expression, and in the induction of antiproliferative genes Lastly, our analysis further confirms that the relative levels of TR isoforms lead to dramatic differential effects on gene expression ... comprising genes with tissue-specific expression and genes with similar or contrasting expression in multiple tissues Category analysis of expression patterns identified genes that were modulated by T3-dependent ... Figure Concordance of gene expression determined by microarrays and RT-PCR Concordance of gene expression determined by microarrays and RT-PCR Expression ratios of representative genes in (a) cerebellum...

Ngày tải lên: 09/08/2014, 20:20

... Bioconductor package for differential expression analysis of digital gene expression data Bioinformatics 2010, 26:139-140 Bioconductor [http://www.bioconductor.org/] WEHI Bioinformatics - Resources ... normalization is an essential step for inferring true differences in expression between samples The number of reads for a gene is dependent not only on the gene s expression level and length, but ... total reads for gene g in experimental condition zk Their analysis utilizes an offset to account for the library size and a likelihood ratio (LR) statistic to test for differences in expression...

Ngày tải lên: 09/08/2014, 20:21

... for HCE3.5 software with parameters set for Pearson correlation coefficient for similarity/distance measure and average linkage method for hierarchical clustering BLASTX analysis of flax unigenes ... in sequences reported for any organism, suggesting that this category represents genes that are likely unique to flax Digital analyses revealed gene expression dynamics for the biosynthesis of ... our unigene dataset indicative of a broad coverage of expressed genes in the flax genome Hierarchical cluster analysis of flax tissue based EST collections In order to compare the gene expression...

Ngày tải lên: 11/08/2014, 11:22

... Selected genes Figure Clustering of genes changing during fruit development Clustering of genes changing during fruit development Cluster analysis of gene expression A and B, Expression patterns for ... 50th gene) Several genes were also chosen for qRTPCR to confirm expression patterns of genes in particular pathways (see below) Three housekeeping genes were Page of 29 (page number not for citation ... relative qRT-PCR expression; the right Y axes shows absolute array expression 10 0 150 Days after anthesis Figure Expression pattern for candidate fruit development genes Expression pattern for candidate...

Ngày tải lên: 12/08/2014, 05:20

... informative genes from thousands of available genes The informative genes are those that have high discriminative powers, and have low correlations between each pair of them [16] Selecting informative ... effective for microarray data analysis Other than simply picking the top-ranked genes, MRMR also minimizes redundant information in the selected genes by measuring correlations between different genes ... two parts for training and the left part for testing For each method, this procedure was repeated for 100 times, and the averages and standard deviations of accuracy were taken for performance...

Ngày tải lên: 12/08/2014, 17:20

... responsive genes in the brain Oligonucleotide microarrays [25] offer an attractive experimental approach for such global gene expression analyses We therefore performed a microarray analysis of ... independent samples: n = for analysis of P43 Nfia-/-; n = for P43 Nfia+/+; n = for P16 Nfia-/-; and n = for P16 Nfia+/+ Adjacent bars show the P16 and P43 results for the respective gene Car2, carbonic ... -1.45 -1.35 1.33 1.41 1.79 1.86 1.96 2.36 Figure qRT-PCR analysis of gene expression: P43 Nfia-/- versus P43 Nfia+/+ qRT-PCR analysis of gene expression: P43 Nfia-/- versus P43 Nfia+/+ Shown are...

Ngày tải lên: 14/08/2014, 07:21

... Segments TAIR genes (b) Unannotated transcribed region Figure online resources for gene expression analysis At-TAX6 At-TAX online resources for gene expression analysis (a) At-TAX gene expression ... reports expression values for user-specified genes, and a customized generic genome browser [48] The At-TAX gene expression visualization tool can be fed with TAIR (The Arabidopsis Information ... transcription methods used to generate the probes for array hybridization [33,34] To profile the expression of annotated genes on tiling arrays, we extracted probe information for all genes that can be analyzed...

Ngày tải lên: 14/08/2014, 20:22

... tropicalis genome as a surrogate for the Xenopus laevis genome, sequence-level analysis can be pursued Microarray analysis of gene expression Microarray analysis of gene expression is the parallelization ... pathways that are critical for cardiogenesis Chapter describes one technique for studying early targets of Nkx2-5: the analysis of changes in global gene expression caused by over -expression of Nkx2-5 ... to be used for gene expression analysis Changes in global gene expression were measured by comparing the abundance of transcripts using the Affymetrix Xenopus laevis Genome Array GeneChip in...

Ngày tải lên: 24/08/2014, 12:29

... 1.1 Introduction to bioinformatics… 1.2 Gene expressions and microarrays………….………………………… 1.2.1 Understanding gene expressions…………………………… 1.2.2 Analyzing gene expression levels ………………………… ... then performed using a proposed neighborhood analysis method based on the information provided by each gene on the list Each gene votes for the class value of an unknown sample If the expression ... a brief description about the gene The next field is the gene accession number by which we can look for the gene in any genetic database It is just an ID for the gene After this the samples are...

Ngày tải lên: 30/10/2014, 20:03

... data analysis …………………………………………………57 5.8.2 Comparison data analysis ……………………………… ……………58 5.8.3 Gene filtration………………………………………………………….…58 5.8.4 Gene clustering and functional analysis based on Gene ... diabetes alters the expression of genes involved in neuronal migration and neurogenesis in cranial neural tubes of mouse embryos…………… 99 6.1 Expression pattern of developmental control genes is altered ... 2004) 3.4 Data analysis strategies There are three steps for data analysis: data normalization, data filtering and pattern identification Initially data are normalized before comparing expression...

Ngày tải lên: 11/09/2015, 16:07

... al (2005) Analysis of long-lived C elegans daf-2 mutants using serial analysis of gene expression Genome Res 15, 603–615 10 Ryu EJ, Angelastro JM & Greene LA (2005) Analysis of gene expression ... serial analysis of gene expression tags for gene identification Proc Natl Acad Sci USA 97, 349–353 35 Richards M, Tan SP, Chan WK & Bongso A (2006) Reverse serial analysis of gene expression (SAGE) ... Serial analysis of gene expression: rapid RT-PCR analysis of unknown SAGE tags Nucleic Acids Res 27, e17 34 Chen JJ, Rowley JD & Wang SM (2000) Generation of longer cDNA fragments from serial analysis...

Ngày tải lên: 07/03/2014, 00:20

... Microarray analysis of gene expression in drug resistant ovarian cancer cell lines To identify genes and pathways important in the development of drug resistance, we performed gene expression ... identified changes in gene expression patterns using Illumina wholegenome expression microarrays Validation of selected genes was performed by RT-PCR and immunoblotting Pathway enrichment analysis using ... the Gene Expression Omnibus database [GEO:GSE26465] Multidimensional scaling (MDS) analysis based on gene expression data showed that the cell lines clustered according to the drug used in generating...

Ngày tải lên: 20/06/2014, 08:20

... continuous wavelet analysis to transform all expression data by wavelet transform; it decomposes temporal gene expression data in both time and frequency domains In wavelet transform we take a real/complex ... down into spectrum In the gene expression analysis, we assume that any gene expression level is a comprehensive result of gene effects and condition effects, that is, the expression profile shift ... calculation was done by SAS and Matlab 3.1 RESULT AND ANALYSIS The variation of gene expression profile A large data set was generated from a unique gene expression experiment where activity of the promoter...

Ngày tải lên: 22/06/2014, 19:20

... to expressionplot@googlegroups.com Extracting biological meaning from high throughput data ExpressionPlot offers the gene expression community an easy-to-use tool for automated analysis of gene ... and a prototype are available at http://expressionplot.com/ Rationale RNA-Seq has emerged in recent years as the eminent platform for analysis of gene expression and RNA processing [1-3] However, ... 10-4 for RNA-Seq, and fold-change cutoffs are for both platforms Colored numbers show number of genes in each category (b) Similar plot comparing the same x-axis (human heart-enriched gene expression...

Ngày tải lên: 09/08/2014, 23:20

... were able to identify a gene- gene and gene- microRNA network that significantly stratifies patient prognosis By combining gene- expression microarray data with microRNA expression levels, copy ... and prediction accuracy of a prognostic gene signature BMC Bioinformatics 2009, 10:147 Edgar R, Domrachev M, Lash AE: Gene Expression Omnibus: NCBI gene expression and hybridization array data ... heterozygous deletion A standard threshold for copy number alteration of >0.3 for amplification, and

Ngày tải lên: 11/08/2014, 12:21

... 2004, http://www.retrovirology.com/content/1/1/10 Figure of Analysis viral gene expression Analysis of viral gene expression (A) HHV-6B gene expression Only the HHV-6 open reading frames are illustrated ... the expression studies AP performed many of the expression studies and the ChIP-chip analysis VL performed the ChIP-chip analysis CD participated in the design and printing of the array and performed ... hybridizations were performed The data is represented for each gene as the ratio of gene- specific hybridization intensity on the average intensity for all spots The cut-off ratio for high hybridizations...

Ngày tải lên: 13/08/2014, 13:20