Abstract Recent advances in high-throughput cDNA sequencing (RNA-seq) can reveal new genes and splice variants and quantify expression genome-wide in a single assay. The volume and complexity of data from RNA-seq experiments necessitate scalable, fast and mathematically principled analysis software. T...
transcriptomeandshedslightontherarestandmostcell-and context-speci ictranscripts 6 .Furthermore,becausethenumbero readsproduced romanRNAtranscriptisa unctiono thattran- script’sabundance,readdensitycanbeusedtomeasuretranscript 7,8 andgene 2,3,9,10 expressionwithcomparableorsuperioraccuracyto expression...
这种方法被称为3' -Digital Gene Expression (3'-DGE) RNA-Seq,这种方法的测序深度只需要3-10M。如果使用得当,相比于常规的全转录本RNA-Seq(Full-Transcript (FT) RNA-Seq),它可以帮助研究人员节约很大的成本来进行差异表达分析和定量转录组分析。 3'-Digital Gene Expression(3'-DGE)RNA-Seq是一种相对较新...
After the completion of the genomic sequence ofArabidopsis thaliana, it is now a priority to identify all the genes, their patterns of expression and functions. Transcript profiling is playing a substantial role in annotating and determining gene functions, having advanced from one-gene-at-a-time ...
Rather than summing cumulative expression across many genes, we employ an algorithm which compares the relative expression of all possible pairs of genes in a set, and selects those gene pairs which exhibit an order of expression correlated strongly with phenotype- with a relative expression ratio ...
transcript encoding for this latter isoform is significantly reduced in the temporal lobe, suggesting that expression of BIN1 isoform 1 in neurons could be reduced. This observation is in line with decreased BIN1 isoform 1 protein expression in the AD brain compared with controls (our own results)...
昨天12 月 16 日在 Rcran 上刚发的一个 R 包,叫做geneExpressionFromGEO, 它是一个简单的函数,可以读取GEO 芯片表达数据和注释文件, 并返回一个整合注释好的数据框的形式,好像还挺方便的。 注释数据平台包括: GPL11532,GPL23126,GPL6244,GPL8300,GPL80,GPL96,GPL570,GPL571,GPL2115,GPL1293,GPL6102,GPL61...
Since the probesets were linked to transcripts and proteins through rigorous association and alignment procedures, the expression profiles of transcript-level synonymous probesets were supposed to be more consistent than those of gene-level synonymous probesets [14, 15]. This was taken as the basis...
Differential expression of RNA-Seq data at the gene level – the DESeq package First, we need a description of the samples, which we keep in a data.frame whose columns correspond to different types of information, and whose rows correspond to the 7 samples: > pasillaDesign = data.fr...
使用tophat和cufflinks计算RNA-seq数据的表达水平时,当一个基因在一个样本中有多个表达水平时需要合并它们的表达水平。 This code is a solution to collapsing duplicate FPKMs for a gene. Problem/Issue: In the cufflinks output files *_genes.expr (which reports the gene-level coordinates and expression ...