کد مقاله | کد نشریه | سال انتشار | مقاله انگلیسی | نسخه تمام متن |
---|---|---|---|---|
10825811 | 1064676 | 2013 | 20 صفحه PDF | دانلود رایگان |
عنوان انگلیسی مقاله ISI
On the importance of small changes in RNA expression
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کلمات کلیدی
RNAseqLPSMicroArray Quality ControlFDRMAQCinflammation - التهاب( توروم) differential expression - بیان دیفرانسیلDifferential gene expression - بیان ژن دیفرانسیلTranscriptome - ترانسکریپتومfold change - تغییر در برابرSingle molecule sequencing - توالی تک مولکولیfluorescent in situ hybridization - فلورسنت در محل hybridizationlipopolysaccharide - لیپوپلی ساکاریدFish - ماهیfalse discovery rate - میزان کشف کاذبGene ontology - هستیشناسی ژنیSMS - پیامک
موضوعات مرتبط
علوم زیستی و بیوفناوری
بیوشیمی، ژنتیک و زیست شناسی مولکولی
زیست شیمی
پیش نمایش صفحه اول مقاله
چکیده انگلیسی
The analysis of the differential expression of genes has been the key goal of many molecular biology methods for decades and will remain with us for decades to come. It constitutes a fundamental resource at our disposal for determining the relationship between products of transcription, biology and disease. The completed genome sequencing of many common species allowed microarrays and RNA sequencing (RNAseq) to become major tools in Systems Biology. However, we estimate that at least half of all experiments ignore transcripts that change less than some subjectively chosen threshold, typically around 2-3 fold. Here we show that a majority of the informative RNAs and differentially expressed transcripts can exhibit fold changes less than 2. We use highly quantitative single-molecule sequencing of total cellular RNA derived from a time course of inflammatory response, a process critical to a large number of diseases. Furthermore, we show that enrichment of biologically-relevant functions occurs even at very low fold changes in RNA levels. In addition, we show that most of the common statistical methods can reliably detect transcripts with low fold change when as few as 3 biological replicates are sequenced using single-molecule based RNAseq. In conclusion, given the prevalence of expression profiling in current research, the loss of data in half of all expression studies results in a significant, yet needless drain on the discovery process.
ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Methods - Volume 63, Issue 1, 1 September 2013, Pages 18-24
Journal: Methods - Volume 63, Issue 1, 1 September 2013, Pages 18-24
نویسندگان
Georges St. Laurent, Dmitry Shtokalo, Michael R. Tackett, Zhaoqing Yang, Yuri Vyatkin, Patrice M. Milos, Bernd Seilheimer, Timothy A. McCaffrey, Philipp Kapranov,