Identifying the impact of G-Quadruplexes on Affymetrix 3′ Arrays using Cloud Computing

Abstract

SummaryA tetramer quadruplex structure is formed by four parallel strands of DNA/ RNA containing runs of guanine. These quadruplexes are able to form because guanine can Hoogsteen hydrogen bond to other guanines, and a tetrad of guanines can form a stable arrangement. Recently we have discovered that probes on Affymetrix GeneChips that contain runs of guanine do not measure gene expression reliably. We associate this finding with the likelihood that quadruplexes are forming on the surface of GeneChips.In order to cope with the rapidly expanding size of GeneChip array datasets in the public domain, we are exploring the use of cloud computing to replicate our experiments on 3 ′ arrays to look at the effect of the location of G-spots (runs of guanines). Cloud computing is a recently introduced high-performance solution that takes advantage of the computational infrastructure of large organisations such as Amazon and Google.We expect that cloud computing will become widely adopted because it enables bioinformaticians to avoid capital expenditure on expensive computing resources and to only pay a cloud computing provider for what is used. Moreover, as well as financial efficiency, cloud computing is an ecologically-friendly technology, it enables efficient data-sharing and we expect it to be faster for development purposes. Here we propose the advantageous use of cloud computing to perform a large data-mining analysis of public domain 3 ′ arrays.

Transcriptomics: Quantifying Non-Uniform Read Distribution Using MapReduce

“…Sequence-specific motifs are an issue in microarray data [18,35] and have also been shown to affect RNA-seq data [38] as well as RNA primers [9], resulting in sequencespecific deviations in the distribution of mapped reads to a reference genome [27,15]. Furthermore GC content effects have been demonstrated in both Microarray and RNA-seq data [26].…”

“…The effect of extremes of GC content in sequencing data (as well as microarray data) has been discussed in numerous studies [6,18], and we therefore also investigate the effect of the mean GC content of reads within the exonḡe and the GC content of the 4-mer motif itself gm. In order to partition reads by mean GC content (which we will discuss later) we also define binned GC content ranges (30-40%, 40-50%, 50-60% and 60-70%) forḡe as follows:…”

Self-service infrastructure container for data intensive application

“…In this work, some of the experiments which use the Human GeneChip called HG-U133A were downloaded and analyzed. The analysis, carried out using the R statistical language, was to determine whether runs of guanine in the probe sequences (runs of 4 or more 'G's) were producing a significant bias in the gene expression data [14,39].…”

RBioCloud: A Light-Weight Framework for Bioconductor and R-based Jobs on the Cloud

“…The cloud has become an appealing alternative high-performance computing platform for ad-hoc analytics since it offers on-demand computing and storage resources, along with scalability and low maintenance costs [4], [5], [6], [7]. This has led to a variety of research for supporting analytics in computational biology and bioinformatics on the cloud (for example, [8], [9], [10] and [11]). …”