To analyze the candidate genes, we combined gene annotation, qPCR and expression profile from microarray data to investigate the potential functional polymorphisms capable of causing changes in the phenotype.
The advent of RNA-Seq technology, in which the entire polyadenylated transcriptome is sequenced [ 19- 24], is capable of building on this microarray data to provide additional insights into the transcriptome of the airway epithelium and its response to cigarette smoke.
Although many GSA methods are designed to analyze microarray data [ 3, 11, 16– 19], relatively few methods are capable of analyzing RNA-Sequencing data [ 20– 23], and even fewer handle single-nucleotide variant data [ 19, 24, 25] or DNA methylation data [ 26].
HME3M is shown to outperform all comparison methods and further is capable of identifying known biologically active pathways within microarray data.
While useful for microarray data comparison, MADMuscle is not limited to microarray results, and is equally capable of comparing results from other high-throughput technologies (SAGE, ChIP-on-chip or ChIP-seq, Protein-array and other proteomic analyses, large scale Real-time PCR, etc).
For CDC, the company's software is analyzing microarray data obtained from chronic fatigue syndrome patients in an attempt to identify gene expression profiles capable of diagnosing CFS.
Although both IA3902 and NCTC11168 harbor similar pathways for metabolizing serine, proline, glutamate, aspartate, and lactate, the sheep abortion strain IA3902 may be more capable in utilizing of serine and less capable in utilizing proline, glutamate, aspartate, and lactate, as suggested by the microarray data (supplementary table S4, Supplementary Material online).
This investigation, for which all the work, with the exception of the microarray data, was undertaken in Ho Chi Minh City, highlights the benefits of having rapidly available multidisciplinary expertise at the site, capable of conducting detailed clinical, epidemiological, and molecular analysis of the outbreak and the causative microorganism.
Both ΔgB and ΔgH virions are capable of stimulating an NF-kB response (Table 2), a result that correlates with the preliminary microarray data (Table 1).
In this paper we describe a method that is capable of both identifying putative regulatory clusters and predicting approximate expression levels of miRNAs from mRNA microarray data.
