In this work, a novel algorithm for reverse engineering gene networks on a genome-wide scale using a noisy gene expression data is proposed.
This calculation was done on a genome-wide scale using a custom script that implemented a divide-and-conquer algorithm, and which is available upon request.
On the other hand, our results based on MethylCap-seq data further validate changes in the DNAm pattern during culture expansion on a genome-wide scale using a different approach, which does not require bisulfite conversion.
Personalized medicine using stem cells is now a practical possibility because of the convergence of two distinct fields: genomic research, which has developed techniques to analyze cells on a genome-wide scale using a very small sample size (even single cells), and direct reprogramming, which has allowed researchers to obtain cells of virtually any phenotype from any human genotype.
In this study, a carbon and light insensitive (cli186) mutant is identified and its molecular defects characterized on a genome-wide scale, using a multinetwork approach to identify the genes, biological processes and regulatory/metabolic networks affected in the cli186 mutant.
To gain more insight into these motifs, we then conducted reverse analysis of the occurrences of uncapped reads surrounding every candidate motif on a genome-wide scale using a cluster heat map that we named motif-oriented read positioning heat map (MORPH).
Herein, we sought to detail the transcriptional regulatory configuration of PPARγ-RXR-DNA interaction on a genome-wide scale using an established ChIP-PET sequencing approach.
In this study, we sought to analyze methylation on a genome wide scale using human CpG island microarrays to uncover novel methylatled loci within prostate cancer.
This paper recently reported predicted PPRE on a genome wide scale, using computational genomics and also summarized known PPRE.
In the budding yeast, methylation and acetylation patterns have been mapped on a genome wide scale using antibodies that exclusively recognize those motifs (35- 37).
In fact, several groups have examined the global distribution of modified histones on a genome wide scale using ChIP followed by hybridizing the co-precipitating DNA to genomic microarrays (33, 34).
