Accumulating evidence suggests that RNAs interacting with genomic regions play important roles in the regulation of genome functions, including X chromosome inactivation and gene expression. However, to our knowledge, no non-biased methods of identifying RNAs that interact with a specific genomic region have been reported. Here, we used enChIP-RNA-Seq, a combination of engineered DNA-binding mo...

Background: T-helper cells play an essential role in the progression of lymphedema. This study aimed to explore biological significance cell-associated genes (THAGs) a mouse tail model lymphedema by RNA-sequencing (RNA-seq) data.

RNA-seq is a sensitive and accurate technique to compare steady-state levels of RNA between different cellular states. However, as it does not provide an account of transcriptional activity per se, other technologies are needed to more precisely determine acute transcriptional responses. Here, we have developed an easy, sensitive and accurate novel computational method, IRNA-SEQ: , for genome-w...

Crohn disease (CD) is a type of inflammatory bowel that causes inflammation in the digestive tract. Cases CD are increasing worldwide, calling for more research to elucidate pathogenesis CD. For this purpose, usage RNA-sequencing (RNA-seq) technique increasingly appreciated, as it captures RNA expression patterns at particular time point high-throughput manner. Although many RNA-seq datasets ge...

DNA microarrays and RNA sequencing (RNA-seq) are major technologies for performing high-throughput analysis of transcript abundance. Recently, concerns have been raised regarding the concordance of data derived from the two techniques. Using cDNA libraries derived from normal human foreskin fibroblasts, we measured changes in transcript abundance as cells transitioned from proliferative growth ...

RNA-sequencing (RNA-seq) technology has become a major choice in detecting differentially expressed genes across different biological conditions. Although microarray technology is used for the same purpose, statistical methods available for identifying differential expression for microarray data are generally not readily applicable to the analysis of RNA-seq data, as RNA-seq data comprise discr...

Although a large number of clustering algorithms have been proposed to identify groups of co-expressed genes from microarray data, the question of if and how such methods may be applied to RNA sequencing (RNA-seq) data remains unaddressed. In this work, we investigate the use of data transformations in conjunction with Gaussian mixture models for RNA-seq co-expression analyses, as well as a pen...

With advances in molecular biology, various biological phenomena can now be explored at higher resolution using mRNA sequencing (RNA-Seq) and chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq), two powerful high-throughput next-generation sequencing (NGS) technologies. While methods are used widely in mouse, human, etc., less information is available in other animal...

this study was done to gain insights into transcriptional regulation of negative energy balance (neb) assoctiated genes. overexpressed genes in neb were identified using microarray and rna-seq data and promoter analysis of these overexpressed genes was applied to identify novel transcription factors. moreever, string database was used to construct a regulatory network of identified transcriptio...