background: the opening and closing of the implantation window is important for successful pregnancy in eutherians. the recent study demonstrated that the window of uterine receptivity was prepared by the sole action of progesterone in mice, but the mechanism to close the window remained to be elucidated. methods: the pregnant mice were ovariectomized on the evening on the third day of pregnanc...

............................................................................................................................... i DEDICATION .......................................................................................................................... iv ACKNOWLEDGEMENTS ....................................................................................................... v TABLE O...

Despite the fact that many RNA-Seq experiments do not use biological replicates, most of the existing differential gene expression analysis for RNA-Seq data are designed to work with replicates. We present a novel method for differential gene expression analysis based on bootstrapping. We also discuss the use of different normalization methods with Fisher’s exact test. We compare the methods we...

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...