Using nuclear factor-κB (NF-κB) ChIP-Seq data, we present a framework for iterative learning of regulatory networks. For every possible transcription factor-binding site (TFBS)-putatively regulated gene pair, the relative distance and orientation are calculated to learn which TFBSs are most likely to regulate a given gene. Weighted TFBS contributions to putative gene regulation are integrated t...

To identify genes of potential importance to alkalinity tolerance, RNA sequencing (RNA-Seq) was performed to survey gill transcriptome profiles from freshwater (FW) and alkaline water (AW) exposed Nile tilapia (Oreochromis niloticus). A total of 22,724,036 (AW)/16,461,040 (FW) single-end reads were generated in which 20,304,348 (AW)/14,681,290 (FW) reads (90.0/89.72%) were aligned to the refere...

abstract ethanol has a vast consumption around the world. many researches confirmed some adverse effect of this component on human health. in addition, recent studies showed significant alteration in both cellular population, and protein profile of human foreskin fibroblast cell line (hfff2) in the specific dosage of ethanol. here, the role and interaction of some proteins (characterized by sig...

To study the role of WNT/β-catenin signaling in pancreatic adenocarcinoma, human BxPC-3 cell lines deficient of the central canonical WNT signaling protein β-catenin were established by using zinc-finger nuclease mediated targeted genomic disruption of the β-catenin gene (CTNNB1). Comparison of the global transcription levels in wild type cells with two β-catenin gene disrupted clones identifie...

Epigenetics underlying refractory epilepsy is poorly understood, especially in patients without distinctive genetic alterations. DNA methylation may affect gene expression in epilepsy without affecting DNA sequences. Herein, we analyzed genome-wide DNA methylation and gene expression in brain tissues of 10 patients with refractory epilepsy using methylated DNA immunoprecipitation linked with se...

Genome-wide association (GWA) studies have identified a number of loci underlying variation in human serum uric acid (SUA) levels with the SLC2A9 gene having the largest effect identified so far. Gene-gene interactions (epistasis) are largely unexplored in these GWA studies. We performed a full pair-wise genome scan in the Italian MICROS population (n = 1201) to characterise epistasis signals i...

Winter dormancy is an important biological feature for tea plant to survive cold winters, and it also affects the economic output of tea plant, one of the few woody plants in the world whose leaves are harvested and one of the few non-conifer evergreen species with characterized dormancies. To discover the bud dormancy regulation mechanism of tea plant in winter, we analyzed the global gene exp...

Huntington's disease (HD) is an autosomal-dominant neurodegenerative disorder resulting from expansion of CAG repeats in the Huntingtin (HTT) gene. Previous studies have shown mutant HTT can alter expression of genes associated with dysregulated epigenetic modifications. One of the most widely studied chromatin modifications is trimethylated lysine 4 of histone 3 (H3K4me3). Here, we conducted t...

Pathway information provides insight into the biological processes underlying microarray data. Pathway information is widely available for humans and laboratory animals in databases through the internet, but less for other species, for example, livestock. Many software packages use species-specific gene IDs that cannot handle genomics data from other species. We developed a species-independent ...

SUMMARY Rice (Oryza sativa L.) is an important model monocot and cereal crop. While the rice genome sequence has been published and annotated, relatively little is known about the transcriptional networks that regulate rice gene expression. For this reason, we have developed Osiris, a database containing promoter sequences, predicted transcription factor (TF) binding sites, gene ontology annota...