For nearly three decades, R loops have been closely linked with class switch recombination (CSR), the process that generates antibody isotypes and that occurs via a complex cascade initiated by transcription-coupled mutagenesis in switch recombination sequences. R loops form during transcription of switch recombination sequences in vitro and in vivo, and there is solid evidence that R loops are...

Anthocyanin pigmentation patterns in different plant species are controlled in part by members of the myc-like R regulatory gene family. We have examined the molecular evolution of this gene family in seven plant species. Three regions of the R protein show sequence conservation between monocot and dicot R genes. These regions encode the basic helix-loop-helix domain, as well as conserved N-ter...

UNLABELLED The amount of gene and genome data obtained by next-generation sequencing technologies generates a need for comparative visualization tools. Complementing existing software for comparison and exploration of genomics data, genoPlotR automatically creates publication-grade linear maps of gene and genomes, in a highly automatic, flexible and reproducible way. AVAILABILITY genoPlotR is...

GSEPD is a package for streamlining RNA-Seq data analysis, targeting complex samples with low replicate count such as human tissues, where all factors (metabolic, genetic, etc) cannot be controlled statistically. As a prerequisite, you need only your multiple samples’ count data as a matrix whose columns are samples and rows are RefSeq NM and NR transcript identifiers. A second matrix associate...

We used polymorphism analysis to study the evolutionary dynamics of 27 disease resistance (R) genes by resequencing the leucine-rich repeat (LRR) region in 96 Arabidopsis thaliana accessions. We compared single nucleotide polymorphisms (SNPs) in these R genes to an empirical distribution of SNP in the same sample based on 876 fragments selected to sample the entire genome. LRR regions are highl...

“Molecular signatures” or “gene-expression signatures” are used to model patients’ clinically relevant information (e.g., prognosis, survival time) using expression data from coexpressed genes. Signatures are a key feature in cancer research because they can provide insight into biological mechanisms and have potential diagnostic use. However, available methods to search for signatures fail to ...

Gene set analysis methods aim to determine whether an a priori defined set of genes shows statistically significant difference in expression on either categorical or continuous outcomes. Although many methods for gene set analysis have been proposed, a systematic analysis tool for identification of different types of gene set significance modules has not been developed previously. This work pre...

The visualization of cluster solutions in gene expression data analysis gives practitioners an understanding of the cluster structure of their data and makes it easier to interpret the cluster results. Neighborhood graphs allow for visual assessment of relationships between adjacent clusters. The number of clusters in gene expression data is for biological reasons rather large. As a linear proj...

The R gene family of maize comprises a set of regulatory loci that control the tissue-specific synthesis of anihocyanin pigments in various parts of the maize plant. Genetic and molecular analyses of these genes have led to the proposal that they encode functionally identical proteins whose diverse pattern of tissue-specific expression reflects differences in their respective promoter sequences...

Mutant screens have identified several genes in tomato, barley and Arabidopsis that are required for the function of specific plant disease resistance (R) genes. Two of these genes, NDR1 and EDS1, have recently been cloned from Arabidopsis. Most Arabidopsis R genes require NDR1 or EDS1, but not both. In a complementary approach, yeast two-hybrid screens have identified several proteins in tomat...