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The development and performance analysis of the GibbsModule algorithm for de novo detection of cis-regulatory motifs and modules in eukaryote genomes are described. GibbsModule could be applied to analyze the binding regions of the Kruppel-like factor (KLF) transcription factor in embryonic stem cells (ESCs) and identify a motif consistent with mutagenesis analysis.

An experimental strategy was developed by using transient transfection assays to identify silencers and enhancer-blockers (EBs) that are cis-acting, negative regulatory elements (NREs) that control interactions between promoters and enhancers. The studies identified 15 novel NREs, which provide new insights into the prevalence and composition of sequences that negatively regulate gene expression.

A computational approach is used to identify and validate the function of mammalian regulatory motifs in a set of cartilage characteristic genes.

The examination of sequence features and evolutionary rates of viral family-specific genes in three nucleo-cytoplasmic large DNA virus (NCLDV) lineages reveals that the proportion of family-specific genes does not correlate with sequence divergence rate.

The evolutionary roles of some recognized transcriptional regulatory sequences defined by the human genome project-ENCODE are studied. The comparative genomics tools reveal that these regulatory regions are associated with genes that play a role in selection.

The silencing of many associated genes near the transcriptional region of histone acetylation is the major cause of the decrease in histone acetylation.

Gene regulation is well understood by the interaction between transcription factors and their DNA binding sites and thus a genome-wide study of the evolutionary dynamics in yeast promoters is performed to provide a fist global view of the network selection forces in the evolution of transcription factor binding sites. New models for binding site activity, identification of families related binding sites and characterization of the functional similarities among them are discussed.

Research has been conducted on protein interaction. The authors describe the two-hybrid strategy developed for facilitating protein interaction map construction on a genome-wide scale.

Research has been conducted on mouse olfactory receptor genes expressed in clustered populations of olfactory sensory neurons. The authors have investigated the genomic regions of these genes in order to identify characteristics putative regulatory sequence motifs.

This article demonstrates the application of Cytoscape software in case studies in which a search for interaction pathways in relation to gene expression, protein complexes mediating cellular recovery to DNA damage, physical/functional interaction network, and an interface to stochastic/kinetic gene regulatory processes are studied.

Results reveal that the consistency of the transcriptional regulatory network elements is affected by both network structural aspects and functional classes of the genes involved in the element. Daa indicae that using this method regulatory network subcomponents can be defined with consistency between network structure and gene expression.

Research evaluates an in silico genetic regulatory network method for identifying genetic networks using gene expression profiles, prior structural information as to which transcription factors regulate which gene, and mRNA degradation rate constants.

Research describes a mathematical approach for the analysis of genetic networks and how it can be applied to synthetic gene networks. Results suggest that the relationship between network structure and behavior in genetic networks, such as gene expression and regulation, can be explained by the models derived from the new approach.

Research has been conducted on human genomes. The authors describe the development of the functional selection for promoter regions in the human genome which uses a retroviral plasmid library-based system.

Research has been conducted on duplication of proximal chromosome 6. The authors report the analysis of paternally expressed and maternally expressed imprinted genes within 1-Mb region, and demonstrate the existence of a large imprinted gene cluster in this region.

Research has been conducted on high-density lipoprotein cholesterol concentrations. The authors describe the use of mapping quantitative trait loci in backcross progeny fed chow diet in order to detect quantitative trait loci which regulate these high-density lipoprotein cholesterol concentrations.

Research has been conducted on mouse and human genome sequences which contain nonexonic and nonexpressed conserved sequences. The correlation between these conserved intronic sequences and splicing regulation has been investigated, and the results are reported.

Research has been conducted on genetic variation in human and African great ape genomes. The authors have investigated gene-expression profiles in cell populations from humans, bonobos and gorillas in the effort to define transcriptional regulatory network which contribute to the complex phenotypes unique to human and African great apes.

Research has been conducted on protein kinases and phosphatases. The authors describe the computational study carried out in the effort to classify and identify these kinases and phosphatases.

Research has been conducted on Gnas complex locus which provide insights into transcriptional regulation. Results demonstrate that the discovery of new transcripts at this locue provides candidates for a complete functional analysis of this region.

Research has been conducted on sense-antisense transcripts. The authors describe their study of these transcripts which has been based on the FANTOM2 cDNA sequence set, and report that the presence of many natural antisense transcripts suggests that the gene expression regulation by antisense transcripts is common.

Research has been conducted on vertebrate Hox genes which occur in clusters and are uninterrupted by other genes. The authors report that they have recovered putative elements regulating Hox gene expression, and that the conserved elements are involved in different gene regulatory network.

Research has been conducted on NF-kappaB-regulated immune genes in the human genome. The authors discuss the methods developed to predict immune gene functions which are based on transcription factor binding patterns, evolutionary conservation and expression studies.

Research has been conducted on transcription regulatory DNA segments controlling gene development in eukaryotes. The clustering of the binding motifs for transcription factors from Drosophila developmental genes, gene regulatory networks and coregulated genes in the genom have been investigated, and the details are reported.

Research has been conducted on microarray carrying open reading frames from Xylella fastidiosa genome. The authors report the hybridization of the microarray with DNA from different X. fastidiosa strains, and demonstrate the existence of the conserved core gene pool which contains genes involved in major biochemical pathways and cellular functions.

Research has been conducted on genetic code change evolution. The authors report that the study of this evolution involving decoding standard leucine-CTG codon, such as serine in Candida spp., has been carried out via the use of complete genome sequence of the yeasts Candida albicans and Saccharomyces cerevisiae.

Research has been conducted on vertebrate Dlx homneobox genes which can form bigene clusters on chromosomes. The authors suggest that Dlx intergenic regions' rapid divergence has been followed by cis-acting regulatory element fixation early in vertebrate evolution.

Research has been conducted on variation in body weights at different ages. The authors have identified quantitative trait loci in the effort to explain large proportions in body weights and growth between chronological ages in an F (sub)2 intercross between different chichen species, and have presented the results.

Research has been conducted on adaptation of Bacillus subtilis to glucose. The authors have investigated this adaptation via the study of glucose-starved cells in a model system which is common environmental situation for B. subtilis cells.

Research has been conducted on Escherichia coli osmotic shock response. The authors report that increased supercoiling is important for elicitation of this response.

Research has been conducted on genome discrimination. Results demonstrate that discrimination based on individual nucleotide pair frequencies are partially successful.

Results demonstrate that a group of genes coexpress mainly in tissues from breast and ovarian cancers and in cancerous tissues of the lung, brain, and bone marrow as determined by real-time reverse transcriptase-polymerase chain reaction. Data indicate that this group of genes contains at least six members, which are probably involved in either transcriptional regulation or the ubiquitin proteasome pathway.

This article describes the development of an algorithm and visualization method for the analysis of conserved noncoding genomic sequences along with the transcription factor binding sites. Results represented in a Regulogram enables detection of similarities in composition and arrangement of cis-element clusters within nonorthologous genes, promoters, and enhancers, which exhibit coordinate regulatory properties.