Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Genomic profiling”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,225 records · Page 68Linked to original sources
PubMed2004

The use of MPSS for whole-genome transcriptional analysis in Arabidopsis.

We have generated 36,991,173 17-base sequence "signatures" representing transcripts from the model plant Arabidopsis. These data were derived by massively parallel signature sequencing (MPSS) from 14 libraries and comprised 268,132 distinct sequences. Comparable data were also obtained with 20-base signatures. We developed a method for handling these data and for comparing these signatures to the annotated Arabidopsis genome. As part of this procedure, 858,019 potential or "genomic" signatures were extracted from the Arabidopsis genome and classified based on the position and orientation of the signatures relative to annotated genes. A comparison of genomic and expressed signatures matched 67,735 signatures predicted to be derived from distinct transcripts and expressed at significant levels. Expressed signatures were derived from the sense strand of at least 19,088 of 29,084 annotated genes. A comparison of the genomic and expression signatures demonstrated that approximately 7.7% of genomic signatures were underrepresented in the expression data. These genomic signatures contained one of 20 four-base words that were consistently associated with reduced MPSS abundances. More than 89% of the sum of the expressed signature abundances matched the Arabidopsis genome, and many of the unmatched signatures found in high abundances were predicted to match to previously uncharacterized transcripts.

Arabidopsis↗
PubMed2000

Biochemical systems analysis of genome-wide expression data.

MOTIVATION: Modern methods of genomics have produced an unprecedented amount of raw data. The interpretation and explanation of these data constitute a major, well-recognized challenge. RESULTS: Biochemical Systems Theory (BST) is the mathematical basis of a well-established methodological framework for analyzing networks of biochemical reactions. An existing BST model of yeast glycolysis is used here to explain and interpret the glycolytic gene expression pattern of heat shocked yeast. Our analysis demonstrates that the observed gene expression profile satisfies the primary goals of increased ATP, trehalose, and NADPH production, while maintaining intermediate metabolites at reasonable levels. Based on a systematic exploration of alternative, hypothetical expression profiles, we show that the observed profile outperforms other profiles. CONCLUSION: BST is a useful framework for combining DNA microarray data with enzymatic process information to yield new insights into metabolic pathway regulation. AVAILABILITY: All analyses were executed with the software PLAS(Copyright), which is freely available at http://correio.cc.fc.ul.pt/~aenf/plas.html for academic use. CONTACT: VoitEO@MUSC.edu

Computational Biology↗
PubMed2003

Laser capture microdissection of cells from plant tissues.

Laser capture microdissection (LCM) is a technique by which individual cells can be harvested from tissue sections while they are viewed under the microscope, by tacking selected cells to an adhesive film with a laser beam. Harvested cells can provide DNA, RNA, and protein for the profiling of genomic characteristics, gene expression, and protein spectra from individual cell types. We have optimized LCM for a variety of plant tissues and species, permitting the harvesting of cells from paraffin sections that maintain histological detail. We show that RNA can be extracted from LCM-harvested plant cells in amount and quality that are sufficient for the comparison of RNAs among individual cell types. The linear amplification of LCM-captured RNA should permit the expression profiling of plant cell types.

DNA, Plant↗
PubMed2005

Immunization of mice with Neisseria meningitidis serogroup B genomic expression libraries elicits functional antibodies and reduces the level of bacteremia in an infant rat infection model.

The feasibility of expression library immunization against the pathogenic bacterium Neisseria meningitidis was studied. A genomic library of N. meningitidis serogroup B strain CU385, containing 6000 individual clones, was constructed and divided into 10 sublibraries. Immunization of BALB/c mice with plasmid DNA from six sublibraries induced a humoral response, with recognition of several meningococcal proteins by Western blot. Three of these sublibraries elicited bactericidal antibodies against the homologous strain, and sera from mice immunized with one of these sublibraries reduced significantly the number of viable bacteria in blood of infant rats challenged with N. meningitidis. In addition, after DNA immunization, mice were boosted intraperitoneally with 5 x 10(2) colony forming units of strain CU385. Mice immunized with nine of the 10 libraries developed bactericidal antibodies 1 week after the boost and controls did not, demonstrating the priming capacity and specificity of our immunization strategy. Our study demonstrates, for the first time, that genomic immunization offers a novel approach for screening possible vaccine candidates against N. meningitidis.

Animals↗
PubMed2005

Phenotype-first screening for the identification of novel drug targets.

Modern drug discovery is predominantly a target-driven process, where success is intricately linked to the selection of an appropriate molecular target. Ideally, there is conclusive functional evidence that a selected target is disease-relevant and, furthermore, suitable for drug development. Phenotype-first screening is a highly attractive approach for target identification because it offers the unique possibility to analyse entire genomes in an unbiased fashion for disease-related phenotypes. Various studies have demonstrated that phenotype-first screening can be successfully applied to the identification of drug targets, thus establishing this approach as a valuable tool for future target discovery efforts.

Animals↗
PubMed2002

Dermatological applications of DNA array technology.

The Human Genome Project and other large scale sequencing consortia continue to generate huge amounts of DNA sequence data. Despite the identification of specific disease-related genes and genetic markers, we still appear to know little about how diverse gene products actually interact with each other or respond to other chemical or biological stimuli. Such information is of course fundamental to understanding complex disease pathways and biochemical processes and, as such, has spawned new fields of investigative genetics, that of functional genomics and proteomics. DNA array technology is emerging as a powerful, high-throughput and versatile tool that can be applied to the study of functional genomics. This article reviews the methodology involved in array analysis and provides insight into how, as an investigative tool, DNA arrays are becoming increasingly useful in understanding fundamental abnormalities in dermatological disease and also in refining the management of patients with certain skin disorders.

Gene Expression Profiling↗
PubMedDate not supplied

Application of toxicogenomics to toxicology: basic concepts in the analysis of microarray data.

Toxicology and the practice of pathology are rapidly evolving in the postgenomic era. Observable treatment related changes have been the hallmark of toxicology studies. Toxicogenomics is a powerful new tool that may show gene and protein changes earlier and at treatment levels below the limits of detection of traditional measures of toxicity. It may also aid in the understanding of toxic mechanisms. It is important to remember that it is only a tool and will provide meaningful results only when properly applied. As is often the case with new experimental tools, the initial utilization is driven more by the technology than application to problem solving. Toxicogenomics is interdisciplinary in nature including at a minimum, pathology, toxicology, and genomics. Most studies will require the input from the disciplines of toxicology, pathology, molecular biology, bioinformatics, biochemistry, and others depending on the types of questions being asked.

Acetaminophen↗
PubMed2003

MuGeN: simultaneous exploration of multiple genomes and computer analysis results.

MOTIVATION: The availability of increasing amounts of sequence data about completely sequenced genomes spurs the development of new methods in the fields of automated annotation, and of comparative genomics. Tools allowing the visualization of results produced by analysis methods, superimposed on possibly annotated sequence data, and enabling synchronized navigation in multiple genomes, provide new means for interactive genome exploration. This kind of visual inspection can be used as a basis to assess the quality of new analysis algorithms, or to discover genome portions to be subjected to in-depth studies. RESULTS: We propose a software package, MuGeN, built for navigating through multiple annotated genomes. It is capable of retrieving annotated sequences in several formats, stored in local files, or available in databases over the network. From these, it then generates an interactive display, or an image file, in most common formats suitable for printing, further editing or integrating in Web pages. Genome maps may be mixed with computer analysis results loaded from XML files, whose format is generic enough to be adapted to a majority of sequence oriented analysis methods. AVAILABILITY: MuGeN is available at http://www-mig.jouy.inra.fr/bdsi/MuGeN.

Computer Graphics↗
PubMed2005

Changing perspectives in yeast research nearly a decade after the genome sequence.

Research with budding yeast (Saccharomyces cerevisiae) has been transformed by the publication, nearly a decade ago, of the entire genome DNA sequence. The introduction of this first eukaryotic genomic sequence changed the yeast research environment significantly, not just because of dramatic progress in technical means but also because the sequence made accessible a new class of scientific questions. A central goal of yeast research remains the determination of the biological role of every sequence feature in the yeast genome. The most remarkable change has been the shift in perspective from focus on individual genes and functionalities to a more global view of how the cellular networks and systems interact and function together to produce the highly evolved organism we see today.

DNA, Fungal↗
PubMed2006

Extensive low-affinity transcriptional interactions in the yeast genome.

Major experimental and computational efforts are targeted at the characterization of transcriptional networks on a genomic scale. The ultimate goal of many of these studies is to construct networks associating transcription factors with genes via well-defined binding sites. Weaker regulatory interactions other than those occurring at high-affinity binding sites are largely ignored and are not well understood. Here I show that low-affinity interactions are abundant in vivo and quantifiable from current high-throughput ChIP experiments. I develop algorithms that predict DNA-binding energies from sequences and ChIP data across a wide dynamic range of affinities and use them to reveal widespread functionality of low-affinity transcription factor binding. Evolutionary analysis suggests that binding energies of many transcription factors are conserved even in promoters lacking classical binding sites. Gene expression analysis shows that such promoters can generate significant expression. I estimate that while only a small percentage of the genome is strongly regulated by a typical transcription factor, up to an order of magnitude more may be involved in weaker interactions. Low-affinity transcription factor-DNA interaction may therefore be important both evolutionarily and functionally.

Algorithms↗
PubMed1981

A sensitive method for the production of diagnostic fingerprints of the genome segments of field isolates of rotavirus.

The 3'-terminal labelling procedure for analyzing the genome segment profile of field isolates of rotavirus (Clarke and McCrae, 1981, J. Virol. Methods 2, 203) has been further developed to produce a rapid and sensitive method for generating diagnostic fingerprints from individual species of double-stranded RNA. The fingerprints were obtained by a one-dimensional resolution of overlapping terminally labelled oligonucleotides produced by partial nuclease digestion with a base-specific nuclease. This fingerprinting method should be of great value in characterizing the molecular details of genome segment variation and will facilitate detailed molecular epidemiological studies of this important virus group.

Animals↗
PubMed2005

Effect of hypoxic preconditioning on brain genomic response before and following ischemia in the adult mouse: identification of potential neuroprotective candidates for stroke.

The aim of the present study is to better understand oxygen-sensitive adaptative pathways underlying the hypoxic preconditioning-induced protection of the brain against ischemia. Using oligonucleotide microarrays, we examined the brain genomic response of adult mice following hypoxia preconditioning (8% O2 for 1 or 6 h of hypoxia with reoxygenation 12, 18, 24 h or 72 h) and ischemia (6 h), preceeded (tolerant state) or not, by preconditioning. Real-time PCR was used to validate the results. Most gene expression increases occurred during hypoxia, including those of HIF-1-dependent genes (RTP801, AM, VEGF, p21, GLUT-1), early response genes (IER3) and transcriptional factors (ATF3, C/EBPdelta). A second wave of changes occurred 24 h after reoxygenation (S100A5, TH, Calretinin, PBX3). A third one occurred during ischemia itself, revealing that hypoxic preconditioning modifies the brain genomic response to ischemia. In addition, we show that some identical genes are overexpressed by hypoxia in both neonatal and adult brains (VEGF, EPO, GLUT-1, AM, MTs, C/EBPdelta).

Age Factors↗
PubMed2004

Multiple-testing strategy for analyzing cDNA array data on gene expression.

An objective of many functional genomics studies is to estimate treatment-induced changes in gene expression. cDNA arrays interrogate each tissue sample for the levels of mRNA for hundreds to tens of thousands of genes, and the use of this technology leads to a multitude of treatment contrasts. By-gene hypotheses tests evaluate the evidence supporting no effect, but selecting a significance level requires dealing with the multitude of comparisons. The p-values from these tests order the genes such that a p-value cutoff divides the genes into two sets. Ideally one set would contain the affected genes and the other would contain the unaffected genes. However, the set of genes selected as affected will have false positives, i.e., genes that are not affected by treatment. Likewise, the other set of genes, selected as unaffected, will contain false negatives, i.e., genes that are affected. A plot of the observed p-values (1 - p) versus their expectation under a uniform [0, 1] distribution allows one to estimate the number of true null hypotheses. With this estimate, the false positive rates and false negative rates associated with any p-value cutoff can be estimated. When computed for a range of cutoffs, these rates summarize the ability of the study to resolve effects. In our work, we are more interested in selecting most of the affected genes rather than protecting against a few false positives. An optimum cutoff, i.e., the best set given the data, depends upon the relative cost of falsely classifying a gene as affected versus the cost of falsely classifying a gene as unaffected. We select the cutoff by a decision-theoretic method analogous to methods developed for receiver operating characteristic curves. In addition, we estimate the false discovery rate and the false nondiscovery rate associated with any cutoff value. Two functional genomics studies that were designed to assess a treatment effect are used to illustrate how the methods allowed the investigators to determine a cutoff to suit their research goals.

Amphetamine↗
PubMed2005

Progression of secondary hyperparathyroidism involves deregulation of genes related to DNA and RNA stability.

BACKGROUND: Renal secondary hyperparathyroidism in its late stages becomes autonomous, so excessive parathyroid hormone (PTH) secretion no longer responds to physiologic stimuli or to aggressive medical treatment. METHODS: To gain molecular understanding of progression of renal secondary hyperparathyroidism, normal and hyperplastic parathyroid tissue with diffuse and nodular growth were analyzed. The results were also compared to parathyroid adenomas. The analysis was performed by high-density oligonucleotide microarray and bidirectional subtraction library. RESULTS: Analysis of the DNA arrays found 16 overexpressed and 132 repressed genes in the nodules while the subtraction library produced 34 overexpressed and 40 repressed genes. The differentially expressed genes between diffuse and nodular samples included some related to DNA stability and repair (TALDO1, PRDX2, DDB1, XRCC1, and POLB), RNA stability and degradation (OASL and AUF1), protein synthesis and processing (PFDN5, HSPD1, and NACA), cell growth (CDC25C and GRPR), and tumorigenesis and cell cycle (VIL2 and TPD52). CONCLUSION: According to the function described for the deregulated genes, when secondary hyperparathyroidism becomes autonomous and refractory to treatment, RNA degradation may be increased while DNA integrity may be compromised. These two mechanisms, combined with deregulation of genes related to growth and differentiation show the complex pathway of parathyroid glands' evolution in renal hyperparathyroidism and may explain the large amount of molecular cytogenetic aberrations found in refractory hyperparathyroidism. Considering that some of the genes with altered expression in nodular hyperplasia lead to irreversible consequences in the genomic integrity of the cells, an adequate and early management of the secondary hyperparathyroidism of chronic kidney disease becomes mandatory.

Adult↗
PubMed2005

Stage-dependent gene expression profiles during natural killer cell development.

Natural killer (NK) cells develop from hematopoietic stem cells (HSCs) in the bone marrow. To understand the molecular regulation of NK cell development, serial analysis of gene expression (SAGE) was applied to HSCs, NK precursor (pNK) cells, and mature NK cells (mNK) cultured without or with OP9 stromal cells. From 170,464 total individual tags from four SAGE libraries, 35,385 unique genes were identified. A set of genes was expressed in a stage-specific manner: 15 genes in HSCs, 30 genes in pNK cells, and 27 genes in mNK cells. Among them, lipoprotein lipase induced NK cell maturation and cytotoxic activity. Identification of genome-wide profiles of gene expression in different stages of NK cell development affords us a fundamental basis for defining the molecular network during NK cell development.

Animals↗
PubMed2002

Association and linkage analyses of RGS4 polymorphisms in schizophrenia.

Gene expression analyses of postmortem cerebral cortex suggest that transcription of the regulator of G-protein signaling 4 (RGS4) is decreased in a diagnosis-specific manner in subjects with schizophrenia. To evaluate the possible role of RGS4 in the pathogenesis of schizophrenia, we conducted genetic association and linkage studies using samples ascertained independently in Pittsburgh and New Delhi and by the NIMH Collaborative Genetics Initiative. Using the transmission disequilibrium test, significant transmission distortion was observed in the Pittsburgh and NIMH samples. Among single-nucleotide polymorphisms (SNPs) spanning approximately 300 kb, significant associations involved four SNPs localized to a 10 kb region at RGS4, but the associated haplotypes differed. A trend for transmission distortion was also present in the Indian sample for haplotypes incorporating the same SNPs. Consistent with the linkage/association observed from the family-based tests, samples with affected siblings (NIMH, India) showed higher levels of allele sharing, identical by descent, at RGS4. When the US patients were contrasted to two population-based control samples, however, no significant differences were observed. To check the specificity of the transmission bias, we therefore examined US families with bipolar I disorder (BD1) probands. This sample also showed a trend for transmission distortion, and differed significantly from the population-based controls for the four-SNP haplotypes tested in the other samples. The transmission distortion is unlikely to be due to chance, but its mechanism and specificity require further study. Our results illustrate the potential power of combining gene expression profiling and genomic analyses to identify susceptibility genes for genetically complex disorders.

Bipolar Disorder↗
PubMed2006

Phylogenetic analysis of the tenascin gene family: evidence of origin early in the chordate lineage.

BACKGROUND: Tenascins are a family of glycoproteins found primarily in the extracellular matrix of embryos where they help to regulate cell proliferation, adhesion and migration. In order to learn more about their origins and relationships to each other, as well as to clarify the nomenclature used to describe them, the tenascin genes of the urochordate Ciona intestinalis, the pufferfish Tetraodon nigroviridis and Takifugu rubripes and the frog Xenopus tropicalis were identified and their gene organization and predicted protein products compared with the previously characterized tenascins of amniotes. RESULTS: A single tenascin gene was identified in the genome of C. intestinalis that encodes a polypeptide with domain features common to all vertebrate tenascins. Both pufferfish genomes encode five tenascin genes: two tenascin-C paralogs, a tenascin-R with domain organization identical to mammalian and avian tenascin-R, a small tenascin-X with previously undescribed GK repeats, and a tenascin-W. Four tenascin genes corresponding to tenascin-C, tenascin-R, tenascin-X and tenascin-W were also identified in the X. tropicalis genome. Multiple sequence alignment reveals that differences in the size of tenascin-W from various vertebrate classes can be explained by duplications of specific fibronectin type III domains. The duplicated domains are encoded on single exons and contain putative integrin-binding motifs. A phylogenetic tree based on the predicted amino acid sequences of the fibrinogen-related domains demonstrates that tenascin-C and tenascin-R are the most closely related vertebrate tenascins, with the most conserved repeat and domain organization. Taking all lines of evidence together, the data show that the tenascins referred to as tenascin-Y and tenascin-N are actually members of the tenascin-X and tenascin-W gene families, respectively. CONCLUSION: The presence of a tenascin gene in urochordates but not other invertebrate phyla suggests that tenascins may be specific to chordates. Later genomic duplication events led to the appearance of four family members in vertebrates: tenascin-C, tenascin-R, tenascin-W and tenascin-X.

Animals↗