SEARCH · PubMed Health

Results for “Gene Expression”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

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

At least 127 records · Page 7Linked to original sources

PubMedDate not supplied

Novel gene expression patterns in hybrid embryos between species with different modes of development.

Cross-species hybrids between eggs of the direct-developing sea urchin, Heliocidaris erythrogramma, and sperm from its congeneric indirect-developing species, Heliocidaris tuberculata, show restoration of features of the paternal feeding pluteus larva, including the gut, and pluteus spicular skeleton. Unlike other reported sea urchin cross-species hybrids, Heliocidaris hybrids express genes derived from both maternal and paternal species at high levels. Ectodermal cell types, which differ radically between the two parental species, are of intermediate form in the hybrids. Gene expression patterns in hybrid embryo tissues represent a number of combinations of parental gene expression patterns: genes that are not expressed in one paternal species, but are expressed in hybrids as in the expressing parent; genes that show additive expression patterns plus novel sites of expression; a gene that is misexpressed in the hybrids; and genes expressed identically in both parents and in hybrids. The results indicate that both conserved and novel gene regulatory interactions are present. Only one gene, CyIII actin, has lost cell-type-specific regulation in the hybrids. Hybrids thus reveal that disparate parental genomes, each with its own genic regulatory system, can produce in combination a novel gene expression entity with a unique ontogeny. This outcome may derive from conserved gene regulatory regions in downstream genes of both parental species responding in conserved ways to higher-level regulators that determine modular gene expression territories.

Animals↗

PubMed1996

Correlations between intrinsic chemoresistance and HER-2/neu gene expression, p53 gene mutations, and cell proliferation characteristics in non-small cell lung cancer cell lines.

Using a panel of 20 non-small cell lung cancer (NSCLC) cell lines established from previously untreated patients, we investigated the relationships between intrinsic chemoresistance (to four agents used commonly in the therapy of NSCLC) and HER-2/neu gene expression (which encodes glycoprotein p185neu), p53 gene mutations, and cell proliferation characteristics. Our results demonstrated that high p185neu expression was correlated with chemoresistance, low S-phase fractions, and long doubling times. By contrast, cell lines expressing relatively low levels of p185neu were relatively chemosensitive and had higher S-phase fractions and shorter doubling times. Although mutation of the p53 gene was a common event in this panel of cell lines (present in 18 of 20 lines), there was no relationship between mutations at any specific codon and chemoresistance or cell proliferation characteristics. Multivariate analysis revealed that the level of p185neu was the only independent predictor for chemoresistance to doxorubicin, etoposide, and probably cisplatin. Although intrinsic chemoresistance almost certainly is a multifactorial process, overexpression of p185neu may be an important factor in the chemoresistance of NSCLC.

Carcinoma, Non-Small-Cell Lung↗

PubMed1999

Gene expression profiles in HTLV-I-immortalized T cells: deregulated expression of genes involved in apoptosis regulation.

Human T-cell leukemia virus type I (HTLV-I) is the etiologic agent of adult T-cell leukemia, an acute and often fatal T-cell malignancy. A key step in HTLV-I-induced leukemigenesis is induction of abnormal T-cell growth and survival. Unlike antigen-stimulated T cells, which cease proliferation after a finite number of cell division, HTLV-I-infected T cells proliferate indefinitely (immortalized), thus facilitating occurrence of secondary genetic changes leading to malignant transformation. To explore the molecular basis of HTLV-I-induced abnormal T-cell survival, we compared the gene expression profiles of normal and HTLV-I-immortalized T cells using 'gene array'. These studies revealed a strikingly altered expression pattern of a large number of genes along with HTLV-I-mediated T-cell immortalization. Interestingly, many of these deregulated genes are involved in the control of programmed cell death or apoptosis. These findings indicate that disruption of the cellular apoptosis-regulatory network may play a role in the HTLV-I-mediated oncogenesis.

Apoptosis↗

PubMed2004

Gene expression pattern in hepatic stem/progenitor cells during rat fetal development using complementary DNA microarrays.

To identify new and differentially expressed genes in rat fetal liver epithelial stem/progenitor cells during their proliferation, lineage commitment, and differentiation, we used a high throughput method-mouse complementary DNA (cDNA) microarrays-for analysis of gene expression. The gene expression pattern of rat hepatic cells was studied during their differentiation in vivo: from embryonic day (ED) 13 until adulthood. The differentially regulated genes were grouped into two clusters: a cluster of up-regulated genes comprised of 281 clones and a cluster of down-regulated genes comprised of 230 members. The expression of the latter increased abruptly between ED 16 and ED 17. Many of the overexpressed genes from the first cluster fall into distinct, differentially expressed functional groups: genes related to development, morphogenesis, and differentiation; calcium- and phospholipid-binding proteins and signal transducers; and cell adhesion, migration, and matrix proteins. Several other functional groups of genes that are initially down-regulated, then increase during development, also emerged: genes related to inflammation, blood coagulation, detoxification, serum proteins, amino acids, lipids, and carbohydrate metabolism. Twenty-eight genes overexpressed in fetal liver that were not detected in adult liver are suggested as potential markers for identification of liver progenitor cells. In conclusion, our data show that the gene expression program of fetal hepatoblasts differs profoundly from that of adult hepatocytes and that it is regulated in a specific manner with a major switch at ED 16 to 17, marking a dramatic change in the gene expression program during the transition of fetal liver progenitor cells from an undifferentiated to a differentiated state. Supplementary material for this article can be found on the HEPATOLOGY website (http://interscience.wiley.com/jpages/0270-9139/suppmat/index.html).

Aging↗

PubMed2006

[Differential gene expression profile of keloids: a study with cDNA microarray].

OBJECTIVE: To investigate the differentially expressed genes in keloids in comparison with normal skin using cDNA microarray. METHODS: The cDNA microarray consisting of 8064 clones of human genes was employed to detect and screen the differentially expressed genes in keloid and normal skin tissues. Semi-quantitative RT-PCR was applied to verify the results of gene microarray. RESULTS: Totally 277 differentially expressed genes were identified in keloids in comparison with normal skin tissue, including 163 up-regulated genes and 114 down-regulated ones according to the designed data filter criteria. These differentially expressed genes belonged to 26 different functional gene families involving different biological processes. RT-PCR yielded results were consistent with those of microarray study. CONCLUSION: A variety of genes are involved in the formation of keloids. The 277 differentially expressed genes comprise the differential gene expression profile of keloids and describe the general changes in the gene expressions in keloid at transcriptional level. Further analysis of the identified genes might help reveal the molecular mechanism of abnormal scarring.

Connective Tissue Growth Factor↗

PubMed2000

Complexity of transcriptional control in neuropeptide gene expression; enkephalin gene regulation during neurodevelopment.

The gene for enkephalin is expressed only in specific subsets of neurons in the mammalian central nervous system (CNS), whereas the large majority of neurons do not express the gene. This restricted expression is the result of a developmental process during which some of the multipotent neural progenitors express the gene for enkephalin and thereby become enkephalinergic neurons. The regulation of this process is not well understood. We have used a novel approach to identify DNA-protein interactions that regulate the developmental expression of the gene for enkephalin. We have identified four novel DNA regulatory sites and their binding proteins that are expressed in the developing mammalian CNS. These protein-DNA interactions regulate DNA and nuclear structures through DNA bending, DNA sliding, chromatin remodelling and far-distant DNA interactions. The concerted and co-ordinated interactions of these four DNA elements and their binding proteins contribute to the guiding of multipotent neural progenitors into enkephalinergic neurons. The provided examples suggest an important role for architectural transcriptional regulation during CNS development.

Animals↗

PubMed2003

Correlations between gene expression and gene conservation in fission yeast.

Genes can be expressed at a wide range of levels, and they show different degrees of cross-species conservation. We compared gene expression levels to gene conservation by integrating microarray data from fission yeast (Schizosaccharomyces pombe) with lists of "core" genes (present in worm and budding and fission yeasts), "yeast-specific" genes (present in budding and fission yeasts, but not in worm), and "pombe-specific" genes (present in fission yeast only). Whereas a disproportionate number of core genes are highly expressed in vegetatively growing cells, many pombe-specific genes are expressed at lower levels. This bias is less pronounced in cells undergoing sexual development, when many pombe-specific genes become highly expressed. This implies that organism-specific proteins are more likely to function during specialized processes such as cellular differentiation. Accordingly, pombe-specific genes were overrepresented among genes induced during sexual development; they were particularly enriched in a group of genes induced during meiotic prophase, when homologous chromosomes pair and recombine. This raises the possibility that organism-specific genes with functions in meiotic prophase favor speciation by preventing fruitful meiosis between closely related organisms. Finally, the set of genes induced late during sexual differentiation, at the time of spore formation, was enriched in yeast-specific genes, indicating that these genes play specialized roles in ascospore development.

Conserved Sequence↗

PubMed2006

Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana.

BACKGROUND: Genome analyses have revealed that gene duplication in plants is rampant. Furthermore, many of the duplicated genes seem to have been created through ancient genome-wide duplication events. Recently, we have shown that gene loss is strikingly different for large- and small-scale duplication events and highly biased towards the functional class to which a gene belongs. Here, we study the expression divergence of genes that were created during large- and small-scale gene duplication events by means of microarray data and investigate both the influence of the origin (mode of duplication) and the function of the duplicated genes on expression divergence. RESULTS: Duplicates that have been created by large-scale duplication events and that can still be found in duplicated segments have expression patterns that are more correlated than those that were created by small-scale duplications or those that no longer lie in duplicated segments. Moreover, the former tend to have highly redundant or overlapping expression patterns and are mostly expressed in the same tissues, while the latter show asymmetric divergence. In addition, a strong bias in divergence of gene expression was observed towards gene function and the biological process genes are involved in. CONCLUSION: By using microarray expression data for Arabidopsis thaliana, we show that the mode of duplication, the function of the genes involved, and the time since duplication play important roles in the divergence of gene expression and, therefore, in the functional divergence of genes after duplication.

Amino Acid Substitution↗

PubMed1999

Tissue structure, nuclear organization, and gene expression in normal and malignant breast.

Because every cell within the body has the same genetic information, a significant problem in biology is to understand how cells within a tissue express genes selectively. A sophisticated network of physical and biochemical signals converge in a highly orchestrated manner to bring about the exquisite regulation that governs gene expression in diverse tissues. Thus, the ultimate decision of a cell to proliferate, express tissue-specific genes, or apoptose must be a coordinated response to its adhesive, growth factor, and hormonal milieu. The unifying hypothesis examined in this overview is that the unit of function in higher organisms is neither the genome nor the cell alone but the complex, three-dimensional tissue. This is because there are bidirectional connections between the components of the cellular microenvironment (growth factors, hormones, and extracellular matrix) and the nucleus. These connections are made via membrane-bound receptors and transmitted to the nucleus, where the signals result in modifications to the nuclear matrix and chromatin structure and lead to selective gene expression. Thus, cells need to be studied "in context", i.e., within a proper tissue structure, if one is to understand the bidirectional pathways that connect the cellular microenvironment and the genome. In the last decades, we have used well-characterized human and mouse mammary cell lines in "designer microenvironments" to create an appropriate context to study tissue-specific gene expression. The use of a three-dimensional culture assay, developed with reconstituted basement membrane, has allowed us to distinguish normal and malignant human breast cells easily and rapidly. Whereas normal cells become growth arrested and form organized "acini," tumor cells continue to grow, pile up, and in general fail to respond to extracellular matrix and microenvironmental cues. By correcting the extracellular matrix-receptor (integrin) signaling and balance, we have been able to revert the malignant phenotype when a human breast tumor cell is cultured in, or on, a basement membrane. Most recently, we have shown that whereas beta1 integrin and epidermal growth factor receptor signal transduction pathways are integrated reciprocally in three-dimensional cultures, on tissue culture plastic (two-dimensional monolayers), these are not coordinated. Finally, we have demonstrated that, rather than passively reflecting changes in gene expression, nuclear organization itself can modulate cellular and tissue phenotype. We conclude that the structure of the tissue is dominant over the genome, and that we may need a new paradigm for how epithelial-specific genes are regulated in vivo. We also argue that unless the structure of the tissue is critically altered, malignancy will not progress, even in the presence of multiple chromosomal mutations.

Animals↗

PubMed2004

Gene expression profiling of the developing Drosophila CNS midline cells.

The Drosophila CNS midline cells constitute a specialized set of interneurons, motorneurons, and glia. The utility of the CNS midline cells as a neurogenomic system to study CNS development derives from the ability to easily identify CNS midline-expressed genes. For this study, we used a variety of sources to identify 281 putative midline-expressed genes, including enhancer trap lines, microarray data, published accounts, and the Berkeley Drosophila Genome Project (BDGP) gene expression data. For each gene, we analyzed expression at all stages of embryonic CNS development and categorized expression patterns with regard to specific midline cell types. Of the 281 candidates, we identified 224 midline-expressed genes, which include transcription factors, signaling proteins, and transposable elements. We find that 58 genes are expressed in mesectodermal precursor cells, 138 in midline primordium cells, and 143 in mature midline cells--50 in midline glia, 106 in midline neurons. Additionally, we identified 27 genes expressed in glial and mesodermal cells associated with the midline cells. This work provides the basis for future research that will generate a complete cellular and molecular map of CNS midline development, thus allowing for detailed genetic and molecular studies of neuronal and glial development and function.

Animals↗

PubMed2002

Nonparametric methods for identifying differentially expressed genes in microarray data.

MOTIVATION: Gene expression experiments provide a fast and systematic way to identify disease markers relevant to clinical care. In this study, we address the problem of robust identification of differentially expressed genes from microarray data. Differentially expressed genes, or discriminator genes, are genes with significantly different expression in two user-defined groups of microarray experiments. We compare three model-free approaches: (1). nonparametric t-test, (2). Wilcoxon (or Mann-Whitney) rank sum test, and (3). a heuristic method based on high Pearson correlation to a perfectly differentiating gene ('ideal discriminator method'). We systematically assess the performance of each method based on simulated and biological data under varying noise levels and p-value cutoffs. RESULTS: All methods exhibit very low false positive rates and identify a large fraction of the differentially expressed genes in simulated data sets with noise level similar to that of actual data. Overall, the rank sum test appears most conservative, which may be advantageous when the computationally identified genes need to be tested biologically. However, if a more inclusive list of markers is desired, a higher p-value cutoff or the nonparametric t-test may be appropriate. When applied to data from lung tumor and lymphoma data sets, the methods identify biologically relevant differentially expressed genes that allow clear separation of groups in question. Thus the methods described and evaluated here provide a convenient and robust way to identify differentially expressed genes for further biological and clinical analysis.

Carcinoma, Squamous Cell↗

PubMed2001

Changes in gene expression during progression of ovarian carcinoma.

The molecular events leading to the development and progression of serous ovarian carcinoma are not completely understood. We performed a large scale survey for the identification of differentially expressed genes in serous ovarian carcinoma by using cDNA array analysis. Differences in gene expression between serous adenocarcinoma and benign serous adenoma, and between advanced and/or moderately or poorly differentiated and local, highly differentiated serous adenocarcinoma were assessed. The most striking difference between adenocarcinoma and benign adenoma was upregulation of RHOGDI2 in the carcinomas irrespective of the clinical tumor stage. Other changes in carcinoma were upregulation of MET and Ne-dlg, and downregulation of HGFAC, desmin, and PDGFA. The most prominent differences between advanced and local adenocarcinoma were upregulation of COL3A1, CFGR, and MET in advanced carcinoma, and downregulation of HGFAC, FZD3, and BFL1 in the same tumors. In conclusion, significant differences were found in the gene expression between benign and malignant serous ovarian tumors, and between local, highly differentiated and advanced and/or moderately or poorly differentiated serous adenocarcinomas. The differentially expressed genes may be related to the carcinogenesis and progression of the malignant growth.

Blotting, Northern↗

PubMed2002

Analysis of gene expression in genetic epilepsy-prone rat using a cDNA expression array.

UNLABELLED: Our aim is to search the differential expression genes of genetic epilepsy and establish the groundwork of exploring the pathogenesis of epilepsy on the gene level by using cDNA array technology. METHODS: Gene expression profiles of the cerebral cortex of genetic epilepsy-prone P77PMC rats and normal Wistar rats were established using the Atlas Rat cDNA Expression Array. The difference between gene expression profiles was analyzed using an image analysis instrument. RESULTS: Fifteen genes exhibited a differential expression pattern between the P77PMC rats' and Wistar rats' cerebral cortex, while there maybe many other differential expression genes undiscovered due to having no image analysis software. Among them, the levels of expression of 13 genes were elevated in P77PMC rats as compared to their levels in Wistar rats, in contrast, the levels of expression of two genes were decreased in P77PMC rats. CONCLUSION: There were several differential expression genes between P77PMC rats and Wistar rats. All these genes could play important roles in the pathogenesis of epilepsy.

Animals↗

PubMed2006

Gene expression profiling reveals stromal genes expressed in common between Barrett's esophagus and adenocarcinoma.

BACKGROUND & AIMS: Barrett's esophagus is a precursor of esophageal adenocarcinoma. DNA microarrays that enable a genome-wide assessment of gene expression enhance the identification of specific genes as well as gene expression patterns that are expressed by Barrett's esophagus and adenocarcinoma compared with normal tissues. Barrett's esophagus length has also been identified as a risk factor for progression to adenocarcinoma, but whether there are intrinsic biological differences between short-segment and long-segment Barrett's esophagus can be explored with microarrays. METHODS: Gene expression profiles for endoscopically obtained biopsy specimens of Barrett's esophagus or esophageal adenocarcinoma and associated normal esophagus and duodenum were identified for 17 patients using DNA microarrays. Unsupervised and supervised approaches for data analysis defined similarities and differences between the tissues as well as correlations with clinical phenotypes. RESULTS: Each tissue displays a unique expression profile that distinguishes it from others. Barrett's esophagus and esophageal adenocarcinoma express a unique set of stromal genes that is distinct from normal tissues but similar to other cancers. Adenocarcinoma also showed lower and higher expression for many genes compared with Barrett's esophagus. No difference in gene expression was found between short-segment and long-segment Barrett's esophagus. CONCLUSIONS: The genome-wide assessment provided by current DNA microarrays reveals many candidate genes and patterns not previously identified. Stromal gene expression in Barrett's esophagus and adenocarcinoma is similar, indicating that these changes precede malignant transformation.

Adenocarcinoma↗

PubMed2002

Gene expression data analysis of human lymphoma using support vector machines and output coding ensembles.

The large amount of data generated by DNA microarrays was originally analysed using unsupervised methods, such as clustering or self-organizing maps. Recently supervised methods such as decision trees, dot-product support vector machines (SVM) and multi-layer perceptrons (MLP) have been applied in order to classify normal and tumoural tissues. We propose methods based on non-linear SVM with polynomial and Gaussian kernels, and output coding (OC) ensembles of learning machines to separate normal from malignant tissues, to classify different types of lymphoma and to analyse the role of sets of coordinately expressed genes in carcinogenic processes of lymphoid tissues. Using gene expression data from "Lymphochip", a specialised DNA microarray developed at Stanford University School of Medicine, we show that SVM can correctly separate normal from tumoural tissues, and OC ensembles can be successfully used to classify different types of lymphoma. Moreover, we identify a group of coordinately expressed genes related to the separation of two distinct subgroups inside diffuse large B-cell lymphoma (DLBCL), validating a previous Alizadeh's hypothesis about the existence of two distinct diseases inside DLBCL.

Artificial Intelligence↗

PubMed2003

Functional modules by relating protein interaction networks and gene expression.

Genes and proteins are organized on the basis of their particular mutual relations or according to their interactions in cellular and genetic networks. These include metabolic or signaling pathways and protein interaction, regulatory or co-expression networks. Integrating the information from the different types of networks may lead to the notion of a functional network and functional modules. To find these modules, we propose a new technique which is based on collective, multi-body correlations in a genetic network. We calculated the correlation strength of a group of genes (e.g. in the co-expression network) which were identified as members of a module in a different network (e.g. in the protein interaction network) and estimated the probability that this correlation strength was found by chance. Groups of genes with a significant correlation strength in different networks have a high probability that they perform the same function. Here, we propose evaluating the multi-body correlations by applying the superparamagnetic approach. We compare our method to the presently applied mean Pearson correlations and show that our method is more sensitive in revealing functional relationships.

Algorithms↗

PubMed1989

Lithium ions induce prestalk-associated gene expression and inhibit prespore gene expression in Dictyostelium discoideum.

We investigated the effect of Li+ on two types of cyclic AMP-regulated gene expression and on basal and cyclic AMP-stimulated inositol 1,4,5-triphosphate (Ins(1,4,5)P3) levels. Li+ effectively inhibits cyclic AMP-induced prespore gene expression, half-maximal inhibition occurring at about 2 mM-LiCl. In contrast, Li+ (1-3 mM) promotes the cyclic AMP-induced increase of cysteine proteinase-2 mRNA levels, and induces the expression of this prestalk-associated gene in the absence of cyclic AMP stimuli. At concentrations exceeding 4-5 mM, LiCl inhibits cysteine proteinase-2 gene expression. LiCl reduces basal Ins(1,4,5)P3 levels and decreases the cyclic AMP-induced accumulation of Ins(1,4,5)P3; both effects occur half-maximally at 2-3 mM-LiCl. These results indicate that the induction of the cysteine proteinase-2 gene by Li+ is not due to elevated levels of Ins(1,4,5)P3. It is, however, possible that inhibition of prespore gene expression by Li+ is caused by Li+-induced reduction of basal and/or stimulated Ins(1,4,5)P3 levels.

3',5'-Cyclic-AMP Phosphodiesterases↗

PubMed2006

Regulation of NF-kappaB-dependent gene expression by the POU domain transcription factor Oct-1.

Maintenance of the cells of the vessel wall in a quiescent state is an important aspect of normal vascular physiology. Transcriptional repressors are widely believed to regulate this process, yet the exact factors involved and the mechanism of repression are not known. Here, we report that the POU domain transcription factor Oct-1 represses the expression of E-selectin and vascular cell adhesion molecule (VCAM-1), two cytokine-inducible, NF-kappaB-dependent endothelial-leukocyte adhesion molecules that participate in the leukocyte recruitment phase of the inflammatory response. Co-transfection and microinjection studies demonstrate that Oct-1 blocks tumor necrosis factor alpha-stimulated E-selectin and VCAM-1 expression. Gene expression arrays indicate that control of tumor necrosis factor alpha-induced, NF-kappaB-dependent gene expression by Oct-1 is promoter-specific. A DNA-binding mutant of Oct-1 represses NF-kappaB-dependent reporter gene expression. Biochemically, Oct-1 interacts with p65, suggesting that Oct-1 is involved in the regulation of NF-kappaB transactivation function. NF-kappaB-dependent gene expression is more pronounced in Oct-1-deficient than in wild-type murine embryonic fibroblasts, and reintroduction of human Oct-1 abolishes these differences. Finally, the cytokine interleukin-6 induces Oct-1 gene expression, providing a biologically relevant means by which NF-kappaB-dependent gene expression can be selectively reverted by Oct-1 to quiescent levels.

3T3 Cells↗