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At least 145 records · Page 8Linked to original sources
PubMed2003

Missing-value estimation using linear and non-linear regression with Bayesian gene selection.

MOTIVATION: Data from microarray experiments are usually in the form of large matrices of expression levels of genes under different experimental conditions. Owing to various reasons, there are frequently missing values. Estimating these missing values is important because they affect downstream analysis, such as clustering, classification and network design. Several methods of missing-value estimation are in use. The problem has two parts: (1) selection of genes for estimation and (2) design of an estimation rule. RESULTS: We propose Bayesian variable selection to obtain genes to be used for estimation, and employ both linear and nonlinear regression for the estimation rule itself. Fast implementation issues for these methods are discussed, including the use of QR decomposition for parameter estimation. The proposed methods are tested on data sets arising from hereditary breast cancer and small round blue-cell tumors. The results compare very favorably with currently used methods based on the normalized root-mean-square error. AVAILABILITY: The appendix is available from http://gspsnap.tamu.edu/gspweb/zxb/missing_zxb/ (user: gspweb; passwd: gsplab).

Algorithms↗
PubMed2005

Gene selection for classification of cancers using probabilistic model building genetic algorithm.

Recently, DNA microarray-based gene expression profiles have been used to correlate the clinical behavior of cancers with the differential gene expression levels in cancerous and normal tissues. To this end, after selection of some predictive genes based on signal-to-noise (S2N) ratio, unsupervised learning like clustering and supervised learning like k-nearest neighbor (k NN) classifier are widely used. Instead of S2N ratio, adaptive searches like Probabilistic Model Building Genetic Algorithm (PMBGA) can be applied for selection of a smaller size gene subset that would classify patient samples more accurately. In this paper, we propose a new PMBGA-based method for identification of informative genes from microarray data. By applying our proposed method to classification of three microarray data sets of binary and multi-type tumors, we demonstrate that the gene subsets selected with our technique yield better classification accuracy.

Algorithms↗
PubMed2004

High expression of two genes selected by iAFLP: a new prognostic factor of estrogen receptor-positive breast cancer.

To detect patients with poor prognosis among those with estrogen receptor (ER)-positive breast cancer, who generally show good prognosis, we analyzed gene expression profiles of 35 ER-positive tumors by using a high through-put RT-PCR technique, iAFLP. High expression of six genes out of 7,508 was related to poor prognosis in this group. From these six genes, NFE2L2 and TIAL1 were selected as genes associated with poor prognosis by means of a validation study with another set of 56 ER-positive breast cancers. High expression of these two genes was determined to be significantly predictive for poor prognosis of patients with ER-positive breast cancer, and may help to achieve optimal selection of adjuvant treatment for such patients.

Adult↗
PubMed1994

[Selective gene therapy of malignant gliomas using brain-specific promoters: its efficacy and basic investigations].

Retroviral vector is often used for gene therapy of malignant tumors. The main characteristic of this vector is that it integrates only into the genes of dividing and proliferating cells. Glioma cells proliferate actively, while surrounding normal brain cells rarely divide. Thus, we can expect the recombinant retrovirus modified to express cytotoxic genes to kill glioma cells selectively. However, this characteristic of specific toxicity to the dividing cells is also observed in many chemotherapeutic agents, and it is well known that they cause severe side effects, such as bone marrow suppression or diarrhea caused by simultaneous toxicity of the drugs to proliferating bone marrow cells or intestinal epithelial cells, respectively. We have cloned many genes which are specifically expressed in brain, and identified their promoter regions conferring tissue-specific expression. If we use the brain-specific promoters to regulate the expression of the toxic genes, these genes may not be expressed in the myeloid cells or intestinal epithelial cells, even if they were infected with the retrovirus. Therefore, we searched for brain-specific promoters which are also active in glioma cells to kill glioma cells specifically. Then, MBP promoter showed the strongest promoter activity in mouse glioma cells. These mouse glioma cells transduced with retrovirus containing the MBP promoter directing the herpes simplex virus type 1 thymidine kinase (HTK) gene were extremely sensitive to ganciclovir, even when transduced with the MBP promoter-HTK gene-containing retrovirus. And we could get complete remission in the mouse brain tumor models, which were transfected HTK genes in more than 25% glioma cells, with ganciclovir.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed2005

Vascular endothelium-selective gene induction by Tie2 promoter/enhancer in the brain and retina of a transgenic rat.

PURPOSE: To produce a transgenic rat harboring the Tie2 promoter/enhancer linked green fluorescence protein (GFP) gene and investigate the blood-brain barrier (BBB)- and inner blood-retinal barrier (iBRB)-selective GFP expression in the brain and retina. METHODS: Transgenic rats were produced by the microinjection of mouse Tie2/GFP gene into fertilized oocytes of Wistar rats. The expression of GFP was observed in tissue slices by confocal microscopy. RESULTS: One of the obtained transgenic lines showed intense GFP expression in vascular endothelial cells throughout the brain. After double immunostaining with glucose transporter 1, the GFP was found to be localized in the cytoplasmic compartment of brain capillary endothelial cells. In contrast, no fluorescence was observed in neural cells. In the retina of transgenic rats, intense GFP expression was detected in retinal capillary endothelial cells. No fluorescence was detected in other cells. In kidney and liver, GFP expression was detected in vascular endothelial cells, whereas the expressed region was limited. CONCLUSIONS: Mouse Tie2 promoter/enhancer has the ability to induce gene expression selectively in vascular endothelial cells in the brain and retina of transgenic rats.

Animals↗
PubMed2003

Altered expression of randomly selected genes in mouse hippocampus after traumatic brain injury.

Using a cDNA microarray method, we analyzed gene expression profiles in mouse hippocampus after traumatic brain injury (TBI). Of 6,400 randomly selected arrayed genes and expressed sequence tags from a mouse cDNA library, 253 were found to be differentially expressed (106 increased and 147 decreased). Genes involved in cell homeostasis and calcium signaling were primarily up-regulated while those encoding mitochondrial enzymes, metabolic molecules, and structural proteins were predominantly down-regulated. Equal numbers of genes related to inflammatory reactions showed increased or decreased expression. Importantly, a large proportion of the dysregulated genes we identified have not been reported as differentially expressed in TBI models. Semiquantitative reverse-transcriptase polymerase chain reaction (RT-PCR) analyses of representative genes confirmed the validity of the corresponding microarray findings. Thus, our microarray-based evaluation of gene expression in traumatically injured hippocampus identified both known and novel genes that respond to TBI. Further investigation of these candidate molecules may suggest new ways to attenuate the traumatic effects of brain injury.

Animals↗
PubMed1988

Homologous integration in mammalian cells without target gene selection.

Homologous integrations into a nonselectable target locus have been highly enriched for following DNA transfections into mammalian cells. The target gene, the SV40 early region in COS1 cells, provides transcription signals to activate a defective selectable marker, the gpt gene. We find that nearly half of the selected clones have integrated the gpt gene at the homologous sequence in the COS1 genome. This is an estimated 100-fold enrichment for homologous events compared with transfections in which the gpt gene is transcriptionally active. As shown for yeast integration events, a double-strand break at a position of homology between the transfected DNA and the genomic target is necessary to achieve a high frequency of homologous integrations. Furthermore, the arrangement of sequences at the integration site includes a repair of the double-strand gap, which was present on the transfected DNA, suggesting that similarities exist between yeast and mammalian integrations. The experimental design, in which a defective marker is activated following a homologous integration, may have general applications for gene targeting in mammalian cells.

Animals↗
PubMed1985

Genes selectively expressed in proliferating Dictyostelium amoebae.

Few eukaryotic genes are expressed only during cell growth and division. We found that the slime mold Dictyostelium discoideum is unusual in that it expresses many genes only during proliferation. Thirty-two percent (304/950) of the sequences in a cDNA library made from vegetative mRNA were homologous to RNAs that are present at high levels during growth but at low or undetectable levels during differentiation when no cell growth occurs. In vitro translation assays confirmed that one-third of the vegetative cell mRNAs decreased in steady-state levels during differentiation. These vegetative cell-specific transcripts identified a diverse coordinately regulated class of genes: (i) 9 of the 10 cDNAs tested hybridized to unique small transcripts ranging from 400 to 620 bases long; (ii) the sequences showed various degrees of homology to related species; (iii) transcript levels synchronously fell by a factor of greater than 20 during development and synchronously increased during germination. This class of genes may play important roles in normal cell proliferation.

Cell Differentiation↗
PubMed1997

Multilocus evolution in fire ants: effects of selection, gene flow and recombination.

The reproductive success of individual fire ant queens (Solenopsis invicta) previously has been shown to be strongly influenced by their genotype at a single enzyme-encoding gene, designated Pgm-3. This paper presents evidence that a second, tightly linked gene, designated Gp-9, is under similarly strong selection in these ants. Selection appears to act independently on the two genes and is detectable in only one of the two social forms of this species (the "polygyne" social form in which nests contain multiple fertile queens). Strong directional selection on Pgm-3 in this form, involves worker destruction of all queens with genotype Pgm-3AA before they reproduce. Selection on Gp-9 is more complex, involving both lethality of all Gp-9bb females and a strong or even complete survival advantage to reproductive queens with the heterozygous genotype Gp-9Bb. Pgm-3 and Gp-9 are tightly linked (rf = 0.0016) and exhibit strong gametic phase disequilibrium in introduced populations in the U.S. This disequilibrium seems not to have stemmed from the founder event associated with the introduction, because the same associations of alleles found in the U.S. apparently occur also in two native populations in Argentina. Rather, selection acting independently on Pgm-3 and Gp-9, in conjunction with gene flow from the alternate, "monogyne" social form (in which nests contain a single fertile queen), may explain the origin of disequilibrium between the two loci in polygyne fire ants.

Animals↗
PubMed1987

Characterization and sequence of follicle cell genes selectively expressed during vitelline membrane formation in Drosophila.

To isolate genes involved in vitelline membrane production, an ovarian cDNA library was screened with eggchamber RNAs labeled in vivo. Two cDNA clones encoding RNAs that are selectively expressed in follicle cells during the period of vitelline membrane formation were isolated. Following isolation of homologous genomic clones from a Drosophila library, one gene was localized by in situ hybridization to chromosomal region 26A, and the other to 3C. Developmental Northern blots demonstrated that both genes produce 700-800 nucleotide transcripts that accumulate during the stages of vitelline membrane synthesis. In vitro translation products from hybrid selected RNAs and DNA sequence analysis both indicate that the 26A region gene encodes a major protein component of the vitelline membrane. The structural properties of the 3C region follicle cell gene seem more compatible with an intracellular function.

Amino Acid Sequence↗
PubMed2005

Detailed expression analysis of selected genes of the aldehyde dehydrogenase (ALDH) gene superfamily in Arabidopsis thaliana.

Aldehyde dehydrogenase (ALDH) genes have been identified in almost all organisms from prokaryotes to eukaryotes, but particularly in plants knowledge is very limited with respect to their function. The data presented here are a contribution towards a functional analysis of selected Arabidopsis ALDH genes by using expression profiles in wild types and mutants. The Arabidopsis thaliana genome contains 14 genes which represent 9 families. To gain insight into the possible roles of aldehyde dehydrogenases from Arabidopsis, the expression patterns of five selected ALDH genes were analyzed under defined physiological conditions. Three genes (ALDH3I1, 3H1 and ALDH7B4) that belong to two different families are differentially activated by dehydration, high salinity and ABA in a tissue-specific manner. The other two genes (ALDH3F1 and ALDH22A1) are constitutively expressed at a low level. Transcript analysis of ALDH3I1 and ALDH7B4 in Arabidopsis mutants suggests that stress responses are differentially controlled by the phytohormone ABA as well as by pathways that affect sugar metabolism and fatty acid composition of membrane lipids. Our results indicate that the stress-associated ALDH genes participate in several pathways and that their regulation involves diverged signal transduction pathways.

Abscisic Acid↗
PubMed1994

Locus-Control-Region-Coupled Beta (S)(Antilles)- and Alpha(2)-Hemoglobin Genes Select for High Alpha(2)-Hemoglobin Expression in Adult Transgenic Mice.

Two transgenic lines of mice were produced which contained the beta(S)(Antilles)- and alpha(2)-hemoglobin genes tandemly coupled to the 'micro' locus control region (&mgr;LCR). The &mgr;LCRbeta(S)(Antilles)alpha(2)-hemoglobin transgenic mice expressed high levels of alpha(2)-hemoglobin while beta(S)(Antilles)-hemoglobin expression was virtually undetectable. Abundant alpha(2)-hemoglobin protein was observed in the blood of transgenic mice, while beta(S)(Antilles)-hemoglobin chains could not be detected. Transgenic red blood cells had substantially decreased sensitivity to osmotic lysis. Attempts to produce homozygotes containing the transgene were unsuccessful. The phenotype of these mice closely resembles that of beta-thalassemic mice. The &mgr;LCRbeta(S)(Antilles)alpha(2) transgenic mice demonstrate that if the &mgr;LCR is coupled to the beta(S)(Antilles)- and alpha(2)-hemoglobin genes in tandem, only the distal alpha(2)-hemoglobin gene is selected for expression to significant levels in adult mice. These results support a reciprocally competitive model for LCR-hemoglobin developmental switching. Copyright 1994 S. Karger AG, Basel

Journal Article↗
PubMed2006

Chronic smoking and alcoholism change expression of selective genes in the human prefrontal cortex.

BACKGROUND: Alcoholism is commonly associated with chronic smoking. A number of gene expression profiles of regions within the human mesocorticolimbic system have identified potential alcohol-sensitive genes; however, the influence of smoking on these changes was not taken into account. This study addressed the impact of alcohol and smoking on the expression of 4 genes, previously identified as alcoholism-sensitive, in the human prefrontal cortex (PFC). METHODS: mRNA expression of apolipoprotein D, tissue inhibitor of the metalloproteinase 3, high-affinity glial glutamate transporter and midkine, was measured in the PFC of alcoholic subjects and controls with and without smoking comorbidity using real-time polymerase chain reaction. RESULTS: The results show that alcohol affects transcription of some of these genes. Additionally, smoking has a marked influence on gene expression. CONCLUSION: This study emphasizes the need for careful case selection in future gene expression studies to delineate the adaptive molecular process associated with smoking and alcohol.

Adult↗
PubMed2000

Serotonergic regulation of mRNA expression of Arc, an immediate early gene selectively localized at neuronal dendrites.

Arc (activity regulated, cytoskeleton associated protein) is an effector immediate early gene that is selectively localized in the neuronal dendrites. Elevation of brain 5-HT by the combined administration of the monoamine oxidase inhibitor, tranylcypromine (TCP, 5 mg/kg, i.p.), and the 5-HT precursor L-tryptophan (L-TP, 100 mg/kg, i.p.), increased Arc mRNA abundance in the cingulate, orbital, frontal and parietal cortices as well as in the striatum but a reduction was observed in the CA1 region of the hippocampus. The 5-HT releasing agent p-chloroamphetamine (PCA, 5 mg/kg, s.c.) also increased Arc mRNA in the cortical and striatal areas. Depleting brain 5-HT with the tryptophan hydroxylase inhibitor, p-chlorophenylalanine (pCPA, 300 mg/kg, i.p. for two days), on the other hand, significantly attenuated the increase in Arc mRNA induced by tranylcypromine and L-tryptophan (TCP/L-TP). Pretreatment with the 5-HT2 receptor antagonist ketanserin (2 mg/kg, i.p.) significantly attenuated the effect of TCP/L-TP in the cortex but only partially in striatum and did not affect the reduction in the CA1 region. The 5-HT2 agonist DOI (0.2, 1 and 2 mg/kg, i.p.) dose-dependently increased Arc mRNA abundance in cortical areas with a pattern similar to that of TCP/L-TP and PCA. DOI, however, had much weaker effects on Arc mRNA in the striatum and did not have any significant effect in the CA1, CA3 and the dentate gyms (DG) of the hippocampus. Pretreatment with ketanserin completely blocked the effect of DOI on Arc expression. These data suggest that Arc mRNA expression can be induced in the cortex by increases in extracellular 5-HT and that 5-HT2 receptors play a major part in mediating such effects. Additional 5-HT receptors as well as other neurotransmitters may also be involved, particularly in the striatum and in CA1 subfield of the hippocampus. Overall, our data suggest that expression of Arc mRNA is highly responsive to changes in brain 5-HT functions, and may provide a sensitive marker of postsynaptic 5-HT2(2A and 2C) receptor functions.

Animals↗
PubMed2005

Probe rank approaches for gene selection in oligonucleotide arrays with a small number of replicates.

MOTIVATION: One major area of interest in analyzing oligonucleotide gene array data is identifying differentially expressed genes. A challenge to biostatisticians is to develop an approach to summarizing probe-level information that adequately reflects the true expression level while accounting for probe variation, chip variation and interaction effects. Various statistical tools, such as MAS and RMA, have been developed to address this issue. In these approaches, the probe level expression data are summarized into gene level data, which are then used for downstream statistical analysis. Since probe variation is often larger than chip variation and there is also a potential interaction effect between probe affinity and treatment effect, strategies such as a gene level analysis, may not be optimal. In this study, we propose a procedure to analyze probe level data for selecting differentially expressed genes under two treatment conditions (groups) with a small number of replicates. The probe level discrepancy between two groups can be measured by a difference of the percentiles of probe perfect-match (PM) ranks or of probe PM weighted ranks. The difference is then compared with a pre-specified threshold to determine differentially expressed genes. The probe level approach takes into account non-homogenous treatment effects and reduces possible cross-hybridization effects across a set of probes. RESULTS: The proposed approach is compared with MAS and RMA using two benchmark gene array datasets. Positive predictivity and sensitivity are used for evaluation. Results show the proposed approach has higher positive predictivity and higher sensitivity. AVAILABILITY: Available on request from the authors. CONTACT: dtchen@uab.edu.

Algorithms↗
PubMed2006

Carcinoembryonic antigen-targeted selective gene therapy for gastric cancer through FZ33 fiber-modified adenovirus vectors.

PURPOSE: A major problem when using the adenoviral vectors for gene therapy applications is thought to be related to low transduction efficiency in cancer cells or to side effects in normal cells. There is an urgent requirement to improve the specificity of gene delivery in the context of cancer gene therapy. EXPERIMENTAL DESIGN: We constructed a genetically modified adenovirus incorporating an IgG Fc-binding motif from the Staphylococcus protein A, Z33, within the HI loop (Adv-FZ33). A remarkable degree of targeted gene delivery to gastric cancer cells was obtained with Adv-FZ33 with the fully human anti-carcinoembryonic antigen (CEA) monoclonal antibody, C2-45. RESULTS: In vitro LacZ or EGFP gene expression after Adv-FZ33 infection via C2-45 was 20 times higher than control monoclonal antibody in MKN-45 at 1,000 viral particles/cell. We generated Ax3CAUP-FZ33 (UP-FZ33), which is an Adv-FZ33 derivative vector expressing a therapeutic gene (i.e., Escherichia coli uracil phosphoribosyltransferase), which converts 5-fluorouracil (5-FU) directly to 5-fluoro-UMP. UP-FZ33 with C2-45 enhanced the cytotoxicity of 5-FU by 10.5-fold in terms of IC(50) against MKN-45 compared with control IgG4. In a nude mouse peritoneal dissemination model, tumor growth in mice treated with UP-FZ33/C2-45/5-FU was significantly suppressed, and tumor volumes were less than one-fourth of those of the control IgG4 group (P < 0.05). The median survival time of the UP-FZ33/C2-45/5-FU group was significantly longer than those treated with PBS or 5-FU only (P < 0.01). CONCLUSIONS: These data suggest that CEA-targeted FZ33 mutant adenovirus-mediated gene delivery offers a strong and selective therapeutic modality against CEA-producing cancers.

Adenoviridae↗
PubMed2000

[Isobutyramide activates transcription of human fetal gamma-globin gene selectively].

OBJECTIVE: To examine the effect of isobutyramide synthesized in our laboratory on expression of globin genes in MEL cells transfected with the recombinant construct mu LCRA gamma psi beta delta beta MEL. METHODS: The transformant cells were cultured in the medium containing different concentrations of isobutyramide for four days. The human gamma-, beta- and mouse alpha-globin mRNA were determined by RNase protection analysis. RESULTS: The inducible and dose-dependent expression of the human gamma-, beta- and mouse alpha- globin gene were observed. The induction of the human gamma-globin gene was significant stronger than that of the beta-globin gene. Under 2.5 mmol/L-5 mmol/L of isobutyramide, the induction of the human gamma-globin gene was even more effective than that of mouse alpha-globin gene. CONCLUSION: Isobutyramide can effectively and selectively activate transcription of the human gamma-globin gene at a certain degree. This function, together with the advantages of nontoxic and long halflife makes isobutyramide a promising application in the treatment of beta-thalassemia and sickle cell anemia.

Amides↗