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Results for “expression analysis”

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At least 163 records · Page 9Linked to original sources

PubMed2003

Unsupervised feature selection via two-way ordering in gene expression analysis.

MOTIVATION: Selection of genes most relevant and informative for certain phenotypes is an important aspect in gene expression analysis. Most current methods select genes based on known phenotype information. However, certain set of genes may correspond to new phenotypes which are yet unknown, and it is important to develop novel effective selection methods for their discovery without using any prior phenotype information. RESULTS: We propose and study a new method to select relevant genes based on their similarity information only. The method relies on a mechanism for discarding irrelevant genes. A two-way ordering of gene expression data can force irrelevant genes towards the middle in the ordering and thus can be discarded. Mechanisms based on variance and principal component analysis are also studied. When applied to expression profiles of colon cancer and leukemia, the unsupervised method outperforms the baseline algorithm that simply uses all genes, and it also selects relevant genes close to those selected using supervised methods. SUPPLEMENT: More results and software are online: http://www.nersc.gov/~cding/2way.

Algorithms↗

PubMedDate not supplied

[Gene expression analysis by DNA microarray in papillary thyroid cancer].

In our study we present chosen elements of microarray analysis of gene expression profile in papillary thyroid cancer. The study group included 16 papillary thyroid cancer tissues and 16 corresponding normal tissues. Samples were analyzed on high density oligonucleotide microarrays (GeneChip HG-U133A) which contain 22.000 genes. 110 genes, which had significant changed expression, were selected by MAS 5.0 program. 3 genes were chosen to the deeper analysis: dipeptidylpeptidase 4 (DPP4), fibronectin 1 (FN1), tissue inhibitor of metalloproteinase 1 (TIMP1). DPP4-RNA were absent in normal tissue while in cancer tissue it was detected in large amount. FN1 and TIMP1 expression were detected in normal tissue but markedly increased in papillary thyroid cancer. Among these 3 genes DPP4 seems to be the best molecular marker for papillary thyroid cancer.

Adenosine Deaminase↗

PubMed2006

Rosetta error model for gene expression analysis.

MOTIVATION: In microarray gene expression studies, the number of replicated microarrays is usually small because of cost and sample availability, resulting in unreliable variance estimation and thus unreliable statistical hypothesis tests. The unreliable variance estimation is further complicated by the fact that the technology-specific variance is intrinsically intensity-dependent. RESULTS: The Rosetta error model captures the variance-intensity relationship for various types of microarray technologies, such as single-color arrays and two-color arrays. This error model conservatively estimates intensity error and uses this value to stabilize the variance estimation. We present two commonly used error models: the intensity error-model for single-color microarrays and the ratio error model for two-color microarrays or ratios built from two single-color arrays. We present examples to demonstrate the strength of our error models in improving statistical power of microarray data analysis, particularly, in increasing expression detection sensitivity and specificity when the number of replicates is limited.

Algorithms↗

PubMed1997

cDNA cloning and expression analysis of NeuroD mRNA in human retina.

We have shown that bHLH proteins are involved in mammalian retinal development. Here we report the identification and analysis of the expression of a neurogenic differentiation gene, NeuroD, in human retina. In situ hybridization and immunocytochemical analyses of adult retina showed that NeuroD transcripts and NeuroD immunoreactivity are predominantly localized to the outer nuclear layer which contains the photoreceptors. Southern analysis of PCR-amplified cDNA revealed that NeuroD mRNA is also expressed in fetal human retina. Fetal monkey retina was used to analyse the spatial distribution of NeuroD in the developing retina. Both NeuroD transcripts and immunoreactivity are largely detected in the outer neuroblastic layer. Therefore, NeuroD may be involved in the differentiation as well as maintenance of the differentiated properties of photoreceptors.

Adult↗

PubMed2004

Optimizing RNA extraction yield from whole blood for microarray gene expression analysis.

OBJECTIVES: Microarray analysis of gene expression profiles of blood leukocytes has many potential clinical and research applications. DESIGN AND METHODS: We used the PAXgene Blood RNA System to prepare RNA from the whole blood of normal volunteers using two incubation times followed by gene expression profiling using the Affymetrix HU133A GeneChip. CONCLUSIONS: Longer incubation gave a significantly higher RNA yield and samples that were satisfactory for microarray analysis, with excellent pairwise correlations between replicates.

Gene Expression Profiling↗

PubMed2006

In silico assessment of gene function involved in cysteine biosynthesis in Arabidopsis: expression analysis of multiple isoforms of serine acetyltransferase.

In plants, the inorganic sulfur is first fixed into cysteine by the cysteine biosynthetic pathway. This biosynthetic pathway of cysteine involves several enzymatic reactions. In Arabidopsis thaliana, multiple isoforms seem to participate in each enzymatic step for cysteine biosynthesis. To obtain more insights on the specific role of each isoform involved in the cysteine biosynthesis, in silico analysis of these isoforms using Arabidopsis expressed sequence tags (EST) database was carried out. This EST database analysis revealed distinct population distribution of ESTs among multiple isoforms, suggesting that each isoform has its particular expression pattern, presumably associated with its specific role in cysteine biosynthesis. As another in silico analysis, co-expression analysis of genes involved in sulfur metabolism in Arabidopsis was performed using a public transcriptome database of DNA microarrays. This co-expression analysis also suggested specific function and co-regulation of some isoform genes for cysteine biosynthesis by consideration on the clustering of co-expressed genes. From the results of sensitivity to feedback regulation, subcellular localization and expression of mRNA analyses, each serine acetyltransferase (SATase) isoform seems to have its specific role for cysteine biosynthesis. Similar expression patterns were observed between the experimental results of expression data for SATase isoforms and the in silico results of "digital northern" analysis using EST database.

Arabidopsis↗

PubMed2006

Functional annotation of the Arabidopsis P450 superfamily based on large-scale co-expression analysis.

Cytochrome P450 mono-oxygenases play prominent roles in a diverse set of metabolic pathways, but the function of most of these enzymes remains obscure. A bottleneck in the functional genomics of this superfamily constitutes hypothesis generation to identify potential substrates (or substrate classes) individual P450s may act on. We used publicly available large-scale expression data to perform co-expression analysis comparing the expression matrix of each P450 with those from more than 4000 selected genes across thousands of microarrays. Based on functional annotations of co-expressed genes from a diverse set of databases, co-expressed pathways were thus identified for each P450. Using this approach, most P450s with known functions were placed into their respective pathways, thereby proofing the concept. As examples, pathway mapping results identifying novel P450s potentially acting on flower-specific monoterpenes and root-specific triterpenes are described. Co-expression results for all Arabidopsis P450s will be presented as a web resource on the 'CYPedia' web pages (http://ibmp.u-strasbg.fr/CYPedia/).

Arabidopsis↗

PubMed2005

Porcine Toll-like receptor 1, 6, and 10 genes: complete sequencing of genomic region and expression analysis.

Toll-like receptors (TLRs) recognize various microbial components and play key roles in activating the innate immune system. Hence, their function is important in swine infectious diseases. We completely determined 173,804 bp of nucleotide sequence of a genomic region including porcine TLR6 and the newly identified porcine TLR homologues TLR1 and TLR10. The porcine genomic structure of these genes was highly conserved in comparison with the corresponding region in humans. Analysis of their expression in porcine tissues showed differences in expression patterns between porcine TLR10 and TLR1 or TLR6. Moreover, phylogenetic analysis of the cytoplasmic regions of TLR genes suggested that the signal transduction pathway of TLR10 was different from those of TLR1 and TLR6. We also developed six polymorphic microsatellite markers within this genomic region; these markers will be valuable for association studies between TLR genes and resistance or susceptibility to infectious diseases in swine.

Amino Acid Sequence↗

PubMed2004

Isolation and gene expression analysis of Arabidopsis thaliana mutants with constitutive expression of ATL2, an early elicitor-response RING-H2 zinc-finger gene.

Genes with unstable transcripts often encode proteins that play important regulatory roles. ATL2 is a member of a multigene family coding highly related RING-H2 zinc-finger proteins that may function as E3 ubiquitin ligases. ATL2 mRNA accumulation occurs rapidly and transiently after incubation with elicitors of pathogen response. We screened 50,000 M(2) families from a line that carries a fusion of pATL2 to the GUS reporter gene and isolated five mutants, which we named eca (expresión constitutiva de ATL2), that showed constitutive expression of the reporter gene. One mutant exhibits a drastic stunted phenotype while the other four grow similarly to wild type. Two early chitin-induced genes and known pathogenesis-related genes such as NPR1, PAL, and CHS are activated in all the mutants whereas members of the ATL family and PR-1 and PDF2.1, which are markers of the salicylic acid (SA) jasmonate (JA) defense-response pathways, display differential expression between the mutants. These observations indicate that the ECA gene products may function in the early steps of an elicitor-response pathway, although some of them may function at other stages on the SA or JA defense-response pathways. Likewise, the fact that ATL2 and other members of the ATL family are activated in eca mutants links the induction of this putative class of ubiquitin ligases to plant defense signaling pathways.

Arabidopsis↗

PubMed1998

Human ARHGDIG, a GDP-dissociation inhibitor for Rho proteins: genomic structure, sequence, expression analysis, and mapping to chromosome 16p13.3.

GDP-dissociation inhibitors (GDIs) play a primary role in modulating the activity of GTPases. We recently reported the identification of a new GDI for the Rho-related GTPases named RhoGDIgamma. This gene is now designated ARHGDIG by HUGO. Here, in a detailed analysis of tissue expression of ARHGDIG, we observe high levels in the entire brain, with regional variations. The mRNA is also present at high levels in kidney and pancreas and at moderate levels in spinal cord, stomach, and pituitary gland. In other tissues examined, the mRNA levels are very low (lung, trachea, small intestine, colon, placenta) or undetectable. RT-PCR analysis of total RNA isolated from exocrine pancreas and islets shows that the gene is expressed in both tissues. We also report the genomic structure of ARHGDIG. The gene spans over 4 kb and is organized into six exons and five introns. The upstream region lacks a canonical TATA box and contains several putative binding sites for ubiquitous and tissue-specific factors active in central nervous system development. Using FISH, we have mapped the gene to chromosome band 16p13.3. This band is rich in deletion mutants of genes involved in several human diseases, notably polycystic kidney disease, alpha-thalassemia, tuberous sclerosis, mental retardation, and cancer. The promoter structure and the chromosomal location of RhoGDIgamma suggest its importance and underscore the need for further investigation into its biology.

Base Sequence↗

PubMed2002

Gene expression analysis reveals chemical-specific profiles.

The articles highlighted in this issue are "Gene Expression Analysis Reveals Chemical-Specific Profiles" by Hisham K. Hamadeh, Pierre R. Bushel, Supriya Jayadev, Karla Martin, Olimpia DiSorbo, Stella Sieber, Lee Bennett, Raymond Tennant, Raymond Stoll, J. Carl Barrett, Kerry Blanchard, Richard S. Paules, and Cynthia A. Afshari (pp. 219-231) and "Prediction of Compound Signature Using High Density Gene Expression Profiling" by Hisham K. Hamadeh, Pierre R. Bushel, Supriya Jayadev, Olimpia DiSorbo, Leping Li, Raymond Tennant, Raymond Stoll, J. Carl Barrett, Richard S. Paules, Kerry Blanchard, and Cynthia A. Afshari (pp. 232-240).

Animals↗

PubMed2000

Fundamentals of DNA hybridization arrays for gene expression analysis.

DNA hybridization arrays [also known as macroarrays, microarrays and/or high-density oligonucleotide arrays (Gene Chips)] bring gene expression analysis to a genomic scale by permitting investigators to simultaneously examine changes in the expression of literally thousands of genes. For hybridization arrays, the general approach is to immobilize gene-specific sequences (probes) on a solid state matrix (nylon membranes, glass microscope slides, silicon/ceramic chips). These sequences are then queried with labeled copies of nucleic acids from biological samples (targets). The underlying theory is that the greater the expression of a gene, the greater the amount of labeled target, and hence, the greater output signal. In spite of the simplicity of the experimental design, there are at least four different platforms and several different approaches to processing and labeling the biological samples. Moreover, investigators must also determine whether they will utilize commercially available arrays or generate their own. This review will cover the status of the hybridization array field with an eye toward underlying principles and available technologies. Future developments and technological trends will also be evaluated.

Cluster Analysis↗

PubMed2004

Global gene expression analysis by combinatorial optimization.

Generally, there is a trade-off between methods of gene expression analysis that are precise but labor-intensive, e.g. RT-PCR, and methods that scale up to global coverage but are not quite as quantitative, e.g. microarrays. In the present paper, we show how how a known method of gene expression profiling (K. Kato, Nucleic Acids Res. 23, 3685-3690 (1995)), which relies on a fairly small number of steps, can be turned into a global gene expression measurement by advanced data post-processing, with potentially little loss of accuracy. Post-processing here entails solving an ancillary combinatorial optimization problem. Validation is performed on in silico experiments generated from the FANTOM data base of full-length mouse cDNA. We present two variants of the method. One uses state-of-the-art commercial software for solving problems of this kind, the other a code developed by us specifically for this purpose, released in the public domain under GPL license.

Algorithms↗

PubMed2004

Cloning and expression analysis of a water stress-induced gene from Brassica oleracea.

Plant growth and productivity are greatly affected by water stress, such as drought and salinity. Here we report on the cloning and expression analysis of a water stress-induced gene from Brassica oleracea (designated as BoWS, GenBank accession number AY571333) by rapid amplification of cDNA ends (RACE). The full-length cDNA of BoWS consisted of 594 bp and contained a 285 bp open reading frame (ORF) encoding a 95-amino-acid protein. The deduced protein had a calculated molecular mass of 10.53 kDa and an isoelectric point of 6.93. The sequence similarity and comparative analysis showed that BoWS was 84% identical to Arabidopsis thaliana putative water stress-induced protein (GenBank accession number AAM67282). Southern blot analysis indicated that BoWS was a low-copy gene. Northern blot analysis revealed that the expression of BoWS was upregulated by abscisic acid (ABA), mannitol, NaCl, drought, salicylic acid (SA) and hydrogen peroxide (H(2)O(2)). Our results indicate that BoWS is extremely related to the water-deficit stress in B. oleracea.

Amino Acid Sequence↗

PubMed2002

[Expression analysis of protein tyrosine kinases of the FAK (focal adhesion kinase) family in osteosarcoma].

AIMS: Expression analysis of the protein tyrosine kinases, focal adhesion kinase (FAK) and proline-rich tyrosine kinase2 (Pyk2) in high grade osteosarcomas. MATERIALS AND METHODS: Expression of the kinases was evaluated qualitatively by immunohistochemical staining and quantitatively by real-time PCR. RESULTS: Osteoblastic cells of high grade osteosarcomas show a distinct FAK expression but an overexpression at the transcriptional level could not be detected. The Pyk2-mRNA expression was decreased in osteosarcomas. CONCLUSION: An altered relationship of FAK and Pyk2 was observed for different tumors and could also be important for osteosarcoma development.

Adolescent↗

PubMed2000

Sequencing and expression analysis of the serine protease gene cluster located in chromosome 19q13 region.

The human kallikrein gene cluster, located in the chromosome band 19q13, contains several tissue-specific serine protease genes including the prostate-specific KLK2, KLK3 and prostase genes. To further characterize the gene cluster, we have mapped, sequenced, and analyzed the genomic sequence from the region. The results of EST database searches and GENSCAN gene prediction analysis reveal 13 serine protease genes and several pseudogenes in the region. Expression analysis by RT-PCR indicates that most of these protease genes are expressed only in a subset of the 35 different normal tissues that have been examined. Several protease genes expressed in skin show higher expression levels in psoriatic lesion samples than in non-lesional skin samples from the same patient. This suggests that the imbalance of a complex protease cascade in skin may contribute to the pathology of disease. The proteases, excluding the kallikrein genes, share approximately 40% of their sequences suggesting that the serine protease gene cluster on chromosome 19q13 arose from ancient gene duplications.

Amino Acid Sequence↗

PubMed1998

Characterization and expression analysis of a Xanthomonas oryzae pv. oryzae recA.

Nucleotide sequence of Xanthomonas oryzae pv. oryzae (Xoo) DNA from pSM-A1 was determined and sequence analysis revealed an ORF with high homology to RecA proteins. Expression analysis using an anti-RecA antibody demonstrates that MMS treatment induces recA in Xanthomonas strains but not in an Escherichia coli harbouring cloned Xoo recA. This indicates the existence of a recA regulatory mechanism in Xanthomonas that is not function in E. coli. In Xoo, recA was highly induced by treatments with chemical mutagens, UV and peroxides, while superoxides, a thiol agent, a heavy metal and heat shock were not inducers. The increased amount of RecA induced by H2O2 or MMS treatments were due to increased transcription of recA. recA showed no growth phase or starvation regulation. The pattern of recA regulation in Xoo could play important roles in stress survival in the environment and during plant-microbe interactions.

Bacterial Proteins↗

PubMed2006

Gene expression analysis using filter cDNA microarrays.

The analysis of gene expression patterns by filter-based complementary (c)DNA microarray remains an important technique in the molecular biology laboratory, despite the development of large-scale cDNA microarray analysis (see Chapter 27). This chapter provides an overview of the methods necessary to carry out the production of membrane-based cDNA arrays and the subsequent synthesis and hybridization of radiolabeled cDNA probes.

Animals↗