Search results for "Microarray analysis techniques"

Mechanism of action of Rhodiola, salidroside, tyrosol and triandrin in isolated neuroglial cells: An interactive pathway analysis of the downstream e…

2014

Abstract Aim The aim of this study was to identify the targets (genes, interactive signaling pathways, and molecular networks) of Rhodiola rosea extract in isolated neuroglia cells and to predict the effects of Rhodiola extract on cellular functions and diseases. In addition, the potential mechanism of action of Rhodiola rosea extract was elucidated, and the “active principle” among the three isolated constituents (salidroside, triandrin, and tyrosol) was identified. Methods Gene expression profiling was performed using the T98G human neuroglia cell line after treatment with the Rhodiola rosea SHR-5 extract and several of its individual constituents (salidroside, triandrin and tyrosol). An …

COX-2-dependent and COX-2-independent mode of action of celecoxib in human liver cancer cells.

2011

Celecoxib (Celebrex((R)), Pfizer) is a selective cyclooxygenase-2 (COX-2) inhibitor with chemopreventive and antitumor effects. However, it is now well known that celecoxib has several COX-2-independent activities. To better understand COX-2-independent molecular mechanisms underlying the antitumor activity of celecoxib, we investigated the expression profile of the celecoxib-treated COX-2-positive (Huh7) and COX-2-negative (HepG2) liver cancer cell lines, using microarray analysis. Celecoxib treatment resulted in significantly altered expression levels of 240 and 403 transcripts in Huh7 and HepG2 cells, respectively. Confirmation of the microarray results was performed for selected genes b…

LASS6, an additional member of the longevity assurance gene family

2005

Longevity assurance genes (LAGs) represent a subgroup of the homeobox gene family. Five mammalian homologs have been reported, and the corresponding proteins have previously been investigated with respect to their key role in ceramide synthesis. However, members of the LAG family have been shown to be involved in cell growth regulation and cancer differentiation. In an effort to characterize additional members of the LAG family, we have screened the latest releases of genomic databases and report on the bioinformatic characterization of yet another member, LAG1 longevity assurance homolog 6 (LASS6). Like other LAG family members, the LASS6 protein contained a homeodomain and LAG1 domain. In…

Expression profiling of glial genes during Drosophila embryogenesis

2006

AbstractIn the central nervous system of Drosophila, the induction of the glial cell fate is dependent on the transcription factor glial cells missing (gcm). Though a considerable number of other genes have been shown to be expressed in all or in subsets of glial cells, the course of glial cell differentiation and subtype specification is only poorly understood. This prompted us to design a whole genome microarray approach comparing gcm gain-of-function and, for the first time, gcm loss-of-function genetics to wildtype in time course experiments along embryogenesis. The microarray data were analyzed with special emphasis on the temporal profile of differential regulation. A comparison of bo…

A new Multi-Layers Method to Analyze Gene Expression

2007

In the paper a new Multi-Layers approach (called Multi-Layers Model MLM) for the analysis of stochastic signals and its application to the analysis of gene expression data is presented. It consists in the generation of sub-samples from the input signal by applying a threshold technique based on cut-set optimal conditions. The MLM has been applied on synthetic and real microarray data for the identification of particular regions across DNA called nucleosomes and linkers. Nucleosomes are the fundamental repeating subunits of all eukaryotic chromatin, and their positioning provides useful information regarding the regulation of gene expression in eukaryotic cells. Results have shown a good rec…

Tumor-Associated MUC1 Tandem-Repeat Glycopeptide Microarrays to Evaluate Serum- and Monoclonal-Antibody Specificity

2009

A MULTI-LAYER MODEL TO STUDY GENOME-SCALE POSITIONS OF NUCLEOSOMES

2007

The positioning of nucleosomes along chromatin has been implicated in the regulation of gene expression in eukaryotic cells, because packaging DNA into nucleosomes affects sequence accessibility. In this paper we propose a new model (called MLM) for the identification of nucleosomes and linker regions across DNA, consisting in a thresholding technique based on cut-set conditions. For this purpose we have defined a method to generate synthetic microarray data fully inspired from the approach that has been used by Yuan et al. Results have shown a good recognition rate on synthetic data, moreover, the $MLM$ shows a good agreement with the recently published method based on Hidden Markov Model …

A systems biology perspective on cholangiocellular carcinoma development: focus on MAPK-signaling and the extracellular environment.

2008

Background/Aims Multiple genes have been implicated in cholangiocellular carcinoma (CCC) development. However, the overall neoplastic risk is likely associated with a much lower number of critical physiological pathways. Methods To investigate this hypothesis, we extracted all published genetic associations for the development of CCC from PubMed (genetic association studies, but also studies associating genes and CCC in general, i.e. functional studies in cell lines, genetic studies in humans, knockout mice etc.) and integrated CCC microarray data. Results We demonstrated the MAPK pathway was consistently enriched in CCC. Comparing our data to genetic associations in HCC often successfully …

Pathway analysis of high-throughput biological data within a Bayesian network framework

2011

Abstract Motivation: Most current approaches to high-throughput biological data (HTBD) analysis either perform individual gene/protein analysis or, gene/protein set enrichment analysis for a list of biologically relevant molecules. Bayesian Networks (BNs) capture linear and non-linear interactions, handle stochastic events accounting for noise, and focus on local interactions, which can be related to causal inference. Here, we describe for the first time an algorithm that models biological pathways as BNs and identifies pathways that best explain given HTBD by scoring fitness of each network. Results: Proposed method takes into account the connectivity and relatedness between nodes of the p…

A web application for the unspecific detection of differentially expressed DNA regions in strand-specific expression data

2015

Abstract Genomic technologies allow laboratories to produce large-scale data sets, either through the use of next-generation sequencing or microarray platforms. To explore these data sets and obtain maximum value from the data, researchers view their results alongside all the known features of a given reference genome. To study transcriptional changes that occur under a given condition, researchers search for regions of the genome that are differentially expressed between different experimental conditions. In order to identify these regions several algorithms have been developed over the years, along with some bioinformatic platforms that enable their use. However, currently available appli…