scholarly journals Calculation of reliable transcript levels of annotated genes on the basis of multiple probe-sets in Affymetrix microarrays.

2009 ◽  
Vol 56 (2) ◽  
Author(s):  
Roman Jaksik ◽  
Joanna Polańska ◽  
Robert Herok ◽  
Joanna Rzeszowska-Wolny
Keyword(s):  
Global Gene Expression ◽  
Basic Tool ◽  
Annotation Database ◽  
New Approach ◽  
Transcript Levels ◽  
Individual Probe ◽  
Affymetrix Microarrays ◽  
Multiple Probe ◽  
Probe Set ◽  
Outlying Probe

Microarray methods have become a basic tool in studies of global gene expression and changes in transcript levels. Affymetrix microarrays from the HGU133 series contain multiple probe-sets complementary to the same gene (4742 genes are represented by more than one probe-set in a microarray HGU133A). Individual probe-sets annotated to the same gene often show different hybridization signals and even opposite trends, which may result from some of them matching transcripts of more than one gene and from the existence of different splice-variant transcripts. Existing methods that redefine probe-sets and develop custom probe-set definitions use mathematical tools such as Matlab or the R statistical environment with the Bioconductor package (Gentleman et al., 2004, Genome Biol. 5: 280) and thus are directed to researchers with a good knowledge of bioinformatics. We propose here a new approach based on the principle that a probe-set which hybridizes to more than one transcript can be recognized because it produces a signal significantly different from others assigned to the particular gene, allowing it to be detected as an outlier in the group and eliminated from subsequent analyses. A simple freeware application has been developed (available at www.bioinformatics.aei.polsl.pl) that detects and removes outlying probe-sets and calculates average signal values for individual genes using the latest annotation database provided by Affymetrix. We illustrate this procedure using microarray data from our experiments aiming to study changes of transcription profile induced by ionizing radiation in human cells.

Systems Approach to Knowledge Synthesis

2010 ◽  
Vol 1 (1) ◽  
pp. 1-13 ◽  
Author(s):  
Yoshiteru Nakamori ◽  
Andrzej P. Wierzbicki
Keyword(s):  
Systems Thinking ◽  
Knowledge Creation ◽  
Knowledge Integration ◽  
Systems Approach ◽  
Knowledge Synthesis ◽  
Basic Tool ◽  
Systems Methodology ◽  
New Approach

This article presents a systems approach to knowledge synthesis or construction, starting with a new systems thinking named the informed systems thinking, which should serve as the basic tool of knowledge integration and support creativity. Based on this new systems thinking, a new systems approach to knowledge synthesis or construction has been developed as a systems methodology that consists of three fundamental parts: how to collect and synthesize knowledge, how to use our abilities in collecting knowledge, and how to justify the synthesized knowledge. This article first describes the informed systems thinking and then introduces a new systems approach to knowledge synthesis and the features of this new approach from a viewpoint of knowledge creation.

Systems Approach to Knowledge Synthesis

2013 ◽  
pp. 1-14
Author(s):  
Yoshiteru Nakamori ◽  
Andrzej P. Wierzbicki
Keyword(s):  
Systems Thinking ◽  
Knowledge Creation ◽  
Knowledge Integration ◽  
Systems Approach ◽  
Knowledge Synthesis ◽  
Basic Tool ◽  
Systems Methodology ◽  
New Approach

This article presents a systems approach to knowledge synthesis or construction, starting with a new systems thinking named the informed systems thinking, which should serve as the basic tool of knowledge integration and support creativity. Based on this new systems thinking, a new systems approach to knowledge synthesis or construction has been developed as a systems methodology that consists of three fundamental parts: how to collect and synthesize knowledge, how to use our abilities in collecting knowledge, and how to justify the synthesized knowledge. This article first describes the informed systems thinking and then introduces a new systems approach to knowledge synthesis and the features of this new approach from a viewpoint of knowledge creation.

Method of Design Through Structuring of Meanings

2008 ◽  
Author(s):  
Georgi V. Georgiev ◽  
Toshiharu Taura ◽  
Amaresh Chakrabarti ◽  
Yukari Nagai
Keyword(s):  
Product Design ◽  
Design Process ◽  
Design Methodology ◽  
Evaluation Process ◽  
Convergence Criteria ◽  
Lexical Database ◽  
Basic Tool ◽  
New Approach ◽  
Evaluation Techniques ◽  
Method Of Design

This research shows a new approach and development of a design methodology, based on the perspective of meanings. In this study the design process is explored as a development of the structure of meanings. The processes of search and evaluation of meanings form the foundations of developing this structure. In order to facilitate the use and operation of the meanings, the WordNet lexical database and an existing visualization of WordNet — Visuwords — is used for the process of meaning search. The basic tool used for evaluation process is the WordNet::Similarity software, measuring the relatedness of meanings in the database. In this way it is measuring the degree of interconnections between different meanings. This kind of search and evaluation techniques are later on incorporated into our methodology of the structure of meanings to support the design process. The measures of relatedness of meanings are developed as convergence criteria for application in the processes of evaluation. Further on, the methodology for the structure of meanings developed here is used to construct meanings in a verification of product design. The steps of the design methodology, including the search and evaluation processes involved in developing the structure of the meanings, are elucidated. The choices, made by the designer in terms of meanings are supported by consequent searches and evaluations of meanings to be implemented in the designed product. In conclusion, the paper presents directions for developing and further extensions of the proposed design methodology.

scholarly journals Global gene expression and secondary metabolite changes in Arabidopsis thaliana ABI4 over-expression lines

Botany ◽  
2016 ◽  
Vol 94 (8) ◽  
pp. 615-634 ◽  
Author(s):  
Bianyun Yu ◽  
Margaret Y. Gruber ◽  
Shu Wei ◽  
Rong Zhou ◽  
Dwayne Hegedus ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Secondary Metabolite ◽  
Plant Development ◽  
Global Gene Expression ◽  
Comprehensive Overview ◽  
Altered Expression ◽  
Transcript Levels ◽  
Over Expression ◽  
Expression Of Genes ◽  
Genes Encoding

Despite numerous studies on ABI4, its role in plant secondary metabolism has not been fully investigated. Here, we used metabolite profiling together with transcriptome analysis to demonstrate that ABI4 transcript levels regulate a host of secondary metabolite pathways and growth modalities in ABI4 over-expression (ABI4_OE) lines of Arabidopsis thaliana. This strategy provided a unique and comprehensive overview of the regulation of metabolic shifts in response to ABI4 transcription. We show that enhancement of ABI4 transcript levels changed seed proanthocyanidin (PA), flavonoid, and carotenoid levels in ABI4_OE seeds and 30-day-old shoots, as well as the expression of genes encoding enzymes involved in the production of these and other secondary metabolites in ABI4_OE shoots. In seeds, PA accumulated in very large uneven patches, which was dramatically different from the even distribution of PA in wild-type seeds. Shoots of ABI4_OE lines also exhibited altered expression of a range of genes involved in several aspects of plant development, including hormone and cell-wall synthesis. Alteration of such disparate secondary metabolite pathways, along with hormone and developmental pathways, suggests that ABI4 is a master regulator integrating these compounds with plant development.

PROBE-LEVEL UNIVERSAL SEARCH (PLUS) ALGORITHM FOR GENDER DIFFERENTIATION IN AFFYMETRIX DATASETS

2010 ◽  
Vol 08 (03) ◽  
pp. 553-577 ◽  
Author(s):  
ANNA S. KARYAGYNA ◽  
MICHAIL O. VASSILIEV ◽  
ANNA S. ERSHOVA ◽  
RAMIL N. NURTDINOV ◽  
ILYA S. LOSSEV
Keyword(s):  
Gene Expression ◽  
Sex Chromosome ◽  
Perfect Match ◽  
Selection Procedure ◽  
Single Measure ◽  
Gender Differentiation ◽  
Affymetrix Microarrays ◽  
Individual Good ◽  
New Feature ◽  
Probe Set

Affymetrix microarrays measure gene expression based on the intensity of hybridization of a panel of oligonucleotide probes (probe set) with mRNA. The signals from all probes within a probe set are converted into a single measure that represents the expression value of a gene. This step diminishes the number of independently measured parameters and eliminates from consideration individual "good-working" probes. We propose a new feature selection algorithm (Probe Level Universal Search or PLUS algorithm) for probe-level analysis of gene expression datasets. The algorithm evaluates the intensities of perfect-match Affymetrix probes individually and selects probes that allow one to distinguish two given classes of samples. The algorithm was used to differentiate the samples according to their gender ("gender differentiation"). The universal gender differentiating set of 3' Gene Affymetrix microarray probes was selected; the set consists of 38 probes from XIST gene of X-chromosome and 17 probes from five Y-chromosome genes: RPS4Y1, EIF1A, DDX3Y, JARID1D and USP9Y. The selection procedure based on the probes selected by PLUS algorithm differentiates the sex chromosome karyotype of the sample, reveals samples with incorrect gender labels and samples from patients with hereditary syndromes or cancer-associated chromosome abnormalities.

Global Gene Expression of Listeria monocytogenes to Salt Stress

2012 ◽  
Vol 75 (5) ◽  
pp. 906-912 ◽  
Author(s):  
DONGRYEOUL BAE ◽  
CONNIE LIU ◽  
TING ZHANG ◽  
MARCUS JONES ◽  
SCOTT N. PETERSON ◽  
...  
Keyword(s):  
Gene Expression ◽  
Salt Stress ◽  
Listeria Monocytogenes ◽  
Cell Growth ◽  
Expression Profiles ◽  
Brain Heart Infusion ◽  
Global Gene Expression ◽  
Phosphotransferase System ◽  
Transcript Levels ◽  
Qrt Pcr

Outbreaks of listeriosis caused by the ingestion of Listeria-contaminated ready-to-eat foods have been reported worldwide. Many ready-to-eat foods, such as deli meat products, contain high amounts of salt, which can disrupt the maintenance of osmotic balance within bacterial cells. To understand how Listeria monocytogenes adapts to salt stress, we examined the growth and global gene expression profiles of L. monocytogenes strain F2365 under salt stress using oligonucleotide probe-based DNA array and quantitative real-time PCR (qRT-PCR) analyses. The growth of L. monocytogenes in brain heart infusion (BHI) medium with various concentrations of NaCl (2.5, 5, and 10%) was significantly inhibited (P < 0.01) when compared with growth in BHI with no NaCl supplementation. Microarray data indicated that growth in BHI medium with 1.2% NaCl upregulated 4 genes and down-regulated 24 genes in L. monocytogenes, which was confirmed by qRT-PCR. The transcript levels of genes involved in the uptake of glycine betaine/l-proline were increased, whereas genes associated with a putative phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS), metabolic enzymes, and virulence factor were down-regulated. Specifically, the expression levels of PTS transport genes were shown to be dependent on NaCl concentration. To further examine whether the down-regulation of PTS genes is related to decreased cell growth, the transcript levels of genes encoding components of enzyme II, involved in the uptake of various sugars used as the primary carbon source in bacteria, were also measured using qRT-PCR. Our results suggest that the decreased transcript levels of PTS genes may be caused by salt stress or reduced cell growth through salt stress. Here, we report global transcriptional profiles of L. monocytogenes in response to salt stress, contributing to an improved understanding of osmotolerance in this bacterium.

scholarly journals DNA Microarray Analysis of Nitrogen Fixation and Fe(III) Reduction in Geobacter sulfurreducens

2005 ◽  
Vol 71 (5) ◽  
pp. 2530-2538 ◽  
Author(s):  
Barbara A. Methé ◽  
Jennifer Webster ◽  
Kelly Nevin ◽  
Jessica Butler ◽  
Derek R. Lovley
Keyword(s):  
Nitrogen Fixation ◽  
Dna Microarray ◽  
Electron Acceptor ◽  
Global Gene Expression ◽  
Geobacter Sulfurreducens ◽  
Unexpected Result ◽  
Transcript Levels ◽  
Gene Coding ◽  
Global Gene Expression Profiling ◽  
Microarray Analyses

ABSTRACT A DNA microarray representing the genome of Geobacter sulfurreducens was constructed for use in global gene expression profiling of cells under steady-state conditions with acetate as the electron donor and Fe(III) or fumarate as the electron acceptor. Reproducible differences in transcript levels were also observed in comparisons between cells grown with ammonia and those fixing atmospheric nitrogen. There was a high correlation between changes in transcript levels determined with microarray analyses and an evaluation of a subset of the genome with quantitative PCR. As expected, cells required to fix nitrogen had higher levels of transcripts of genes associated with nitrogen fixation, further demonstrating that the microarray approach could reliably detect important physiological changes. Cells grown with Fe(III) as the electron acceptor had higher levels of transcripts for omcB, a gene coding for an outer membrane c-type cytochrome that is essential for Fe(III) reduction. Several other c-type cytochrome genes also appeared to be up-regulated. An unexpected result was significantly higher levels of transcripts for genes which have a role in metal efflux, potentially suggesting the importance of maintaining metal homeostasis during release of soluble metals when reducing Fe(III). A substantial proportion (30%) of significantly expressed genes during Fe(III) reduction were genes of unknown function or hypothetical proteins, suggesting differences in Fe(III) reduction physiology among microorganisms which perform this metabolic process.

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