Relationship between gene co-expression and probe localization on microarray slides

Background  

Microarray technology allows simultaneous measurement of thousands of genes in a single experiment. This is a potentially useful tool for evaluating co-expression of genes and extraction of useful functional and chromosomal structural information about genes.     

Chromosomal loci important for cotyledon opening under UV-B in Arabidopsis thaliana

Background  

Understanding of the genetic architecture of plant UV-B responses allows extensive targeted testing of candidate genes or regions, along with combinations of those genes, for placement in metabolic or signal transduction pathways.     

Non-random clustering of stress-related genes during evolution of the S. cerevisiae genome

Background  

Coordinately regulated genes often physically cluster in eukaryotic genomes, for reasons that remain unclear.     

A hierarchical statistical model for estimating population properties of quantitative genes

Background  

Earlier methods for detecting major genes responsible for a quantitative trait rely critically upon a well-structured pedigree in which the segregation pattern of genes exactly follow Mendelian inheritance laws. However, for many outcrossing species, such pedigrees are not available and genes also display population properties.     

Asymmetric and non-uniform evolution of recently duplicated human genes

Background  

Gene duplications are a source of new genes and protein functions. The innovative role of duplication events makes families of paralogous genes an interesting target for studies in evolutionary biology. Here we study global trends in the evolution of human genes that resulted from recent duplications.     

In search of suitable reference genes for gene expression studies of human renal cell carcinoma by real-time PCR

Background  

Housekeeping genes are commonly used as endogenous reference genes for the relative quantification of target genes in gene expression studies. No conclusive systematic study comparing the suitability of different candidate reference genes in clear cell renal cell carcinoma has been published to date. To remedy this situation, 10 housekeeping genes for normalizing purposes of RT-PCR measurements already recommended in various studies were examined with regard to their usefulness as reference genes.     

Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana

Background  

All sequenced genomes contain a proportion of lineage-specific genes, which exhibit no sequence similarity to any genes outside the lineage. Despite their prevalence, the origins and functions of most lineage-specific genes remain largely unknown. As more genomes are sequenced opportunities for understanding evolutionary origins and functions of lineage-specific genes are increasing.     

Selecting normalization genes for small diagnostic microarrays

Background  

Normalization of gene expression microarrays carrying thousands of genes is based on assumptions that do not hold for diagnostic microarrays carrying only few genes. Thus, applying standard microarray normalization strategies to diagnostic microarrays causes new normalization problems.     

Identifying metabolic enzymes with multiple types of association evidence

Background  

Existing large-scale metabolic models of sequenced organisms commonly include enzymatic functions which can not be attributed to any gene in that organism. Existing computational strategies for identifying such missing genes rely primarily on sequence homology to known enzyme-encoding genes.     

Sparse canonical correlation analysis for identifying, connecting and completing gene-expression networks

Background  

We generalized penalized canonical correlation analysis for analyzing microarray gene-expression measurements for checking completeness of known metabolic pathways and identifying candidate genes for incorporation in the pathway. We used Wold's method for calculation of the canonical variates, and we applied ridge penalization to the regression of pathway genes on canonical variates of the non-pathway genes, and the elastic net to the regression of non-pathway genes on the canonical variates of the pathway genes.     

Iterative class discovery and feature selection using Minimal Spanning Trees

Background  

Clustering is one of the most commonly used methods for discovering hidden structure in microarray gene expression data. Most current methods for clustering samples are based on distance metrics utilizing all genes. This has the effect of obscuring clustering in samples that may be evident only when looking at a subset of genes, because noise from irrelevant genes dominates the signal from the relevant genes in the distance calculation.     

Protein evolution of ANTP and PRD homeobox genes

Background  

Although homeobox genes have been the subject of many studies, little is known about the main amino acid changes that occurred early in the evolution of genes belonging to different classes.     

Generation of an external guide sequence library for a reverse genetic screen in Caenorhabditis elegans

Background  

A method for inhibiting the expression of particular genes using external guide sequences (EGSs) has been developed in bacteria, mammalian cells and maize cells.     

Chromosomal patterns of gene expression from microarray data: methodology, validation and clinical relevance in gliomas

Background  

Expression microarrays represent a powerful technique for the simultaneous investigation of thousands of genes. The evidence that genes are not randomly distributed in the genome and that their coordinated expression depends on their position on chromosomes has highlighted the need for mathematical approaches to exploit this dependency for the analysis of expression data-sets.     

Different cDNA microarray patterns of gene expression reflecting changes during metastatic progression in adenoid cystic carcinoma

Background  

The metastatic ability of tumor cells is determined by level of expression of specific genes that may be identified with the aid of cDNA microarray containing thousands of genes and can be used to establish the expression profile of disease related genes in complex biological system.     

Library on a slide for bacterial comparative genomics

Background  

We describe a novel application of microarray technology for comparative genomics of bacteria in which libraries of entire genomes rather than the sequence of a single genome or sets of genes are arrayed on the slide and then probed for the presence or absence of specific genes and/or gene alleles.