A systematic approach for testing expression of human full-length proteins in cell-free expression systems

Background  

The growing field of proteomics and systems biology is resulting in an ever increasing demand for purified recombinant proteins for structural and functional studies. Here, we show a systematic approach to successfully express a full-length protein of interest by using cell-free and cell-based expression systems.     

Genomic expression dominance in allopolyploids

Background  

Allopolyploid speciation requires rapid evolutionary reconciliation of two diverged genomes and gene regulatory networks. Here we describe global patterns of gene expression accompanying genomic merger and doubling in inter-specific crosses in the cotton genus (Gossypium L.).     

The utility of MAS5 expression summary and detection call algorithms

Background  

Used alone, the MAS5.0 algorithm for generating expression summaries has been criticized for high False Positive rates resulting from exaggerated variance at low intensities.     

Gene expression profiling predicts a three-gene expression signature of endometrial adenocarcinoma in a rat model

Background  

In the Western world, endometrial cancers are the most common gynaecological neoplastic disorders among women. Initial symptoms are often vague and may be confused with several other conditions or disorders. Thus, there is a need for an easy and reliable diagnostic tool. The objective of this work was to identify a gene expression signature specific for endometrial adenocarcinomas to be used for testing potential endometrial biomarkers.     

Coordinate regulation of DNA methyltransferase expression during oogenesis

Background  

Normal mammalian development requires the action of DNA methyltransferases (DNMTs) for the establishment and maintenance of DNA methylation within repeat elements and imprinted genes. Here we report the expression dynamics of Dnmt3a and Dnmt3b, as well as a regulator of DNA methylation, Dnmt3L, in isolated female germ cells.     

Washing scaling of GeneChip microarray expression

Background  

Post-hybridization washing is an essential part of microarray experiments. Both the quality of the experimental washing protocol and adequate consideration of washing in intensity calibration ultimately affect the quality of the expression estimates extracted from the microarray intensities.     

Normal uniform mixture differential gene expression detection for cDNA microarrays

Background  

One of the primary tasks in analysing gene expression data is finding genes that are differentially expressed in different samples. Multiple testing issues due to the thousands of tests run make some of the more popular methods for doing this problematic.     

Placental thrombomodulin expression in recurrent miscarriage

Background  

Early pregnancy loss can be associated with trophoblast insufficiency and coagulation defects. Thrombomodulin is an endothelial-associated anticoagulant protein involved in the control of hemostasis and inflammation at the vascular beds and it's also a cofactor of the protein C anticoagulant pathway.     

Controlled expression of functional miR-122 with a ligand inducible expression system

Background  

To study the biological function of miRNAs, and to achieve sustained or conditional gene silencing with siRNAs, systems that allow controlled expression of these small RNAs are desirable. Methods for cell delivery of siRNAs include transient transfection of synthetic siRNAs and expression of siRNAs in the form of short hairpins using constitutive RNA polymerase III promoters. Systems employing constitutive RNA polymerase II promoters have been used to express miRNAs. However, for many experimental systems these methods do not offer sufficient control over expression.     

HOX cofactors expression and regulation in the human ovary

Background  

HOX cofactors enhance HOX binding affinities and specificities and increase HOX's unique functional activities. The expression and the regulation of HOX cofactors in human ovaries are unknown.     

Measuring gene expression divergence: the distance to keep

Background  

Gene expression divergence is a phenotypic trait reflecting evolution of gene regulation and characterizing dissimilarity between species and between cells and tissues within the same species. Several distance measures, such as Euclidean and correlation-based distances have been proposed for measuring expression divergence.     

Multivariate analysis of microarray data: differential expression and differential connection

Background  

Typical analysis of microarray data ignores the correlation between gene expression values. In this paper we present a model for microarray data which specifically allows for correlation between genes. As a result we combine gene network ideas with linear models and differential expression.     

A consensus prognostic gene expression classifier for ER positive breast cancer

Background  

A consensus prognostic gene expression classifier is still elusive in heterogeneous diseases such as breast cancer.     

Identification and expression analysis of genes associated with bovine blastocyst formation

Background  

Normal preimplantation embryo development encompasses a series of events including first cleavage division, activation of the embryonic genome, compaction and blastocyst formation.     

ANMM4CBR: a case-based reasoning method for gene expression data classification

Background  

Accurate classification of microarray data is critical for successful clinical diagnosis and treatment. The "curse of dimensionality" problem and noise in the data, however, undermines the performance of many algorithms.     

Mouse ribonuclease III. cDNA structure, expression analysis, and chromosomal location

Background  

Two-hybrid screening for proteins that interact with the core domain of human topoisomerase I identified two novel proteins, BTBD1 and BTBD2, which share 80% amino acid identities.     

TLR3 and TLR4 expression in healthy and diseased human endometrium

Background  

Toll-like receptors (TLRs) play an essential role in the innate immune system by initiating and directing immune response to pathogens. TLRs are expressed in the human endometrium and their regulation might be crucial for the pathogenesis of endometrial diseases.     

An interactive tool for visualization of relationships between gene expression profiles

Background  

Application of phenetic methods to gene expression analysis proved to be a successful approach. Visualizing the results in a 3-dimentional space may further enhance these techniques.     

mRNA stability and the unfolding of gene expression in the long-period yeast metabolic cycle

Background  

In yeast, genome-wide periodic patterns associated with energy-metabolic oscillations have been shown recently for both short (approx. 40 min) and long (approx. 300 min) periods.