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Expression Signature as a Biomarker for Prenatal Diagnosis of Trisomy 21

A universal biomarker panel with the potential to predict high-risk pregnancies or adverse pregnancy outcome does not exist. Transcriptome analysis is a powerful tool to capture differentially expressed genes (DEG), which can be used as biomarker-diagnostic-predictive tool for various conditions in prenatal setting. In search of biomarker set for predicting high-risk pregnancies...

Hidden Disease Susceptibility and Sexual Dimorphism in the Heterozygous Knockout of Cyp51 from Cholesterol Synthesis

We examined the genotype-phenotype interactions of Cyp51+/− mice carrying one functional allele of lanosterol 14α-demethylase from cholesterol biosynthesis. No distinct developmental or morphological abnormalities were observed by routine visual inspection of Cyp51+/− and Cyp51+/+ mice and fertility was similar. We further collected a large data-set from female and male Cyp51...

RNAmotifs: prediction of multivalent RNA motifs that control alternative splicing

RNA-binding proteins (RBPs) regulate splicing according to position-dependent principles, which can be exploited for analysis of regulatory motifs. Here we present RNAmotifs, a method that evaluates the sequence around differentially regulated alternative exons to identify clusters of short and degenerate sequences, referred to as multivalent RNA motifs. We show that diverse RBPs...

Cumulus Cells Gene Expression Profiling in Terms of Oocyte Maturity in Controlled Ovarian Hyperstimulation Using GnRH Agonist or GnRH Antagonist

In in vitro fertilization (IVF) cycles controlled ovarian hyperstimulation (COH) is established by gonadotropins in combination with gonadotropin-releasing hormone (GnRH) agonists or antagonists, to prevent premature luteinizing hormone (LH) surge. The aim of our study was to improve the understanding of gene expression profile of cumulus cells (CC) in terms of ovarian...

Novel Insights into the Downstream Pathways and Targets Controlled by Transcription Factors CREM in the Testis

The essential role of the Crem gene in normal sperm development is widely accepted and is confirmed by azoospermia in male mice lacking the Crem gene. The exact number of genes affected by Crem absence is not known, however a large difference has been observed recently between the estimated number of differentially expressed genes found in Crem knock-out (KO) mice compared to the...

Obesity resistant mechanisms in the Lean polygenic mouse model as indicated by liver transcriptome and expression of selected genes in skeletal muscle

Juvan Damjana Rozman Gregor Fazarinc Catherine Fievet Bart Staels Simon Horvat 0 0 University of Ljubljana, Biotechnical Faculty, Department of Animal Science , Groblje 3, 1230 Domzale , Slovenia

Tools and data services registry: a community effort to document bioinformatics resources

Manuela Helmer-Citterich 14 Hans Ienasescu 15 Vassilios Ioannidis 10 Martin Closter Jespersen 22 Rafael Jimenez 24 Nick Juty 24 Peter Juvan 16 Maximilian Koch 24 Camille Laibe 24 Jing-Woei Li 17 18 Luana

GenePath: from mutations to genetic networks and back

GenePath is a web-based application for the analysis of mutant-based experiments and synthesis of genetic networks. Here, we introduce GenePath and describe a number of new approaches, including conflict resolution, handling cyclic pathways, confidence level assignment, what-if analysis and new experiment proposal. We illustrate the key concepts using data from a study of...

The Sterolgene v0 cDNA microarray: a systemic approach to studies of cholesterol homeostasis and drug metabolism

Background Cholesterol homeostasis and xenobiotic metabolism are complex biological processes, which are difficult to study with traditional methods. Deciphering complex regulation and response of these two processes to different factors is crucial also for understanding of disease development. Systems biology tools as are microarrays can importantly contribute to this knowledge...

GenePath: a system for automated construction of genetic networks from mutant data

Motivation: Genetic networks are often used in the analysis of biological phenomena. In classical genetics, they are constructed manually from experimental data on mutants. The field lacks formalism to guide such analysis, and accounting for all the data becomes complicated when large amounts of data are considered. Results: We have developed GenePath, an intelligent assistant...