Search results for "Gene chip analysis"
showing 9 items of 19 documents
A Tutorial on Computational Cluster Analysis with Applications to Pattern Discovery in Microarray Data
2008
Background Inferring cluster structure in microarray datasets is a fundamental task for the so-called -omic sciences. It is also a fundamental question in Statistics, Data Analysis and Classification, in particular with regard to the prediction of the number of clusters in a dataset, usually established via internal validation measures. Despite the wealth of internal measures available in the literature, new ones have been recently proposed, some of them specifically for microarray data. Results We consider five such measures: Clest, Consensus (Consensus Clustering), FOM (Figure of Merit), Gap (Gap Statistics) and ME (Model Explorer), in addition to the classic WCSS (Within Cluster Sum-of-S…
Determinants of endometrial receptivity.
2005
Understanding the molecular changes that occur during the window of implantation is fundamental to our knowledge of human reproduction. Lately, the development of microarray technology has allowed this process to be studied from a global molecular perspective. In the last 2 years, researchers have focused their efforts on throwing light on the gene expression profile of the receptive endometrium. The genes hold the key to the development of the endometrium at any stage, and we have focused our work on the window of implantation. The four most recently published works in this field have revealed a long list of genes that are up- or downregulated at the time of implantation. Although these st…
Plasma circulating miRNAs as diagnostic and prognostic biomarkers in alpha-1 antitrypsin deficiency
2019
Introduction: Alpha-1 antitrypsin (AATD) deficiency is an inherited condition that leads to decreased circulating AAT levels, significantly increasing the risk of lung and liver disease. AATD is underdiagnosed. Severity of symptoms in AATD patients are highly variable and neither protein levels nor phenotype are sufficient to identify which patients will develop lung and/or liver disease. Therefore, new strategies and biomarkers for early diagnosis and prognosis of the disease are needed. Rationale and Aims: MicroRNAs (miRNAs) regulate gene expression and have been associated with the pathogenesis of various lung and liver diseases. Circulating miRNAs may serve as diagnostic and prognostic …
Two independent epigenetic biomarkers predict survival in neuroblastoma.
2015
Background Neuroblastoma (NB) is the most common extracranial pediatric solid tumor with a highly variable clinical course, ranging from spontaneous regression to life-threatening disease. Survival rates for high-risk NB patients remain disappointingly low despite multimodal treatment. Thus, there is an urgent clinical need for additional biomarkers to improve risk stratification, treatment management, and survival rates in children with aggressive NB. Results Using gene promoter methylation analysis in 48 neuroblastoma tumors with microarray technology, we found a strong association between survival and gene promoter hypermethylation (P = 0.036). Hypermethylation of 70 genes significantly …
Poster Presentations
2014
Administration of recombinant human erythropoietin (rHuEpo) improves performance and hence is subject to abuse by athletes. The detection of rHuEpo doping remains a major challenge at present. The aim of the current study was to investigate whether circulating microRNA (miRNA) can be used for detecting r-HuEpo doping. Twenty trained males received rHuEpo injections of 50 IU∙kg -1 body mass every two days for 4 weeks. Blood was obtained 2 weeks before, during and 4 weeks after administration. For this pilot analysis, plasma miRNA expression was assessed at selected time points using the Affymetrix GeneChip 3.0 and the miScript 384 HC PCR Array (Qiagen). For the Affymetrix microarray data, GC…
RNA-Seq Atlas—a reference database for gene expression profiling in normal tissue by next-generation sequencing
2012
Abstract Motivation: Next-generation sequencing technology enables an entirely new perspective for clinical research and will speed up personalized medicine. In contrast to microarray-based approaches, RNA-Seq analysis provides a much more comprehensive and unbiased view of gene expression. Although the perspective is clear and the long-term success of this new technology obvious, bioinformatics resources making these data easily available especially to the biomedical research community are still evolving. Results: We have generated RNA-Seq Atlas, a web-based repository of RNA-Seq gene expression profiles and query tools. The website offers open and easy access to RNA-Seq gene expression pr…
Prognostic Impact of let-7e MicroRNA and Its Target Genes in Localized High-Risk Intestinal GIST: A Spanish Group for Research on Sarcoma (GEIS) Study
2020
MicroRNAs (miRNAs) are small non-coding RNAs that negatively regulate gene expression at the post-transcriptional level, and they have been described as being associated with tumor prognosis. Here, miRNA profiling was planned to explore new molecular prognostic biomarkers in localized intestinal high-risk GIST. Paraffin tumor blocks of 14 and 86 patients were used in the discovery and expansion sets, respectively. GeneChip miRNA v3.0 was employed to identify the miRNAs differentially expressed between relapsed and non-relapsed patient samples, which were validated in the expansion set, by qRT-PCR. RT2 Profiler PCR Array was used for the screening of let-7e targets. Expression levels were co…
Computational cluster validation for microarray data analysis: experimental assessment of Clest, Consensus Clustering, Figure of Merit, Gap Statistic…
2008
Abstract Background Inferring cluster structure in microarray datasets is a fundamental task for the so-called -omic sciences. It is also a fundamental question in Statistics, Data Analysis and Classification, in particular with regard to the prediction of the number of clusters in a dataset, usually established via internal validation measures. Despite the wealth of internal measures available in the literature, new ones have been recently proposed, some of them specifically for microarray data. Results We consider five such measures: Clest, Consensus (Consensus Clustering), FOM (Figure of Merit), Gap (Gap Statistics) and ME (Model Explorer), in addition to the classic WCSS (Within Cluster…
Controlled Ovarian Stimulation Induces a Functional Genomic Delay of the Endometrium with Potential Clinical Implications
2008
Context: Controlled ovarian stimulation induces morphological, biochemical, and functional genomic modifications of the human endometrium during the window of implantation. Objective: Our objective was to compare the gene expression profile of the human endometrium in natural vs. controlled ovarian stimulation cycles throughout the early-mid secretory transition using microarray technology. Method: Microarray data from 49 endometrial biopsies obtained from LH+1 to LH+9 (n = 25) in natural cycles and from human chorionic gonadotropin (hCG) +1 to hCG+9 in controlled ovarian stimulation cycles (n = 24) were analyzed using different methods, such as clustering, profiling of biological processes…