Search results for "Microarrays"
showing 9 items of 49 documents
Quantification of the heterogeneity of prognostic cellular biomarkers in ewing sarcoma using automated image and random survival forest analysis
2014
Driven by genomic somatic variation, tumour tissues are typically heterogeneous, yet unbiased quantitative methods are rarely used to analyse heterogeneity at the protein level. Motivated by this problem, we developed automated image segmentation of images of multiple biomarkers in Ewing sarcoma to generate distributions of biomarkers between and within tumour cells. We further integrate high dimensional data with patient clinical outcomes utilising random survival forest (RSF) machine learning. Using material from cohorts of genetically diagnosed Ewing sarcoma with EWSR1 chromosomal translocations, confocal images of tissue microarrays were segmented with level sets and watershed algorithm…
Models of Biobanking and Tissue Preservation: RNA Quality in Archival Samples in Pathology Laboratories and “In Vivo Biobanking” by Tumor Xenografts …
2011
Tissue banks represent essential resources and platforms for biomedical research serving basic, translational, and clinical research projects. In this article, we describe 2 models of biobanking and tissue preservation with different approaches and aims. Archive tissue biobanking is described here as a resource of residual pathology tissues for translational research, which represents the huge clinical heterogeneity. In this context, managing of tissues and RNA quality in archive tissue are discussed. The other model of tissue biobanking is referred to as xenograft tissue banking, which represents an alternative method for obtaining large amounts of tissue, over an indefinite period, in so …
Control of dataset bias in combined Affymetrix cohorts of triple negative breast cancer
2014
AbstractHeterogenous subtypes of breast cancer need to be analyzed separately. Pooling of datasets can provide reasonable sample sizes but dataset bias is an important concern. We assembled a combined dataset of 579 Affymetrix microarrays from triple negative breast cancer (TNBC) in Gene Expression Omnibus (GEO) series GSE31519. We developed a method for selecting comparable datasets and to control for the amount of dataset bias of individual probesets.
Expression profiling of glial genes during Drosophila embryogenesis
2006
AbstractIn the central nervous system of Drosophila, the induction of the glial cell fate is dependent on the transcription factor glial cells missing (gcm). Though a considerable number of other genes have been shown to be expressed in all or in subsets of glial cells, the course of glial cell differentiation and subtype specification is only poorly understood. This prompted us to design a whole genome microarray approach comparing gcm gain-of-function and, for the first time, gcm loss-of-function genetics to wildtype in time course experiments along embryogenesis. The microarray data were analyzed with special emphasis on the temporal profile of differential regulation. A comparison of bo…
iGEMS : an integrated model for identification of alternative exon usage events
2016
DNA microarrays and RNAseq are complementary methods for studying RNA molecules. Current computational methods to determine alternative exon usage (AEU) using such data require impractical visual inspection and still yield high false-positive rates. Integrated Gene and Exon Model of Splicing (iGEMS) adapts a gene-level residuals model with a gene size adjusted false discovery rate and exon-level analysis to circumvent these limitations. iGEMS was applied to two new DNA microarray datasets, including the high coverage Human Transcriptome Arrays 2.0 and performance was validated using RT-qPCR. First, AEU was studied in adipocytes treated with (n = 9) or without (n = 8) the anti-diabetes drug,…
Gene Expression Profile of Chronic Myeloid Leukemia Innately Resistant to Imatinib
2007
Background. Most chronic myeloid leukemia patients who receive imatinib as first line-terapy will obtain, after 12 months treatment, complete cytogenetic and molecular response . However several cases will not achieve molecular response, but their innate mechanism(s) of resistance remain poorly understood. We tried to explore the molecular events involved in innate resistance in CML. Study design. Five patients who were molecular “non responder” and seven “major” responder were investigated by using the expression profile of a set of 380 genes. Multiple testing procedure (MTP), Significance Analysis of Microarrays (SAM), Empirical Bayes Analysis of Microarrays (EBAM), False Discovery Rate (…
Rare variant analyses across multiethnic cohorts identify novel genes for refractive error
2023
Refractive error, measured here as mean spherical equivalent (SER), is a complex eye condition caused by both genetic and environmental factors. Individuals with strong positive or negative values of SER require spectacles or other approaches for vision correction. Common genetic risk factors have been identified by genome-wide association studies (GWAS), but a great part of the refractive error heritability is still missing. Some of this heritability may be explained by rare variants (minor allele frequency [MAF] ≤ 0.01.). We performed multiple gene-based association tests of mean Spherical Equivalent with rare variants in exome array data from the Consortium for Refractive Error and Myopi…
Estudio de la adaptación a estrés por etanol en cepas de Saccharomyces cerevisiae
2016
Los mecanismos de tolerancia a etanol han sido ampliamente estudiados en la levadura Saccharomyces cerevisiae debido a su importancia en el sector industrial de bebidas fermentadas y obtención de biocombustibles, siendo las cepas de laboratorio las más utilizadas en los estudios experimentales. A pesar del gran número de estudios llevados a cabo, nuestra comprensión de la respuesta transcripcional y fisiológica al etanol continúa siendo limitada debido al uso de cepas no adecuadas para este fin y la gran disparidad en las condiciones utilizadas. Además se ha dejado de lado el estudio de ciertas rutas de respuesta a estrés en levaduras, como la respuesta a proteínas desplegadas (UPR), cuya a…
Implicación de los microARNs en la hipertensión pulmonar idiopática. Regulación farmacológica
2014
La hipertensión pulmonar (HP) es un desorden complejo que se caracteriza por un aumento progresivo de la presión arterial pulmonar, ocasionado por el remodelado de las arterias pulmonares de pequeño calibre, que origina un aumento de resistencias pulmonares y como consecuencia sobrecarga y fallo del ventrículo derecho que puede llevar al fallecimiento del paciente. La Organización mundial de la salud la clasifica en 5 grupos, en nuestro estudio nos hemos centrado en el grupo I, que se caracteriza por la afección de los vasos pulmonares de pequeño calibre, con una presión arterial pulmonar (PAP) media de ≥ 25 mmHg y ausencia de causas secundarias, este así mismo se subdivide en hipertensión …